From b9ea1a80fedb01c46ea9c87d2c8f0e80c26b8128 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 14 Aug 2018 16:19:56 +0100
Subject: [PATCH 01/32] checkpoint: no compile error in mvn package

---
 .../plugins/example/layout/Bundle.properties  |   2 +-
 modules/NodeWeight/README.md                  |   4 +
 modules/NodeWeight/pom.xml                    |  99 +++
 .../layout/NodeWeight/AbstractLayout.java     | 104 +++
 .../layout/NodeWeight/ForceAtlas2.java        | 619 ++++++++++++++++++
 .../layout/NodeWeight/ForceAtlas2Builder.java | 105 +++
 .../NodeWeight/ForceAtlas2LayoutData.java     |  61 ++
 .../layout/NodeWeight/ForceFactory.java       | 577 ++++++++++++++++
 .../layout/NodeWeight/NodesThread.java        | 102 +++
 .../plugins/layout/NodeWeight/Operation.java  |  51 ++
 .../NodeWeight/OperationNodeNodeAttract.java  |  70 ++
 .../NodeWeight/OperationNodeNodeRepulse.java  |  68 ++
 .../OperationNodeRegionRepulse.java           |  70 ++
 .../NodeWeight/OperationNodeRepulse.java      |  68 ++
 .../plugins/layout/NodeWeight/Region.java     | 222 +++++++
 modules/NodeWeight/src/main/nbm/manifest.mf   |   5 +
 .../layout/NodeWeight/Bundle.properties       |  16 +
 pom.xml                                       |  22 +-
 18 files changed, 2254 insertions(+), 11 deletions(-)
 create mode 100644 modules/NodeWeight/README.md
 create mode 100644 modules/NodeWeight/pom.xml
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/AbstractLayout.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2Builder.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2LayoutData.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceFactory.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/NodesThread.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Operation.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeAttract.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeRepulse.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRegionRepulse.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRepulse.java
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Region.java
 create mode 100644 modules/NodeWeight/src/main/nbm/manifest.mf
 create mode 100644 modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties

diff --git a/modules/LayoutPluginExample/src/main/resources/org/gephi/plugins/example/layout/Bundle.properties b/modules/LayoutPluginExample/src/main/resources/org/gephi/plugins/example/layout/Bundle.properties
index 26f6990..f5c97d7 100644
--- a/modules/LayoutPluginExample/src/main/resources/org/gephi/plugins/example/layout/Bundle.properties
+++ b/modules/LayoutPluginExample/src/main/resources/org/gephi/plugins/example/layout/Bundle.properties
@@ -1,4 +1,4 @@
-OpenIDE-Module-Display-Category=Plugin
+OpenIDE-Module-Display-Category=Layout
 OpenIDE-Module-Long-Description=\
     Example of Layout Plugins:\n<ul>\n<li><b>Grid Layout:</b> Place all nodes in a simple grid. \
     Users can configure the size of the area and the speed.\
diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
new file mode 100644
index 0000000..95d48ca
--- /dev/null
+++ b/modules/NodeWeight/README.md
@@ -0,0 +1,4 @@
+## Node Weight
+
+This README supports Markdown, see [syntax](https://help.github.com/articles/markdown-basics/)
+
diff --git a/modules/NodeWeight/pom.xml b/modules/NodeWeight/pom.xml
new file mode 100644
index 0000000..0cacab7
--- /dev/null
+++ b/modules/NodeWeight/pom.xml
@@ -0,0 +1,99 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <parent>
+        <artifactId>gephi-plugin-parent</artifactId>
+        <groupId>org.gephi</groupId>
+        <version>0.9.0</version>
+    </parent>
+
+    <groupId>imperial</groupId>
+    <artifactId>node-weight</artifactId>
+    <version>1.0.0</version>
+    <packaging>nbm</packaging>
+
+    <name>Node Weight</name>
+
+    <dependencies>
+        <dependency>
+            <groupId>org.netbeans.api</groupId>
+            <artifactId>org-openide-util-lookup</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>graph-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>layout-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>ui-propertyeditor</artifactId>
+        </dependency>
+        <!-- <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>graph-api</artifactId>
+            <type>jar</type>
+        </dependency> -->
+        <!-- <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>ui-propertyeditor</artifactId>
+            <type>jar</type>
+        </dependency> -->
+        <!-- <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>graph-api</artifactId>
+        </dependency> -->
+       <!--  <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>layout-api</artifactId>
+        </dependency> -->
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>project-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>core-library-wrapper</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.gephi</groupId>
+            <artifactId>utils-longtask</artifactId>
+        </dependency>
+        <!-- <dependency>
+            <groupId>org.netbeans.api</groupId>
+            <artifactId>org-openide-util-lookup</artifactId>
+        </dependency> -->
+        <dependency>
+            <groupId>org.netbeans.api</groupId>
+            <artifactId>org-openide-util</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.netbeans.api</groupId>
+            <artifactId>org-openide-nodes</artifactId>
+        </dependency>
+    </dependencies>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>nbm-maven-plugin</artifactId>
+                <configuration>
+                    <licenseName>Apache 2.0</licenseName>
+                    <author>Julianne Joswiak</author>
+                    <authorEmail>jj2816@imperial.ac.uk</authorEmail>
+                    <authorUrl></authorUrl>
+                    <sourceCodeUrl>http://github.com/gephi/gephi-plugins-bootcamp</sourceCodeUrl>
+                    <homePageUrl>$homepage_url</homePageUrl>
+                    <publicPackages>
+                        <!-- Insert public packages -->
+                    </publicPackages>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+</project>
+
+
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/AbstractLayout.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/AbstractLayout.java
new file mode 100644
index 0000000..c4c2ed5
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/AbstractLayout.java
@@ -0,0 +1,104 @@
+/*
+ Copyright 2008-2010 Gephi
+ Authors : Helder Suzuki <heldersuzuki@gephi.org>
+ Website : http://www.gephi.org
+ This file is part of Gephi.
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ Copyright 2011 Gephi Consortium. All rights reserved.
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+ Contributor(s):
+ Portions Copyrighted 2011 Gephi Consortium.
+ */
+package org.gephi.layout.plugins.layout.NodeWeight;
+
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.NodeIterable;
+import org.gephi.layout.spi.Layout;
+import org.gephi.layout.spi.LayoutBuilder;
+
+/**
+ * Base class for layout algorithms.
+ *
+ * @author Helder Suzuki <heldersuzuki@gephi.org>
+ */
+public abstract class AbstractLayout implements Layout {
+
+    private final LayoutBuilder layoutBuilder;
+    protected GraphModel graphModel;
+    private boolean converged;
+
+    public AbstractLayout(LayoutBuilder layoutBuilder) {
+        this.layoutBuilder = layoutBuilder;
+    }
+
+    @Override
+    public LayoutBuilder getBuilder() {
+        return layoutBuilder;
+    }
+
+    @Override
+    public void setGraphModel(GraphModel graphModel) {
+        this.graphModel = graphModel;
+    }
+
+    @Override
+    public boolean canAlgo() {
+        return !isConverged() && graphModel != null;
+    }
+
+    public void setConverged(boolean converged) {
+        this.converged = converged;
+    }
+
+    public boolean isConverged() {
+        return converged;
+    }
+
+    /**
+     * See https://github.com/gephi/gephi/issues/603 Nodes position to NaN on applied layout
+     *
+     * @param graphModel
+     */
+    public static void ensureSafeLayoutNodePositions(GraphModel graphModel) {
+        Graph graph = graphModel.getGraph();
+        NodeIterable nodesIterable = graph.getNodes();
+        for (Node node : nodesIterable) {
+            if (node.x() != 0 || node.y() != 0) {
+                nodesIterable.doBreak();
+                return;
+            }
+        }
+
+        //All at 0.0, init some random positions
+        nodesIterable = graph.getNodes();
+        for (Node node : nodesIterable) {
+            node.setX((float) ((0.01 + Math.random()) * 1000) - 500);
+            node.setY((float) ((0.01 + Math.random()) * 1000) - 500);
+        }
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
new file mode 100644
index 0000000..9f9973f
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -0,0 +1,619 @@
+/*
+ Copyright 2008-2011 Gephi
+ Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2011 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2011 Gephi Consortium.
+ */
+package org.gephi.layout.plugins.layout.NodeWeight;
+// org.gephi.layout.plugins.layout.NodeWeight
+
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+import org.gephi.layout.spi.Layout;
+import org.gephi.layout.spi.LayoutBuilder;
+import org.gephi.layout.spi.LayoutProperty;
+
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import org.gephi.graph.api.Interval;
+// import org.gephi.layout.plugin.AbstractLayout;
+import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
+
+
+import org.openide.util.Exceptions;
+import org.openide.util.NbBundle;
+
+/**
+ * ForceAtlas 2 Layout, manages each step of the computations.
+ *
+ * @author Mathieu Jacomy
+ */
+public class ForceAtlas2 implements Layout {
+
+    private GraphModel graphModel;
+    private Graph graph;
+    private final ForceAtlas2Builder layoutBuilder;
+    private double edgeWeightInfluence;
+    private double jitterTolerance;
+    private double scalingRatio;
+    private double gravity;
+    private double speed;
+    private double speedEfficiency;
+    private boolean outboundAttractionDistribution;
+    private boolean adjustSizes;
+    private boolean barnesHutOptimize;
+    private double barnesHutTheta;
+    private boolean linLogMode;
+    private boolean strongGravityMode;
+    private int threadCount;
+    private int currentThreadCount;
+    private Region rootRegion;
+    double outboundAttCompensation = 1;
+    private ExecutorService pool;
+
+    public ForceAtlas2(ForceAtlas2Builder layoutBuilder) {
+        this.layoutBuilder = layoutBuilder;
+        this.threadCount = Math.min(4, Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
+    }
+
+    @Override
+    public void initAlgo() {
+        AbstractLayout.ensureSafeLayoutNodePositions(graphModel);
+
+        speed = 1.;
+        speedEfficiency = 1.;
+
+        graph = graphModel.getGraphVisible();
+
+        graph.readLock();
+        try {
+            Node[] nodes = graph.getNodes().toArray();
+
+            // Initialise layout data
+            for (Node n : nodes) {
+                if (n.getLayoutData() == null || !(n.getLayoutData() instanceof ForceAtlas2LayoutData)) {
+                    ForceAtlas2LayoutData nLayout = new ForceAtlas2LayoutData();
+                    n.setLayoutData(nLayout);
+                }
+                ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                nLayout.mass = 1 + graph.getDegree(n);
+                nLayout.old_dx = 0;
+                nLayout.old_dy = 0;
+                nLayout.dx = 0;
+                nLayout.dy = 0;
+            }
+
+            pool = Executors.newFixedThreadPool(threadCount);
+            currentThreadCount = threadCount;
+        } finally {
+            graph.readUnlockAll();
+        }
+    }
+
+    private double getEdgeWeight(Edge edge, boolean isDynamicWeight, Interval interval) {
+        if (isDynamicWeight) {
+            return edge.getWeight(interval);
+        } else {
+            return edge.getWeight();
+        }
+    }
+
+    private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
+        if (isDynamicNodeWeight) {
+            // node_weight = (Double) n.getAttribute("gravity_x");
+            return (Double) node.getAttribute("weight", interval);
+        } else {
+            return (Double) node.getAttribute("weight");
+        }
+    }
+
+
+    @Override
+    public void goAlgo() {
+        // Initialize graph data
+        if (graphModel == null) {
+            return;
+        }
+        graph = graphModel.getGraphVisible();
+        graph.readLock();
+        boolean isDynamicWeight = graphModel.getEdgeTable().getColumn("weight").isDynamic();
+        boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn("weight").isDynamic();
+        Interval interval = graph.getView().getTimeInterval();
+
+        try {
+            Node[] nodes = graph.getNodes().toArray();
+            Edge[] edges = graph.getEdges().toArray();
+
+            // Initialise layout data
+            for (Node n : nodes) {
+                if (n.getLayoutData() == null || !(n.getLayoutData() instanceof ForceAtlas2LayoutData)) {
+                    ForceAtlas2LayoutData nLayout = new ForceAtlas2LayoutData();
+                    n.setLayoutData(nLayout);
+                }
+                ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                nLayout.mass = 1 + graph.getDegree(n);
+                nLayout.old_dx = nLayout.dx;
+                nLayout.old_dy = nLayout.dy;
+                nLayout.dx = 0;
+                nLayout.dy = 0;
+            }
+
+            // If Barnes Hut active, initialize root region
+            if (isBarnesHutOptimize()) {
+                rootRegion = new Region(nodes);
+                rootRegion.buildSubRegions();
+            }
+
+            // If outboundAttractionDistribution active, compensate.
+            if (isOutboundAttractionDistribution()) {
+                outboundAttCompensation = 0;
+                for (Node n : nodes) {
+                    ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                    outboundAttCompensation += nLayout.mass;
+                }
+                outboundAttCompensation /= nodes.length;
+            }
+
+            // Repulsion (and gravity)
+            // NB: Muti-threaded
+            RepulsionForce Repulsion = ForceFactory.builder.buildRepulsion(isAdjustSizes(), getScalingRatio());
+
+            int taskCount = 8 * currentThreadCount;  // The threadPool Executor Service will manage the fetching of tasks and threads.
+            // We make more tasks than threads because some tasks may need more time to compute.
+            ArrayList<Future> threads = new ArrayList();
+            for (int t = taskCount; t > 0; t--) {
+                int from = (int) Math.floor(nodes.length * (t - 1) / taskCount);
+                int to = (int) Math.floor(nodes.length * t / taskCount);
+                Future future = pool.submit(new NodesThread(nodes, from, to, isBarnesHutOptimize(), getBarnesHutTheta(), getGravity(), (isStrongGravityMode()) ? (ForceFactory.builder.getStrongGravity(getScalingRatio())) : (Repulsion), getScalingRatio(), rootRegion, Repulsion));
+                threads.add(future);
+            }
+            for (Future future : threads) {
+                try {
+                    future.get();
+                } catch (Exception e) {
+                    throw new RuntimeException("Unable to layout " + this.getClass().getSimpleName() + ".", e);
+                }
+            }
+//BOOKMARK
+          // Attraction
+            // Edge Weight
+            AttractionForce Attraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
+            if (getEdgeWeightInfluence() == 0) {
+                for (Edge e : edges) {
+                    Attraction.apply(e.getSource(), e.getTarget(), 1);
+                }
+            } else if (getEdgeWeightInfluence() == 1) {
+                for (Edge e : edges) {
+                    Attraction.apply(e.getSource(), e.getTarget(), getEdgeWeight(e, isDynamicWeight, interval));
+                }
+            } else {
+                for (Edge e : edges) {
+                    Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
+                }
+            }
+            // Node Weight
+            AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
+            for (Edge e : edges) {
+              Node node_a = e.getSource();
+              Node node_b = e.getTarget();
+
+              Double wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
+              Double wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
+
+              NodeAttraction.apply(node_a, node_b, (getNodeWeight(node_a, isDynamicNodeWeight, interval) + getNodeWeight(node_b, isDynamicNodeWeight, interval))/2);
+
+
+
+
+              // Attraction.apply(node_a, node_b, getNodeWeight())
+            }
+            // if (getEdgeWeightInfluence() == 0) {
+            //     for (Edge e : edges) {
+            //         Attraction.apply(e.getSource(), e.getTarget(), 1);
+            //     }
+            // } else if (getEdgeWeightInfluence() == 1) {
+            //     for (Edge e : edges) {
+            //         Attraction.apply(e.getSource(), e.getTarget(), getEdgeWeight(e, isDynamicWeight, interval));
+            //     }
+            // } else {
+            //     for (Edge e : edges) {
+            //         Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
+            //     }
+            // }
+
+            // Auto adjust speed
+            double totalSwinging = 0d;  // How much irregular movement
+            double totalEffectiveTraction = 0d;  // Hom much useful movement
+            for (Node n : nodes) {
+                ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                if (!n.isFixed()) {
+                    double swinging = Math.sqrt(Math.pow(nLayout.old_dx - nLayout.dx, 2) + Math.pow(nLayout.old_dy - nLayout.dy, 2));
+                    totalSwinging += nLayout.mass * swinging;   // If the node has a burst change of direction, then it's not converging.
+                    totalEffectiveTraction += nLayout.mass * 0.5 * Math.sqrt(Math.pow(nLayout.old_dx + nLayout.dx, 2) + Math.pow(nLayout.old_dy + nLayout.dy, 2));
+                }
+            }
+            // We want that swingingMovement < tolerance * convergenceMovement
+
+            // Optimize jitter tolerance
+            // The 'right' jitter tolerance for this network. Bigger networks need more tolerance. Denser networks need less tolerance. Totally empiric.
+            double estimatedOptimalJitterTolerance = 0.05 * Math.sqrt(nodes.length);
+            double minJT = Math.sqrt(estimatedOptimalJitterTolerance);
+            double maxJT = 10;
+            double jt = jitterTolerance * Math.max(minJT, Math.min(maxJT, estimatedOptimalJitterTolerance * totalEffectiveTraction / Math.pow(nodes.length, 2)));
+
+            double minSpeedEfficiency = 0.05;
+
+            // Protection against erratic behavior
+            if (totalSwinging / totalEffectiveTraction > 2.0) {
+                if (speedEfficiency > minSpeedEfficiency) {
+                    speedEfficiency *= 0.5;
+                }
+                jt = Math.max(jt, jitterTolerance);
+            }
+
+            double targetSpeed = jt * speedEfficiency * totalEffectiveTraction / totalSwinging;
+
+            // Speed efficiency is how the speed really corresponds to the swinging vs. convergence tradeoff
+            // We adjust it slowly and carefully
+            if (totalSwinging > jt * totalEffectiveTraction) {
+                if (speedEfficiency > minSpeedEfficiency) {
+                    speedEfficiency *= 0.7;
+                }
+            } else if (speed < 1000) {
+                speedEfficiency *= 1.3;
+            }
+
+            // But the speed shoudn't rise too much too quickly, since it would make the convergence drop dramatically.
+            double maxRise = 0.5;   // Max rise: 50%
+            speed = speed + Math.min(targetSpeed - speed, maxRise * speed);
+
+            // Apply forces
+            if (isAdjustSizes()) {
+                // If nodes overlap prevention is active, it's not possible to trust the swinging mesure.
+                for (Node n : nodes) {
+                    ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                    if (!n.isFixed()) {
+
+                        // Adaptive auto-speed: the speed of each node is lowered
+                        // when the node swings.
+                        double swinging = nLayout.mass * Math.sqrt((nLayout.old_dx - nLayout.dx) * (nLayout.old_dx - nLayout.dx) + (nLayout.old_dy - nLayout.dy) * (nLayout.old_dy - nLayout.dy));
+                        double factor = 0.1 * speed / (1f + Math.sqrt(speed * swinging));
+
+                        double df = Math.sqrt(Math.pow(nLayout.dx, 2) + Math.pow(nLayout.dy, 2));
+                        factor = Math.min(factor * df, 10.) / df;
+
+                        double x = n.x() + nLayout.dx * factor;
+                        double y = n.y() + nLayout.dy * factor;
+
+                        n.setX((float) x);
+                        n.setY((float) y);
+                    }
+                }
+            } else {
+                for (Node n : nodes) {
+                    ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                    if (!n.isFixed()) {
+
+                        // Adaptive auto-speed: the speed of each node is lowered
+                        // when the node swings.
+                        double swinging = nLayout.mass * Math.sqrt((nLayout.old_dx - nLayout.dx) * (nLayout.old_dx - nLayout.dx) + (nLayout.old_dy - nLayout.dy) * (nLayout.old_dy - nLayout.dy));
+                        //double factor = speed / (1f + Math.sqrt(speed * swinging));
+                        double factor = speed / (1f + Math.sqrt(speed * swinging));
+
+                        double x = n.x() + nLayout.dx * factor;
+                        double y = n.y() + nLayout.dy * factor;
+
+                        n.setX((float) x);
+                        n.setY((float) y);
+                    }
+                }
+            }
+        } finally {
+            graph.readUnlockAll();
+        }
+    }
+
+    @Override
+    public boolean canAlgo() {
+        return graphModel != null;
+    }
+
+    @Override
+    public void endAlgo() {
+        graph.readLock();
+        try {
+            for (Node n : graph.getNodes()) {
+                n.setLayoutData(null);
+            }
+            pool.shutdown();
+        } finally {
+            graph.readUnlockAll();
+        }
+    }
+
+    // BOOKMARK FOR POSSIBLE NAME CHANGE
+
+    @Override
+    public LayoutProperty[] getProperties() {
+        List<LayoutProperty> properties = new ArrayList<LayoutProperty>();
+        final String FORCEATLAS2_TUNING = NbBundle.getMessage(getClass(), "ForceAtlas2.tuning");
+        final String FORCEATLAS2_BEHAVIOR = NbBundle.getMessage(getClass(), "ForceAtlas2.behavior");
+        final String FORCEATLAS2_PERFORMANCE = NbBundle.getMessage(getClass(), "ForceAtlas2.performance");
+        final String FORCEATLAS2_THREADS = NbBundle.getMessage(getClass(), "ForceAtlas2.threads");
+
+        try {
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.scalingRatio.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.scalingRatio.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.scalingRatio.desc"),
+                    "getScalingRatio", "setScalingRatio"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.strongGravityMode.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.desc"),
+                    "isStrongGravityMode", "setStrongGravityMode"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.gravity.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.gravity.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.gravity.desc"),
+                    "getGravity", "setGravity"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.distributedAttraction.name"),
+                    FORCEATLAS2_BEHAVIOR,
+                    "ForceAtlas2.distributedAttraction.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.distributedAttraction.desc"),
+                    "isOutboundAttractionDistribution", "setOutboundAttractionDistribution"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.linLogMode.name"),
+                    FORCEATLAS2_BEHAVIOR,
+                    "ForceAtlas2.linLogMode.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.linLogMode.desc"),
+                    "isLinLogMode", "setLinLogMode"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.adjustSizes.name"),
+                    FORCEATLAS2_BEHAVIOR,
+                    "ForceAtlas2.adjustSizes.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.adjustSizes.desc"),
+                    "isAdjustSizes", "setAdjustSizes"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.edgeWeightInfluence.name"),
+                    FORCEATLAS2_BEHAVIOR,
+                    "ForceAtlas2.edgeWeightInfluence.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.edgeWeightInfluence.desc"),
+                    "getEdgeWeightInfluence", "setEdgeWeightInfluence"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.jitterTolerance.name"),
+                    FORCEATLAS2_PERFORMANCE,
+                    "ForceAtlas2.jitterTolerance.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.jitterTolerance.desc"),
+                    "getJitterTolerance", "setJitterTolerance"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.barnesHutOptimization.name"),
+                    FORCEATLAS2_PERFORMANCE,
+                    "ForceAtlas2.barnesHutOptimization.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.barnesHutOptimization.desc"),
+                    "isBarnesHutOptimize", "setBarnesHutOptimize"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.barnesHutTheta.name"),
+                    FORCEATLAS2_PERFORMANCE,
+                    "ForceAtlas2.barnesHutTheta.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.barnesHutTheta.desc"),
+                    "getBarnesHutTheta", "setBarnesHutTheta"));
+
+            properties.add(LayoutProperty.createProperty(
+                    this, Integer.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.threads.name"),
+                    FORCEATLAS2_THREADS,
+                    "ForceAtlas2.threads.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.threads.desc"),
+                    "getThreadsCount", "setThreadsCount"));
+
+        } catch (Exception e) {
+            Exceptions.printStackTrace(e);
+        }
+
+        return properties.toArray(new LayoutProperty[0]);
+    }
+
+    @Override
+    public void resetPropertiesValues() {
+        int nodesCount = 0;
+
+        if (graphModel != null) {
+            nodesCount = graphModel.getGraphVisible().getNodeCount();
+        }
+
+        // Tuning
+        if (nodesCount >= 100) {
+            setScalingRatio(2.0);
+        } else {
+            setScalingRatio(10.0);
+        }
+        setStrongGravityMode(false);
+        setGravity(1.);
+
+        // Behavior
+        setOutboundAttractionDistribution(false);
+        setLinLogMode(false);
+        setAdjustSizes(false);
+        setEdgeWeightInfluence(1.);
+
+        // Performance
+        setJitterTolerance(1d);
+        if (nodesCount >= 1000) {
+            setBarnesHutOptimize(true);
+        } else {
+            setBarnesHutOptimize(false);
+        }
+        setBarnesHutTheta(1.2);
+        setThreadsCount(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
+    }
+
+    @Override
+    public LayoutBuilder getBuilder() {
+        return layoutBuilder;
+    }
+
+    @Override
+    public void setGraphModel(GraphModel graphModel) {
+        this.graphModel = graphModel;
+        // Trick: reset here to take the profile of the graph in account for default values
+        resetPropertiesValues();
+    }
+
+    public Double getBarnesHutTheta() {
+        return barnesHutTheta;
+    }
+
+    public void setBarnesHutTheta(Double barnesHutTheta) {
+        this.barnesHutTheta = barnesHutTheta;
+    }
+
+    public Double getEdgeWeightInfluence() {
+        return edgeWeightInfluence;
+    }
+
+    public void setEdgeWeightInfluence(Double edgeWeightInfluence) {
+        this.edgeWeightInfluence = edgeWeightInfluence;
+    }
+
+    public Double getJitterTolerance() {
+        return jitterTolerance;
+    }
+
+    public void setJitterTolerance(Double jitterTolerance) {
+        this.jitterTolerance = jitterTolerance;
+    }
+
+    public Boolean isLinLogMode() {
+        return linLogMode;
+    }
+
+    public void setLinLogMode(Boolean linLogMode) {
+        this.linLogMode = linLogMode;
+    }
+
+    public Double getScalingRatio() {
+        return scalingRatio;
+    }
+
+    public void setScalingRatio(Double scalingRatio) {
+        this.scalingRatio = scalingRatio;
+    }
+
+    public Boolean isStrongGravityMode() {
+        return strongGravityMode;
+    }
+
+    public void setStrongGravityMode(Boolean strongGravityMode) {
+        this.strongGravityMode = strongGravityMode;
+    }
+
+    public Double getGravity() {
+        return gravity;
+    }
+
+    public void setGravity(Double gravity) {
+        this.gravity = gravity;
+    }
+
+    public Integer getThreadsCount() {
+        return threadCount;
+    }
+
+    public void setThreadsCount(Integer threadCount) {
+        this.threadCount = Math.max(1, threadCount);
+    }
+
+    public Boolean isOutboundAttractionDistribution() {
+        return outboundAttractionDistribution;
+    }
+
+    public void setOutboundAttractionDistribution(Boolean outboundAttractionDistribution) {
+        this.outboundAttractionDistribution = outboundAttractionDistribution;
+    }
+
+    public Boolean isAdjustSizes() {
+        return adjustSizes;
+    }
+
+    public void setAdjustSizes(Boolean adjustSizes) {
+        this.adjustSizes = adjustSizes;
+    }
+
+    public Boolean isBarnesHutOptimize() {
+        return barnesHutOptimize;
+    }
+
+    public void setBarnesHutOptimize(Boolean barnesHutOptimize) {
+        this.barnesHutOptimize = barnesHutOptimize;
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2Builder.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2Builder.java
new file mode 100644
index 0000000..cd8ab06
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2Builder.java
@@ -0,0 +1,105 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+package org.gephi.layout.plugins.layout.NodeWeight;
+// package org.gephi.layout.plugin.NodeWeight;
+
+import javax.swing.Icon;
+import javax.swing.JPanel;
+import org.gephi.layout.spi.Layout;
+import org.gephi.layout.spi.LayoutBuilder;
+import org.gephi.layout.spi.LayoutUI;
+import org.openide.util.NbBundle;
+import org.openide.util.lookup.ServiceProvider;
+
+/**
+ * Layout Builder
+ * @author Mathieu Jacomy
+ */
+@ServiceProvider(service = LayoutBuilder.class)
+public class ForceAtlas2Builder implements LayoutBuilder {
+
+    private ForceAtlas2UI ui = new ForceAtlas2UI();
+
+    @Override
+    public String getName() {
+        return NbBundle.getMessage(ForceAtlas2.class, "NodeWeight.name");
+    }
+
+    @Override
+    public LayoutUI getUI() {
+        return ui;
+    }
+
+    @Override
+    public ForceAtlas2 buildLayout() {
+        ForceAtlas2 layout = new ForceAtlas2(this);
+        return layout;
+    }
+
+    private class ForceAtlas2UI implements LayoutUI {
+
+        @Override
+        public String getDescription() {
+            return NbBundle.getMessage(ForceAtlas2.class, "NodeWeight.description");
+        }
+
+        @Override
+        public Icon getIcon() {
+            return null;
+        }
+
+        @Override
+        public JPanel getSimplePanel(Layout layout) {
+            return null;
+        }
+
+        @Override
+        public int getQualityRank() {
+            return 4;
+        }
+
+        @Override
+        public int getSpeedRank() {
+            return 4;
+        }
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2LayoutData.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2LayoutData.java
new file mode 100644
index 0000000..ddeb8c7
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2LayoutData.java
@@ -0,0 +1,61 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.spi.LayoutData;
+
+/**
+ * Data stored in Nodes and used by ForceAtlas2
+ * @author Mathieu Jacomy
+ */
+public class ForceAtlas2LayoutData implements LayoutData {
+    //Data
+
+
+    public double dx = 0;
+    public double dy = 0;
+    public double old_dx = 0;
+    public double old_dy = 0;
+    public double mass = 1;
+    // weight
+    public double weight = 0;
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceFactory.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceFactory.java
new file mode 100644
index 0000000..7a9639e
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceFactory.java
@@ -0,0 +1,577 @@
+/*
+ Copyright 2008-2011 Gephi
+ Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2011 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.api.Node;
+
+/**
+ * Generates the forces on demand, here are all the formulas for attraction and
+ * repulsion.
+ *
+ * @author Mathieu Jacomy
+ */
+public class ForceFactory {
+
+    public static ForceFactory builder = new ForceFactory();
+
+    private ForceFactory() {
+    }
+
+    public RepulsionForce buildRepulsion(boolean adjustBySize, double coefficient) {
+        if (adjustBySize) {
+            return new linRepulsion_antiCollision(coefficient);
+        } else {
+            return new linRepulsion(coefficient);
+        }
+    }
+
+    public RepulsionForce getStrongGravity(double coefficient) {
+        return new strongGravity(coefficient);
+    }
+
+    public AttractionForce buildAttraction(boolean logAttraction, boolean distributedAttraction, boolean adjustBySize, double coefficient) {
+        if (adjustBySize) {
+            if (logAttraction) {
+                if (distributedAttraction) {
+                    return new logAttraction_degreeDistributed_antiCollision(coefficient);
+                } else {
+                    return new logAttraction_antiCollision(coefficient);
+                }
+            } else {
+                if (distributedAttraction) {
+                    return new linAttraction_degreeDistributed_antiCollision(coefficient);
+                } else {
+                    return new linAttraction_antiCollision(coefficient);
+                }
+            }
+        } else {
+            if (logAttraction) {
+                if (distributedAttraction) {
+                    return new logAttraction_degreeDistributed(coefficient);
+                } else {
+                    return new logAttraction(coefficient);
+                }
+            } else {
+                if (distributedAttraction) {
+                    return new linAttraction_massDistributed(coefficient);
+                } else {
+                    return new linAttraction(coefficient);
+                }
+            }
+        }
+    }
+
+    public abstract class AttractionForce {
+
+        public abstract void apply(Node n1, Node n2, double e); // Model for node-node attraction (e is for edge weight if needed)
+    }
+
+    public abstract class RepulsionForce {
+
+        public abstract void apply(Node n1, Node n2);           // Model for node-node repulsion
+
+        public abstract void apply(Node n, Region r);           // Model for Barnes Hut approximation
+
+        public abstract void apply(Node n, double g);           // Model for gravitation (anti-repulsion)
+    }
+
+    /*
+     * Repulsion force: Linear
+     */
+    private class linRepulsion extends RepulsionForce {
+
+        private double coefficient;
+
+        public linRepulsion(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * n1Layout.mass * n2Layout.mass / distance / distance;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+
+        @Override
+        public void apply(Node n, Region r) {
+            ForceAtlas2LayoutData nLayout = n.getLayoutData();
+
+            // Get the distance
+            double xDist = n.x() - r.getMassCenterX();
+            double yDist = n.y() - r.getMassCenterY();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * nLayout.mass * r.getMass() / distance / distance;
+
+                nLayout.dx += xDist * factor;
+                nLayout.dy += yDist * factor;
+            }
+        }
+
+        @Override
+        public void apply(Node n, double g) {
+            ForceAtlas2LayoutData nLayout = n.getLayoutData();
+
+            // Get the distance
+            double xDist = n.x();
+            double yDist = n.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * nLayout.mass * g / distance;
+
+                nLayout.dx -= xDist * factor;
+                nLayout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Repulsion force: Strong Gravity (as a Repulsion Force because it is easier)
+     */
+    private class linRepulsion_antiCollision extends RepulsionForce {
+
+        private double coefficient;
+
+        public linRepulsion_antiCollision(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = Math.sqrt(xDist * xDist + yDist * yDist) - n1.size() - n2.size();
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * n1Layout.mass * n2Layout.mass / distance / distance;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+
+            } else if (distance < 0) {
+                double factor = 100 * coefficient * n1Layout.mass * n2Layout.mass;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+
+        @Override
+        public void apply(Node n, Region r) {
+            ForceAtlas2LayoutData nLayout = n.getLayoutData();
+
+            // Get the distance
+            double xDist = n.x() - r.getMassCenterX();
+            double yDist = n.y() - r.getMassCenterY();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * nLayout.mass * r.getMass() / distance / distance;
+
+                nLayout.dx += xDist * factor;
+                nLayout.dy += yDist * factor;
+            } else if (distance < 0) {
+                double factor = -coefficient * nLayout.mass * r.getMass() / distance;
+
+                nLayout.dx += xDist * factor;
+                nLayout.dy += yDist * factor;
+            }
+        }
+
+        @Override
+        public void apply(Node n, double g) {
+            ForceAtlas2LayoutData nLayout = n.getLayoutData();
+
+            // Get the distance
+            double xDist = n.x();
+            double yDist = n.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * nLayout.mass * g / distance;
+
+                nLayout.dx -= xDist * factor;
+                nLayout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    private class strongGravity extends RepulsionForce {
+
+        private double coefficient;
+
+        public strongGravity(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2) {
+            // Not Relevant
+        }
+
+        @Override
+        public void apply(Node n, Region r) {
+            // Not Relevant
+        }
+
+        @Override
+        public void apply(Node n, double g) {
+            ForceAtlas2LayoutData nLayout = n.getLayoutData();
+
+            // Get the distance
+            double xDist = n.x();
+            double yDist = n.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = coefficient * nLayout.mass * g;
+
+                nLayout.dx -= xDist * factor;
+                nLayout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Attraction force: Linear
+     */
+    private class linAttraction extends AttractionForce {
+
+        private double coefficient;
+
+        public linAttraction(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+
+            // NB: factor = force / distance
+            double factor = -coefficient * e;
+
+            n1Layout.dx += xDist * factor;
+            n1Layout.dy += yDist * factor;
+
+            n2Layout.dx -= xDist * factor;
+            n2Layout.dy -= yDist * factor;
+        }
+    }
+
+    /*
+     * Attraction force: Linear, distributed by mass (typically, degree)
+     */
+    private class linAttraction_massDistributed extends AttractionForce {
+
+        private double coefficient;
+
+        public linAttraction_massDistributed(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+
+            // NB: factor = force / distance
+            double factor = -coefficient * e / n1Layout.mass;
+
+            n1Layout.dx += xDist * factor;
+            n1Layout.dy += yDist * factor;
+
+            n2Layout.dx -= xDist * factor;
+            n2Layout.dy -= yDist * factor;
+        }
+    }
+
+    /*
+     * Attraction force: Logarithmic
+     */
+    private class logAttraction extends AttractionForce {
+
+        private double coefficient;
+
+        public logAttraction(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+
+                // NB: factor = force / distance
+                double factor = -coefficient * e * Math.log(1 + distance) / distance;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Attraction force: Linear, distributed by Degree
+     */
+    private class logAttraction_degreeDistributed extends AttractionForce {
+
+        private double coefficient;
+
+        public logAttraction_degreeDistributed(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = (float) Math.sqrt(xDist * xDist + yDist * yDist);
+
+            if (distance > 0) {
+
+                // NB: factor = force / distance
+                double factor = -coefficient * e * Math.log(1 + distance) / distance / n1Layout.mass;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Attraction force: Linear, with Anti-Collision
+     */
+    private class linAttraction_antiCollision extends AttractionForce {
+
+        private double coefficient;
+
+        public linAttraction_antiCollision(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = Math.sqrt(xDist * xDist + yDist * yDist) - n1.size() - n2.size();
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = -coefficient * e;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Attraction force: Linear, distributed by Degree, with Anti-Collision
+     */
+    private class linAttraction_degreeDistributed_antiCollision extends AttractionForce {
+
+        private double coefficient;
+
+        public linAttraction_degreeDistributed_antiCollision(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = Math.sqrt(xDist * xDist + yDist * yDist) - n1.size() - n2.size();
+
+            if (distance > 0) {
+                // NB: factor = force / distance
+                double factor = -coefficient * e / n1Layout.mass;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Attraction force: Logarithmic, with Anti-Collision
+     */
+    private class logAttraction_antiCollision extends AttractionForce {
+
+        private double coefficient;
+
+        public logAttraction_antiCollision(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = Math.sqrt(xDist * xDist + yDist * yDist) - n1.size() - n2.size();
+
+            if (distance > 0) {
+
+                // NB: factor = force / distance
+                double factor = -coefficient * e * Math.log(1 + distance) / distance;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+    }
+
+    /*
+     * Attraction force: Linear, distributed by Degree, with Anti-Collision
+     */
+    private class logAttraction_degreeDistributed_antiCollision extends AttractionForce {
+
+        private double coefficient;
+
+        public logAttraction_degreeDistributed_antiCollision(double c) {
+            coefficient = c;
+        }
+
+        @Override
+        public void apply(Node n1, Node n2, double e) {
+            ForceAtlas2LayoutData n1Layout = n1.getLayoutData();
+            ForceAtlas2LayoutData n2Layout = n2.getLayoutData();
+
+            // Get the distance
+            double xDist = n1.x() - n2.x();
+            double yDist = n1.y() - n2.y();
+            double distance = Math.sqrt(xDist * xDist + yDist * yDist) - n1.size() - n2.size();
+
+            if (distance > 0) {
+
+                // NB: factor = force / distance
+                double factor = -coefficient * e * Math.log(1 + distance) / distance / n1Layout.mass;
+
+                n1Layout.dx += xDist * factor;
+                n1Layout.dy += yDist * factor;
+
+                n2Layout.dx -= xDist * factor;
+                n2Layout.dy -= yDist * factor;
+            }
+        }
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/NodesThread.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/NodesThread.java
new file mode 100644
index 0000000..170b0b8
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/NodesThread.java
@@ -0,0 +1,102 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu Jacomy
+ */
+public class NodesThread implements Runnable {
+
+    private Node[] nodes;
+    private int from;
+    private int to;
+    private Region rootRegion;
+    private boolean barnesHutOptimize;
+    private RepulsionForce Repulsion;
+    private double barnesHutTheta;
+    private double gravity;
+    private RepulsionForce GravityForce;
+    private double scaling;
+
+    public NodesThread(Node[] nodes, int from, int to, boolean barnesHutOptimize, double barnesHutTheta, double gravity, RepulsionForce GravityForce, double scaling, Region rootRegion, RepulsionForce Repulsion) {
+        this.nodes = nodes;
+        this.from = from;
+        this.to = to;
+        this.rootRegion = rootRegion;
+        this.barnesHutOptimize = barnesHutOptimize;
+        this.Repulsion = Repulsion;
+        this.barnesHutTheta = barnesHutTheta;
+        this.gravity = gravity;
+        this.GravityForce = GravityForce;
+        this.scaling = scaling;
+    }
+
+    @Override
+    public void run() {
+        // Repulsion
+        if (barnesHutOptimize) {
+            for (int nIndex = from; nIndex < to; nIndex++) {
+                Node n = nodes[nIndex];
+                rootRegion.applyForce(n, Repulsion, barnesHutTheta);
+            }
+        } else {
+            for (int n1Index = from; n1Index < to; n1Index++) {
+                Node n1 = nodes[n1Index];
+                for (int n2Index = 0; n2Index < n1Index; n2Index++) {
+                    Node n2 = nodes[n2Index];
+                    Repulsion.apply(n1, n2);
+                }
+            }
+        }
+
+        // Gravity
+        for (int nIndex = from; nIndex < to; nIndex++) {
+            Node n = nodes[nIndex];
+            GravityForce.apply(n, gravity / scaling);
+        }
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Operation.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Operation.java
new file mode 100644
index 0000000..771b0a6
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Operation.java
@@ -0,0 +1,51 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+/**
+ *
+ * @author Mathieu Jacomy
+ */
+public abstract class Operation {
+
+    public abstract void execute();
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeAttract.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeAttract.java
new file mode 100644
index 0000000..5e8bcea
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeAttract.java
@@ -0,0 +1,70 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
+
+/**
+ *
+ * @author Mathieu Jacomy
+ */
+public class OperationNodeNodeAttract extends Operation {
+
+    private final Node n1;
+    private final Node n2;
+    private final AttractionForce f;
+    private final double coefficient;
+
+    public OperationNodeNodeAttract(Node n1, Node n2, AttractionForce f, double coefficient) {
+        this.n1 = n1;
+        this.n2 = n2;
+        this.f = f;
+        this.coefficient = coefficient;
+    }
+
+    @Override
+    public void execute() {
+        f.apply(n1, n2, coefficient);
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeRepulse.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeRepulse.java
new file mode 100644
index 0000000..4f78bd8
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeNodeRepulse.java
@@ -0,0 +1,68 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu Jacomy
+ */
+public class OperationNodeNodeRepulse extends Operation {
+
+    private final Node n1;
+    private final Node n2;
+    private final RepulsionForce f;
+
+    public OperationNodeNodeRepulse(Node n1, Node n2, RepulsionForce f) {
+        this.n1 = n1;
+        this.n2 = n2;
+        this.f = f;
+    }
+
+    @Override
+    public void execute() {
+        f.apply(n1, n2);
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRegionRepulse.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRegionRepulse.java
new file mode 100644
index 0000000..76ba361
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRegionRepulse.java
@@ -0,0 +1,70 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu Jacomy
+ */
+public class OperationNodeRegionRepulse extends Operation {
+
+    private final Node n;
+    private final Region r;
+    private final RepulsionForce f;
+    private final double theta;
+
+    public OperationNodeRegionRepulse(Node n, Region r, RepulsionForce f, double theta) {
+        this.n = n;
+        this.f = f;
+        this.r = r;
+        this.theta = theta;
+    }
+
+    @Override
+    public void execute() {
+        r.applyForce(n, f, theta);
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRepulse.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRepulse.java
new file mode 100644
index 0000000..cf5fd1e
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/OperationNodeRepulse.java
@@ -0,0 +1,68 @@
+/*
+Copyright 2008-2011 Gephi
+Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+Website : http://www.gephi.org
+
+This file is part of Gephi.
+
+DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+Copyright 2011 Gephi Consortium. All rights reserved.
+
+The contents of this file are subject to the terms of either the GNU
+General Public License Version 3 only ("GPL") or the Common
+Development and Distribution License("CDDL") (collectively, the
+"License"). You may not use this file except in compliance with the
+License. You can obtain a copy of the License at
+http://gephi.org/about/legal/license-notice/
+or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+specific language governing permissions and limitations under the
+License.  When distributing the software, include this License Header
+Notice in each file and include the License files at
+/cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+License Header, with the fields enclosed by brackets [] replaced by
+your own identifying information:
+"Portions Copyrighted [year] [name of copyright owner]"
+
+If you wish your version of this file to be governed by only the CDDL
+or only the GPL Version 3, indicate your decision by adding
+"[Contributor] elects to include this software in this distribution
+under the [CDDL or GPL Version 3] license." If you do not indicate a
+single choice of license, a recipient has the option to distribute
+your version of this file under either the CDDL, the GPL Version 3 or
+to extend the choice of license to its licensees as provided above.
+However, if you add GPL Version 3 code and therefore, elected the GPL
+Version 3 license, then the option applies only if the new code is
+made subject to such option by the copyright holder.
+
+Contributor(s):
+
+Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+/**
+ *
+ * @author Mathieu Jacomy
+ */
+public class OperationNodeRepulse extends Operation {
+
+    private Node n;
+    private RepulsionForce f;
+    private double coefficient;
+
+    public OperationNodeRepulse(Node n, RepulsionForce f, double coefficient) {
+        this.n = n;
+        this.f = f;
+        this.coefficient = coefficient;
+    }
+
+    @Override
+    public void execute() {
+        f.apply(n, coefficient);
+    }
+}
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Region.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Region.java
new file mode 100644
index 0000000..1277929
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/Region.java
@@ -0,0 +1,222 @@
+/*
+ Copyright 2008-2011 Gephi
+ Authors : Mathieu Jacomy <mathieu.jacomy@gmail.com>
+ Website : http://www.gephi.org
+
+ This file is part of Gephi.
+
+ DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+
+ Copyright 2011 Gephi Consortium. All rights reserved.
+
+ The contents of this file are subject to the terms of either the GNU
+ General Public License Version 3 only ("GPL") or the Common
+ Development and Distribution License("CDDL") (collectively, the
+ "License"). You may not use this file except in compliance with the
+ License. You can obtain a copy of the License at
+ http://gephi.org/about/legal/license-notice/
+ or /cddl-1.0.txt and /gpl-3.0.txt. See the License for the
+ specific language governing permissions and limitations under the
+ License.  When distributing the software, include this License Header
+ Notice in each file and include the License files at
+ /cddl-1.0.txt and /gpl-3.0.txt. If applicable, add the following below the
+ License Header, with the fields enclosed by brackets [] replaced by
+ your own identifying information:
+ "Portions Copyrighted [year] [name of copyright owner]"
+
+ If you wish your version of this file to be governed by only the CDDL
+ or only the GPL Version 3, indicate your decision by adding
+ "[Contributor] elects to include this software in this distribution
+ under the [CDDL or GPL Version 3] license." If you do not indicate a
+ single choice of license, a recipient has the option to distribute
+ your version of this file under either the CDDL, the GPL Version 3 or
+ to extend the choice of license to its licensees as provided above.
+ However, if you add GPL Version 3 code and therefore, elected the GPL
+ Version 3 license, then the option applies only if the new code is
+ made subject to such option by the copyright holder.
+
+ Contributor(s):
+
+ Portions Copyrighted 2011 Gephi Consortium.
+ */
+// package org.gephi.layout.plugin.NodeWeight;
+package org.gephi.layout.plugins.layout.NodeWeight;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import org.gephi.graph.api.Node;
+// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+/**
+ * Barnes Hut optimization
+ *
+ * @author Mathieu Jacomy
+ */
+public class Region {
+
+    private double mass;
+    private double massCenterX;
+    private double massCenterY;
+    private double size;
+    private final List<Node> nodes;
+    private final List<Region> subregions = new ArrayList<Region>();
+
+    public Region(Node[] nodes) {
+        this.nodes = new ArrayList<Node>();
+        this.nodes.addAll(Arrays.asList(nodes));
+        updateMassAndGeometry();
+    }
+
+    public Region(ArrayList<Node> nodes) {
+        this.nodes = new ArrayList<Node>(nodes);
+        updateMassAndGeometry();
+    }
+
+    private void updateMassAndGeometry() {
+        if (nodes.size() > 1) {
+            // Compute Mass
+            mass = 0;
+            double massSumX = 0;
+            double massSumY = 0;
+            for (Node n : nodes) {
+                ForceAtlas2LayoutData nLayout = n.getLayoutData();
+                mass += nLayout.mass;
+                massSumX += n.x() * nLayout.mass;
+                massSumY += n.y() * nLayout.mass;
+            }
+            massCenterX = massSumX / mass;
+            massCenterY = massSumY / mass;
+
+            // Compute size
+            size = Double.MIN_VALUE;
+            for (Node n : nodes) {
+                double distance = Math.sqrt((n.x() - massCenterX) * (n.x() - massCenterX) + (n.y() - massCenterY) * (n.y() - massCenterY));
+                size = Math.max(size, 2 * distance);
+            }
+        }
+    }
+
+    public synchronized void buildSubRegions() {
+        if (nodes.size() > 1) {
+            ArrayList<Node> leftNodes = new ArrayList<Node>();
+            ArrayList<Node> rightNodes = new ArrayList<Node>();
+            for (Node n : nodes) {
+                ArrayList<Node> nodesColumn = (n.x() < massCenterX) ? (leftNodes) : (rightNodes);
+                nodesColumn.add(n);
+            }
+
+            ArrayList<Node> topleftNodes = new ArrayList<Node>();
+            ArrayList<Node> bottomleftNodes = new ArrayList<Node>();
+            for (Node n : leftNodes) {
+                ArrayList<Node> nodesLine = (n.y() < massCenterY) ? (topleftNodes) : (bottomleftNodes);
+                nodesLine.add(n);
+            }
+
+            ArrayList<Node> bottomrightNodes = new ArrayList<Node>();
+            ArrayList<Node> toprightNodes = new ArrayList<Node>();
+            for (Node n : rightNodes) {
+                ArrayList<Node> nodesLine = (n.y() < massCenterY) ? (toprightNodes) : (bottomrightNodes);
+                nodesLine.add(n);
+            }
+
+            if (topleftNodes.size() > 0) {
+                if (topleftNodes.size() < nodes.size()) {
+                    Region subregion = new Region(topleftNodes);
+                    subregions.add(subregion);
+                } else {
+                    for (Node n : topleftNodes) {
+                        ArrayList<Node> oneNodeList = new ArrayList<Node>();
+                        oneNodeList.add(n);
+                        Region subregion = new Region(oneNodeList);
+                        subregions.add(subregion);
+                    }
+                }
+            }
+            if (bottomleftNodes.size() > 0) {
+                if (bottomleftNodes.size() < nodes.size()) {
+                    Region subregion = new Region(bottomleftNodes);
+                    subregions.add(subregion);
+                } else {
+                    for (Node n : bottomleftNodes) {
+                        ArrayList<Node> oneNodeList = new ArrayList<Node>();
+                        oneNodeList.add(n);
+                        Region subregion = new Region(oneNodeList);
+                        subregions.add(subregion);
+                    }
+                }
+            }
+            if (bottomrightNodes.size() > 0) {
+                if (bottomrightNodes.size() < nodes.size()) {
+                    Region subregion = new Region(bottomrightNodes);
+                    subregions.add(subregion);
+                } else {
+                    for (Node n : bottomrightNodes) {
+                        ArrayList<Node> oneNodeList = new ArrayList<Node>();
+                        oneNodeList.add(n);
+                        Region subregion = new Region(oneNodeList);
+                        subregions.add(subregion);
+                    }
+                }
+            }
+            if (toprightNodes.size() > 0) {
+                if (toprightNodes.size() < nodes.size()) {
+                    Region subregion = new Region(toprightNodes);
+                    subregions.add(subregion);
+                } else {
+                    for (Node n : toprightNodes) {
+                        ArrayList<Node> oneNodeList = new ArrayList<Node>();
+                        oneNodeList.add(n);
+                        Region subregion = new Region(oneNodeList);
+                        subregions.add(subregion);
+                    }
+                }
+            }
+
+            for (Region subregion : subregions) {
+                subregion.buildSubRegions();
+            }
+        }
+    }
+
+    public void applyForce(Node n, RepulsionForce Force, double theta) {
+        if (nodes.size() < 2) {
+            Node regionNode = nodes.get(0);
+            Force.apply(n, regionNode);
+        } else {
+            double distance = Math.sqrt((n.x() - massCenterX) * (n.x() - massCenterX) + (n.y() - massCenterY) * (n.y() - massCenterY));
+            if (distance * theta > size) {
+                Force.apply(n, this);
+            } else {
+                for (Region subregion : subregions) {
+                    subregion.applyForce(n, Force, theta);
+                }
+            }
+        }
+    }
+
+    public double getMass() {
+        return mass;
+    }
+
+    public void setMass(double mass) {
+        this.mass = mass;
+    }
+
+    public double getMassCenterX() {
+        return massCenterX;
+    }
+
+    public void setMassCenterX(double massCenterX) {
+        this.massCenterX = massCenterX;
+    }
+
+    public double getMassCenterY() {
+        return massCenterY;
+    }
+
+    public void setMassCenterY(double massCenterY) {
+        this.massCenterY = massCenterY;
+    }
+}
diff --git a/modules/NodeWeight/src/main/nbm/manifest.mf b/modules/NodeWeight/src/main/nbm/manifest.mf
new file mode 100644
index 0000000..9e84c49
--- /dev/null
+++ b/modules/NodeWeight/src/main/nbm/manifest.mf
@@ -0,0 +1,5 @@
+Manifest-Version: 1.0
+OpenIDE-Module-Name: Node Weight
+OpenIDE-Module-Display-Category: Layout
+OpenIDE-Module-Short-Description: adds node to FA2
+OpenIDE-Module-Long-Description: see above
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
new file mode 100644
index 0000000..0d8c4b7
--- /dev/null
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -0,0 +1,16 @@
+#OpenIDE-Module-Display-Category=Layout
+#OpenIDE-Module-Long-Description=\
+#    Example of Layout Plugins:\n<ul>\n<li><b>Grid Layout:</b> Place all nodes in a simple grid. \
+#    Users can configure the size of the area and the speed.\
+#    </li>\n<li><b>Sorted Grid Layout:</b> Same example as Grid Layout but users can sort nodes with an attribute column.\
+#    </li>\n</ul>
+#OpenIDE-Module-Name=NodeWeight
+#OpenIDE-Module-Short-Description=add node weight to FA2 algorithm
+
+
+
+
+NodeWeight.name=Node Weight
+NodeWeight.description=Quality layout: a linear-attraction linear-repulsion model with few approximations (BarnesHut). Speed automatically computed.
+
+
diff --git a/pom.xml b/pom.xml
index f13a911..0123888 100644
--- a/pom.xml
+++ b/pom.xml
@@ -8,11 +8,11 @@
     <packaging>pom</packaging>
 
     <name>gephi-plugins</name>
-    
+
     <!-- List of modules -->
     <modules>
         <!-- Add here the paths of all modules (e.g. <module>modules/MyModule</module>) -->
-        <module>modules/PluginsSubMenuExample</module>
+        <!-- <module>modules/PluginsSubMenuExample</module>
         <module>modules/StatisticsPluginExample</module>
         <module>modules/ToolPluginExample</module>
         <module>modules/ImportPluginExample</module>
@@ -25,8 +25,10 @@
         <module>modules/ExportPluginExample</module>
         <module>modules/PreviewPluginExample</module>
         <module>modules/LayoutPluginExample</module>
+        <module>modules/LayoutPluginExample</module> -->
+        <module>modules/NodeWeight</module>
     </modules>
-    
+
     <!-- Properties -->
     <properties>
         <!-- Version of Gephi building plugins against. Plugins with anterior versions will be ignored -->
@@ -34,7 +36,7 @@
         <clusters.path>${project.build.directory}/plugins_clusters</clusters.path>
         <github.global.server>github</github.global.server>
     </properties>
-    
+
     <!-- SCM -->
     <scm>
         <connection>scm:git:git://github.com/gephi/gephi-plugins.git</connection>
@@ -53,7 +55,7 @@
             </snapshots>
         </repository>
     </repositories>
-    
+
     <!-- Plugin Repositories -->
     <pluginRepositories>
         <pluginRepository>
@@ -76,7 +78,7 @@
             <type>tar.gz</type>
         </dependency>
     </dependencies>
-    
+
     <build>
         <!-- Plugins installed with versions -->
         <pluginManagement>
@@ -109,7 +111,7 @@
                 </plugin>
             </plugins>
         </pluginManagement>
-        
+
         <!-- Plugins -->
         <plugins>
             <!-- Configure gephi-maven-plugin -->
@@ -126,7 +128,7 @@
                     </execution>
                 </executions>
             </plugin>
-            
+
             <!-- Unpack the localization dependency -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
@@ -148,7 +150,7 @@
                     </execution>
                 </executions>
             </plugin>
-            
+
             <!-- NBM Plugin -->
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
@@ -167,7 +169,7 @@
             </plugin>
         </plugins>
     </build>
-    
+
     <!-- Custom profile only used to build and package all modules at once -->
     <profiles>
         <profile>

From c09f5a8e9c90795cf027d5b7e131ce16fd3c902d Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Thu, 16 Aug 2018 19:48:22 +0100
Subject: [PATCH 02/32] hot fix on putting in weight column

---
 .../layout/plugins/layout/NodeWeight/#TODO    |  6 ++++
 .../layout/NodeWeight/ForceAtlas2.java        | 19 +++++++++++++
 .../layout/NodeWeight/Bundle.properties       | 28 +++++++++++++++++++
 3 files changed, 53 insertions(+)
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
new file mode 100644
index 0000000..d368b57
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
@@ -0,0 +1,6 @@
+#TODO
+
+1. check and validate if the column already exists
+  1a. check whether the column is dynamic
+2. add a column that can accept dynamic or not dynamic value
+  called "weight"
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 9f9973f..56a2929 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -46,6 +46,7 @@ Development and Distribution License("CDDL") (collectively, the
 import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.Node;
+import org.gephi.graph.api.Table;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
 import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
@@ -109,6 +110,11 @@ public void initAlgo() {
         speed = 1.;
         speedEfficiency = 1.;
 
+        Table table = graphModel.getNodeTable();
+        table.addColumn("weight", "weight", Double.class, (Double) 0.0);
+
+
+
         graph = graphModel.getGraphVisible();
 
         graph.readLock();
@@ -153,6 +159,13 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
+    // public void addWeightCol(graph){
+    //   graph.addColumn();
+    // }
+
+    // public void switchToDynamic(col){
+    //   return 0;
+    // }
 
     @Override
     public void goAlgo() {
@@ -160,7 +173,13 @@ public void goAlgo() {
         if (graphModel == null) {
             return;
         }
+
+        // Table table = graphModel.getNodeTable();
+        // table.addColumn("weight", Double.class);
+
+
         graph = graphModel.getGraphVisible();
+
         graph.readLock();
         boolean isDynamicWeight = graphModel.getEdgeTable().getColumn("weight").isDynamic();
         boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn("weight").isDynamic();
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index 0d8c4b7..16253ca 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -14,3 +14,31 @@ NodeWeight.name=Node Weight
 NodeWeight.description=Quality layout: a linear-attraction linear-repulsion model with few approximations (BarnesHut). Speed automatically computed.
 
 
+ForceAtlas2.tuning=Tuning
+ForceAtlas2.behavior=Behavior Alternatives
+ForceAtlas2.performance=Performance
+ForceAtlas2.threads=Threads
+
+ForceAtlas2.scalingRatio.name=Scaling
+ForceAtlas2.scalingRatio.desc=How much repulsion you want. More makes a more sparse graph.
+
+ForceAtlas2.gravity.name=Gravity
+ForceAtlas2.gravity.desc=Attracts nodes to the center. Prevents islands from drifting away.
+ForceAtlas2.strongGravityMode.name=Stronger Gravity
+ForceAtlas2.strongGravityMode.desc=A stronger gravity law
+ForceAtlas2.distributedAttraction.name=Dissuade Hubs
+ForceAtlas2.distributedAttraction.desc=Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
+ForceAtlas2.linLogMode.name=LinLog mode
+ForceAtlas2.linLogMode.desc=Switch ForceAtlas' model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight.
+ForceAtlas2.adjustSizes.name=Prevent Overlap
+ForceAtlas2.adjustSizes.desc=Use only when spatialized. Should not be used with "Approximate Repulsion"
+ForceAtlas2.jitterTolerance.name=Tolerance (speed)
+ForceAtlas2.jitterTolerance.desc=How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision.
+ForceAtlas2.barnesHutOptimization.name=Approximate Repulsion
+ForceAtlas2.barnesHutOptimization.desc=Barnes Hut optimization: n\u00b2 complexity to n.ln(n) ; allows larger graphs.
+ForceAtlas2.barnesHutTheta.name=Approximation
+ForceAtlas2.barnesHutTheta.desc=Theta of the Barnes Hut optimization.
+ForceAtlas2.edgeWeightInfluence.name=Edge Weight Influence
+ForceAtlas2.edgeWeightInfluence.desc=How much influence you give to the edges weight. 0 is "no influence" and 1 is "normal".
+ForceAtlas2.threads.name=Threads number
+ForceAtlas2.threads.desc=More threads means more speed if your cores can handle it.

From 46c559d8f45a388e88cf01bf745301003df1c29c Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Thu, 16 Aug 2018 22:25:39 +0100
Subject: [PATCH 03/32] real fix for nullpointer issue

---
 .../layout/NodeWeight/ForceAtlas2.java        | 24 +++++++++++++++----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 56a2929..0af0b73 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -111,7 +111,9 @@ public void initAlgo() {
         speedEfficiency = 1.;
 
         Table table = graphModel.getNodeTable();
-        table.addColumn("weight", "weight", Double.class, (Double) 0.0);
+        // table.addColumn("weight", "weight", Double.class, (Double) 0.0);
+        table.addColumn("weight", Double.class);
+
 
 
 
@@ -150,6 +152,14 @@ private double getEdgeWeight(Edge edge, boolean isDynamicWeight, Interval interv
         }
     }
 
+    private boolean hasNodeWeight(Node node) {
+      if (node.getAttribute("weight") != null) {
+        return true;
+      } else {
+        return false;
+      }
+    }
+
     private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
         if (isDynamicNodeWeight) {
             // node_weight = (Double) n.getAttribute("gravity_x");
@@ -240,7 +250,7 @@ public void goAlgo() {
                 }
             }
 //BOOKMARK
-          // Attraction
+        // Attractions (weights)
             // Edge Weight
             AttractionForce Attraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
             if (getEdgeWeightInfluence() == 0) {
@@ -256,16 +266,20 @@ public void goAlgo() {
                     Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
                 }
             }
+
             // Node Weight
             AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
             for (Edge e : edges) {
               Node node_a = e.getSource();
               Node node_b = e.getTarget();
 
-              Double wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
-              Double wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
+              if (hasNodeWeight(node_a) && hasNodeWeight(node_b)) {
+                Double wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
+                Double wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
+
+                NodeAttraction.apply(node_a, node_b, (getNodeWeight(node_a, isDynamicNodeWeight, interval) + getNodeWeight(node_b, isDynamicNodeWeight, interval))/2);
 
-              NodeAttraction.apply(node_a, node_b, (getNodeWeight(node_a, isDynamicNodeWeight, interval) + getNodeWeight(node_b, isDynamicNodeWeight, interval))/2);
+              }
 
 
 

From 6b048d2045e3359571a20f140b633804a7d80175 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Fri, 17 Aug 2018 14:16:35 +0100
Subject: [PATCH 04/32] it works, gephi 0.9.2

---
 .../layout/plugins/layout/NodeWeight/#TODO      | 17 +++++++++++++++--
 .../plugins/layout/NodeWeight/ForceAtlas2.java  | 11 ++++++++---
 pom.xml                                         |  4 ++--
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
index d368b57..8230d23 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
@@ -1,6 +1,19 @@
 #TODO
 
-1. check and validate if the column already exists
+To-do:
+1. add hsv transparency
+2. add size change
+3. make the node weight attraction more meaningful
+4. try out many use-cases to test plugin
+5. make good visualizations to be tested
+
+
+
+
+
+
+Done:
+ check and validate if the column already exists
   1a. check whether the column is dynamic
-2. add a column that can accept dynamic or not dynamic value
+ add a column that can accept dynamic or not dynamic value
   called "weight"
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 0af0b73..8fa6ba6 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -111,8 +111,12 @@ public void initAlgo() {
         speedEfficiency = 1.;
 
         Table table = graphModel.getNodeTable();
+
+        if (!(table.hasColumn("weight"))) {
+          table.addColumn("weight", Double.class);
+        }
         // table.addColumn("weight", "weight", Double.class, (Double) 0.0);
-        table.addColumn("weight", Double.class);
+        // table.addColumn("weight", Double.class);
 
 
 
@@ -250,7 +254,7 @@ public void goAlgo() {
                 }
             }
 //BOOKMARK
-        // Attractions (weights)
+          // Attraction
             // Edge Weight
             AttractionForce Attraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
             if (getEdgeWeightInfluence() == 0) {
@@ -266,8 +270,8 @@ public void goAlgo() {
                     Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
                 }
             }
-
             // Node Weight
+
             AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
             for (Edge e : edges) {
               Node node_a = e.getSource();
@@ -392,6 +396,7 @@ public void goAlgo() {
         }
     }
 
+
     @Override
     public boolean canAlgo() {
         return graphModel != null;
diff --git a/pom.xml b/pom.xml
index 0123888..6d0c3d6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -4,7 +4,7 @@
 
     <groupId>org.gephi</groupId>
     <artifactId>gephi-plugins</artifactId>
-    <version>0.9.0</version>
+    <version>0.9.2</version>
     <packaging>pom</packaging>
 
     <name>gephi-plugins</name>
@@ -32,7 +32,7 @@
     <!-- Properties -->
     <properties>
         <!-- Version of Gephi building plugins against. Plugins with anterior versions will be ignored -->
-        <gephi.version>0.9.0</gephi.version>
+        <gephi.version>0.9.2</gephi.version>
         <clusters.path>${project.build.directory}/plugins_clusters</clusters.path>
         <github.global.server>github</github.global.server>
     </properties>

From 44fcaf6ffb5a11f93f6664f2b4397c0555e7d8a4 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Sun, 19 Aug 2018 19:28:30 +0100
Subject: [PATCH 05/32] created a NullPointerException when trying to turn
 weight column dynamic in dataobservatory

---
 .../layout/plugins/layout/NodeWeight/ForceAtlas2.java     | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 8fa6ba6..47c0f4f 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -63,6 +63,10 @@ Development and Distribution License("CDDL") (collectively, the
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
 import org.gephi.graph.api.Interval;
+
+import org.gephi.graph.api.types.IntervalMap;
+import org.gephi.graph.api.types.TimeMap;
+import org.gephi.graph.api.types.TimestampMap;
 // import org.gephi.layout.plugin.AbstractLayout;
 import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
 
@@ -167,7 +171,9 @@ private boolean hasNodeWeight(Node node) {
     private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
         if (isDynamicNodeWeight) {
             // node_weight = (Double) n.getAttribute("gravity_x");
-            return (Double) node.getAttribute("weight", interval);
+            TimestampMap map = (TimestampMap) node.getAttribute("weight");
+            return (Double) map.get(interval, 0);
+
         } else {
             return (Double) node.getAttribute("weight");
         }

From b920a1a7465d0fa77f5281de0b7338e3a384e973 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Sun, 19 Aug 2018 20:03:21 +0100
Subject: [PATCH 06/32] dynamic workinggit add .git add .git add .git add .

---
 .../plugins/layout/NodeWeight/ForceAtlas2.java    | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 47c0f4f..fa50015 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -47,6 +47,7 @@ Development and Distribution License("CDDL") (collectively, the
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.Node;
 import org.gephi.graph.api.Table;
+import org.gephi.graph.api.Estimator;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
 import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
@@ -57,6 +58,7 @@ Development and Distribution License("CDDL") (collectively, the
 import org.gephi.layout.spi.LayoutProperty;
 
 
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
@@ -74,6 +76,7 @@ Development and Distribution License("CDDL") (collectively, the
 import org.openide.util.Exceptions;
 import org.openide.util.NbBundle;
 
+
 /**
  * ForceAtlas 2 Layout, manages each step of the computations.
  *
@@ -172,7 +175,17 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         if (isDynamicNodeWeight) {
             // node_weight = (Double) n.getAttribute("gravity_x");
             TimestampMap map = (TimestampMap) node.getAttribute("weight");
-            return (Double) map.get(interval, 0);
+            // Estimator estimator = (Estimator) AVERAGE;
+            Double prev_value = 0.0;
+            Double value = (Double) map.get(interval, Estimator.AVERAGE);
+            if (value != null) {
+              prev_value = value;
+              return value;
+            } else {
+              return prev_value;
+            }
+
+
 
         } else {
             return (Double) node.getAttribute("weight");

From 491add06e821bdb60a4ab2c5e10e044b0fc3d825 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Sun, 19 Aug 2018 23:20:16 +0100
Subject: [PATCH 07/32] put in method declarations with pseudocode for
 normalization, transparency, and nodesize

---
 .../layout/NodeWeight/ForceAtlas2.java        | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 8fa6ba6..74987ad 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -173,6 +173,36 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
+
+    private double normalizeNodeWeight(Node node, Double weight) {
+      /**
+      * 1. find the max and min in the column
+      * 2. add to make all numbers positive
+      * 3. divide by ten's place of the new max
+      * 3b. functionality to choose desired max?
+      */
+    }
+
+    private void adjustNodeTransparency(Node node), Double normalized_weight {
+      /**
+      * DO: Adjust transparency based on weight normalization
+      * void  setAlpha(float a)
+      * Sets the alpha (transparency) color component.
+      ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/ElementProperties.html#alpha--
+      */
+    }
+
+    private void adjustNodeSize(Node node, Double normalized_weight) {
+      /**
+      * DO: Adjust size based on weight normalization
+      * void setSize(float size)
+      * Sets the size.
+      * Parameters:
+      * size - the size
+      ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/NodeProperties.html#setSize-float-
+      */
+    }
+
     // public void addWeightCol(graph){
     //   graph.addColumn();
     // }

From d932fbf896326e4345146969ba556c677d3e86b0 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Mon, 20 Aug 2018 15:03:42 +0100
Subject: [PATCH 08/32] first attempt at adding transparency feature

---
 .../layout/NodeWeight/ForceAtlas2.java        | 118 +++++++++++++-----
 .../layout/NodeWeight/Bundle.properties       |   7 ++
 2 files changed, 97 insertions(+), 28 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 74987ad..f4ddd84 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -47,6 +47,10 @@ Development and Distribution License("CDDL") (collectively, the
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.Node;
 import org.gephi.graph.api.Table;
+import org.gephi.graph.api.Estimator;
+import org.gephi.graph.api.types.IntervalMap;
+import org.gephi.graph.api.types.TimeMap;
+import org.gephi.graph.api.types.TimestampMap;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
 import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
@@ -97,6 +101,8 @@ public class ForceAtlas2 implements Layout {
     private Region rootRegion;
     double outboundAttCompensation = 1;
     private ExecutorService pool;
+    private double minWeight;
+    private double maxWeight;
 
     public ForceAtlas2(ForceAtlas2Builder layoutBuilder) {
         this.layoutBuilder = layoutBuilder;
@@ -165,42 +171,65 @@ private boolean hasNodeWeight(Node node) {
     }
 
     private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
-        if (isDynamicNodeWeight) {
-            // node_weight = (Double) n.getAttribute("gravity_x");
-            return (Double) node.getAttribute("weight", interval);
-        } else {
-            return (Double) node.getAttribute("weight");
-        }
+      if (isDynamicNodeWeight) {
+          // node_weight = (Double) n.getAttribute("gravity_x");
+          TimestampMap map = (TimestampMap) node.getAttribute("weight");
+          // Estimator estimator = (Estimator) AVERAGE;
+          Double prev_value = 0.0;
+          Double value = (Double) map.get(interval, Estimator.AVERAGE);
+          if (value != null) {
+            prev_value = value;
+            return value;
+          } else {
+            return prev_value;
+          }
+
+
+
+      } else {
+          return (Double) node.getAttribute("weight");
+      }
     }
 
 
-    private double normalizeNodeWeight(Node node, Double weight) {
-      /**
-      * 1. find the max and min in the column
-      * 2. add to make all numbers positive
-      * 3. divide by ten's place of the new max
-      * 3b. functionality to choose desired max?
-      */
+    private float normalizeNodeWeight(Node node, Double weight) {
+      double d_weight = weight;
+      double d_max = getMaxWeight();
+      double d_min = getMinWeight();
+      float maxWeight = (float) d_max;
+      float minWeight = (float) d_min;
+      float f_weight = (float) d_weight;
+      Float normalized = (f_weight-minWeight)/(maxWeight-minWeight);
+
+      return normalized;
+      // /**
+      // * 1. find the max and min in the column
+      // * 2. add to make all numbers positive
+      // * 3. divide by ten's place of the new max
+      // * 3b. functionality to choose desired max?
+      // */
     }
 
-    private void adjustNodeTransparency(Node node), Double normalized_weight {
-      /**
-      * DO: Adjust transparency based on weight normalization
-      * void  setAlpha(float a)
-      * Sets the alpha (transparency) color component.
-      ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/ElementProperties.html#alpha--
-      */
+    private void adjustNodeTransparency(Node node, Double weight) {
+      Float normalized_weight = normalizeNodeWeight(node, weight);
+      node.setAlpha(normalized_weight);
+      // /**
+      // * DO: Adjust transparency based on weight normalization
+      // * void  setAlpha(float a)
+      // * Sets the alpha (transparency) color component.
+      // ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/ElementProperties.html#alpha--
+      // */
     }
 
     private void adjustNodeSize(Node node, Double normalized_weight) {
-      /**
-      * DO: Adjust size based on weight normalization
-      * void setSize(float size)
-      * Sets the size.
-      * Parameters:
-      * size - the size
-      ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/NodeProperties.html#setSize-float-
-      */
+      // /**
+      // * DO: Adjust size based on weight normalization
+      // * void setSize(float size)
+      // * Sets the size.
+      // * Parameters:
+      // * size - the size
+      // ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/NodeProperties.html#setSize-float-
+      // */
     }
 
     // public void addWeightCol(graph){
@@ -311,6 +340,9 @@ public void goAlgo() {
                 Double wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
                 Double wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
 
+                adjustNodeTransparency(node_a, wt_a);
+                adjustNodeTransparency(node_b, wt_b);
+
                 NodeAttraction.apply(node_a, node_b, (getNodeWeight(node_a, isDynamicNodeWeight, interval) + getNodeWeight(node_b, isDynamicNodeWeight, interval))/2);
 
               }
@@ -456,6 +488,20 @@ public LayoutProperty[] getProperties() {
         final String FORCEATLAS2_THREADS = NbBundle.getMessage(getClass(), "ForceAtlas2.threads");
 
         try {
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.maxWeight.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.desc"),
+                    "getMaxWeight", "setMaxWeight"));
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.minWeight.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.desc"),
+                    "getMinWeight", "setMinWeight"));
             properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.scalingRatio.name"),
@@ -629,6 +675,22 @@ public void setLinLogMode(Boolean linLogMode) {
         this.linLogMode = linLogMode;
     }
 
+    public Double getMaxWeight() {
+      return maxWeight;
+    }
+
+    public void setMaxWeight(Double maxWeight) {
+      this.maxWeight = maxWeight;
+    }
+
+    public Double getMinWeight() {
+      return minWeight;
+    }
+
+    public void setMinWeight(Double minWeight) {
+        this.minWeight = minWeight;
+    }
+
     public Double getScalingRatio() {
         return scalingRatio;
     }
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index 16253ca..b4ea3eb 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -19,6 +19,13 @@ ForceAtlas2.behavior=Behavior Alternatives
 ForceAtlas2.performance=Performance
 ForceAtlas2.threads=Threads
 
+ForceAtlas2.minWeight.name=Minimum Weight
+ForceAtlas2.minWeight.desc=Minimum weight possible in your data
+ForceAtlas2.maxWeight.name=Maximum Weight
+ForceAtlas2.maxWeight.desc=Maxium weight possible in your data
+
+
+
 ForceAtlas2.scalingRatio.name=Scaling
 ForceAtlas2.scalingRatio.desc=How much repulsion you want. More makes a more sparse graph.
 

From a06adb6bb9ec391f54f4df86d644673dd68905cf Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Mon, 20 Aug 2018 15:12:46 +0100
Subject: [PATCH 09/32] inserted print statement to test then commented out

---
 .../org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java  | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index f4ddd84..5429b15 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -213,6 +213,7 @@ private float normalizeNodeWeight(Node node, Double weight) {
     private void adjustNodeTransparency(Node node, Double weight) {
       Float normalized_weight = normalizeNodeWeight(node, weight);
       node.setAlpha(normalized_weight);
+      // System.out.println("\"TESTING\"" + String.valueOf(getMinWeight()));
       // /**
       // * DO: Adjust transparency based on weight normalization
       // * void  setAlpha(float a)

From cbe4cd232476460c7755ab4d074d7265373eed8b Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 21 Aug 2018 14:21:49 +0100
Subject: [PATCH 10/32] removed sizing objective

---
 .../layout/plugins/layout/NodeWeight/#TODO    | 13 ++-
 .../layout/NodeWeight/ForceAtlas2.java        | 85 +++++++++++++------
 2 files changed, 69 insertions(+), 29 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
index 8230d23..40c0672 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
@@ -2,14 +2,16 @@
 
 To-do:
 1. add hsv transparency
-2. add size change
-3. make the node weight attraction more meaningful
-4. try out many use-cases to test plugin
-5. make good visualizations to be tested
 
+3. make the node weight attraction more meaningful
+4. make good visualizations to be tested
+5. Make app more robust (OR CATCH EXCEPTIONS AND TELL USER WHAT TO DO)
 
+  ii. Figure out exception if data in incorrect (non-double) format…. Either be able to handle this or catch exception
 
+  iii. Catch exception if there exists a node weight outside of the provided range
 
+6. test some use-cases to see what errors appear
 
 
 Done:
@@ -17,3 +19,6 @@ Done:
   1a. check whether the column is dynamic
  add a column that can accept dynamic or not dynamic value
   called "weight"
+
+    i. Resolve use of weight vs weight_dynamic
+  Check if weight is dynamic; check if dynamic_weight is dynamic; use whichever one exists
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 5429b15..ddf5e03 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -162,33 +162,50 @@ private double getEdgeWeight(Edge edge, boolean isDynamicWeight, Interval interv
         }
     }
 
+    private boolean hasNodeWeightStop(Node node) {
+
+      if (graphModel.getNodeTable().hasColumn("weight") && node.getAttribute("weight") != null) {
+        return true;
+      } else {
+        return false;
+      }
+    }
+
+    private boolean hasNodeWeightDynamic(Node node) {
+      if (graphModel.getNodeTable().hasColumn("weight_dynamic") && node.getAttribute("weight_dynamic") != null) {
+        return true;
+      } else {
+        return false;
+      }
+    }
+
+    //// DYNAMIC
     private boolean hasNodeWeight(Node node) {
-      if (node.getAttribute("weight") != null) {
+      if (hasNodeWeightStop(node) || hasNodeWeightDynamic(node)){
         return true;
       } else {
         return false;
       }
     }
 
-    private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
+
+    private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval, String column_name) {
       if (isDynamicNodeWeight) {
           // node_weight = (Double) n.getAttribute("gravity_x");
-          TimestampMap map = (TimestampMap) node.getAttribute("weight");
+          TimestampMap map = (TimestampMap) node.getAttribute(column_name);
           // Estimator estimator = (Estimator) AVERAGE;
           Double prev_value = 0.0;
           Double value = (Double) map.get(interval, Estimator.AVERAGE);
-          if (value != null) {
+        if (value != null) {
             prev_value = value;
             return value;
           } else {
             return prev_value;
           }
 
-
-
-      } else {
-          return (Double) node.getAttribute("weight");
-      }
+        } else {
+          return (Double) node.getAttribute(column_name);
+        }
     }
 
 
@@ -222,16 +239,6 @@ private void adjustNodeTransparency(Node node, Double weight) {
       // */
     }
 
-    private void adjustNodeSize(Node node, Double normalized_weight) {
-      // /**
-      // * DO: Adjust size based on weight normalization
-      // * void setSize(float size)
-      // * Sets the size.
-      // * Parameters:
-      // * size - the size
-      // ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/NodeProperties.html#setSize-float-
-      // */
-    }
 
     // public void addWeightCol(graph){
     //   graph.addColumn();
@@ -256,7 +263,22 @@ public void goAlgo() {
 
         graph.readLock();
         boolean isDynamicWeight = graphModel.getEdgeTable().getColumn("weight").isDynamic();
-        boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn("weight").isDynamic();
+        // to-do: make compatible with weight_dynamic
+        // provide exception catch otherwise
+        // boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn("weight").isDynamic();
+        boolean isDynamicNodeWeight = false;
+
+        Table node_table = graphModel.getNodeTable();
+        if (node_table.hasColumn("weight") && node_table.getColumn("weight").isDynamic()){
+          isDynamicNodeWeight = true;
+        } else if (node_table.hasColumn("weight_dynamic") && node_table.getColumn("weight_dynamic").isDynamic()){
+          isDynamicNodeWeight = true;
+        }
+
+
+
+
+
         Interval interval = graph.getView().getTimeInterval();
 
         try {
@@ -313,7 +335,7 @@ public void goAlgo() {
                     throw new RuntimeException("Unable to layout " + this.getClass().getSimpleName() + ".", e);
                 }
             }
-//BOOKMARK
+
           // Attraction
             // Edge Weight
             AttractionForce Attraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
@@ -338,15 +360,28 @@ public void goAlgo() {
               Node node_b = e.getTarget();
 
               if (hasNodeWeight(node_a) && hasNodeWeight(node_b)) {
-                Double wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
-                Double wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
+                Double wt_a = 0.0;
+                Double wt_b = 0.0;
+                if (hasNodeWeightStop(node_a) && hasNodeWeightStop(node_b)) {
+
+                  wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval, "weight");
+                  wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval, "weight");
+
+                }
+
+                if (hasNodeWeightDynamic(node_a) && hasNodeWeightDynamic(node_b)) {
+
+                  wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval, "weight_dynamic");
+                  wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval, "weight_dynamic");
+
+                }
 
                 adjustNodeTransparency(node_a, wt_a);
                 adjustNodeTransparency(node_b, wt_b);
 
-                NodeAttraction.apply(node_a, node_b, (getNodeWeight(node_a, isDynamicNodeWeight, interval) + getNodeWeight(node_b, isDynamicNodeWeight, interval))/2);
+                NodeAttraction.apply(node_a, node_b, ((wt_a + wt_b)/2));
 
-              }
+            }
 
 
 

From ebcea4e5d7d3e2210bfb47766ff8a032197dfc7e Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 21 Aug 2018 14:23:01 +0100
Subject: [PATCH 11/32] TODO updated

---
 .../java/org/gephi/layout/plugins/layout/NodeWeight/#TODO     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
index 40c0672..f62f9fd 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
@@ -1,8 +1,8 @@
 #TODO
 
 To-do:
-1. add hsv transparency
-
+1. add transparency for nodes based on weight
+2. make transparency for nodes optional
 3. make the node weight attraction more meaningful
 4. make good visualizations to be tested
 5. Make app more robust (OR CATCH EXCEPTIONS AND TELL USER WHAT TO DO)

From ab23b5c4819da1414ca2e7e12143fc282c49c3bb Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 21 Aug 2018 14:29:40 +0100
Subject: [PATCH 12/32] TODO updated'

---
 .../gephi/layout/plugins/layout/NodeWeight/#TODO  | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
index 8230d23..f62f9fd 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
@@ -1,15 +1,17 @@
 #TODO
 
 To-do:
-1. add hsv transparency
-2. add size change
+1. add transparency for nodes based on weight
+2. make transparency for nodes optional
 3. make the node weight attraction more meaningful
-4. try out many use-cases to test plugin
-5. make good visualizations to be tested
-
+4. make good visualizations to be tested
+5. Make app more robust (OR CATCH EXCEPTIONS AND TELL USER WHAT TO DO)
 
+  ii. Figure out exception if data in incorrect (non-double) format…. Either be able to handle this or catch exception
 
+  iii. Catch exception if there exists a node weight outside of the provided range
 
+6. test some use-cases to see what errors appear
 
 
 Done:
@@ -17,3 +19,6 @@ Done:
   1a. check whether the column is dynamic
  add a column that can accept dynamic or not dynamic value
   called "weight"
+
+    i. Resolve use of weight vs weight_dynamic
+  Check if weight is dynamic; check if dynamic_weight is dynamic; use whichever one exists

From 34b8ddc65501962fc440350fa9943299d04ff9cc Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Wed, 22 Aug 2018 17:18:02 +0100
Subject: [PATCH 13/32] min achieved and compiles

---
 hs_err_pid44976.log                           | 707 ++++++++++++++++++
 .../layout/plugins/layout/NodeWeight/#TODO    |   5 +
 .../layout/NodeWeight/ForceAtlas2.java        | 189 ++++-
 3 files changed, 871 insertions(+), 30 deletions(-)
 create mode 100644 hs_err_pid44976.log

diff --git a/hs_err_pid44976.log b/hs_err_pid44976.log
new file mode 100644
index 0000000..3d6fe11
--- /dev/null
+++ b/hs_err_pid44976.log
@@ -0,0 +1,707 @@
+#
+# A fatal error has been detected by the Java Runtime Environment:
+#
+#  SIGILL (0x4) at pc=0x00007fff48537454, pid=44976, tid=0x0000000000000307
+#
+# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
+# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode bsd-amd64 compressed oops)
+# Problematic frame:
+# C  [AppKit+0x36c454]  -[NSApplication _crashOnException:]+0x6d
+#
+# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
+#
+# If you would like to submit a bug report, please visit:
+#   http://bugreport.java.com/bugreport/crash.jsp
+# The crash happened outside the Java Virtual Machine in native code.
+# See problematic frame for where to report the bug.
+#
+
+---------------  T H R E A D  ---------------
+
+Current thread (0x00007f8b6587a000):  JavaThread "AWT-AppKit" daemon [_thread_in_native, id=775, stack(0x00007ffee1e1f000,0x00007ffee261f000)]
+
+siginfo: si_signo: 4 (SIGILL), si_code: 1 (ILL_ILLOPC), si_addr: 0x00007fff48537454
+
+Registers:
+RAX=0x00007f8b65737200, RBX=0x00007f8b697977f0, RCX=0x0000000000000000, RDX=0x0000000000000ead
+RSP=0x00007ffee2616e90, RBP=0x00007ffee2616ea0, RSI=0x00007f8b6c266ea1, RDI=0x0000000008000101
+R8 =0x0000000000000000, R9 =0x0000000000000000, R10=0x00007ffee2616998, R11=0xfffffffff94d11ff
+R12=0x00007f8b694bc200, R13=0x00007f8b65391068, R14=0x00007fff71e8ae80, R15=0x00007fff4ac8f6d0
+RIP=0x00007fff48537454, EFLAGS=0x0000000000010206, ERR=0x0000000000000000
+  TRAPNO=0x0000000000000006
+
+Top of Stack: (sp=0x00007ffee2616e90)
+0x00007ffee2616e90:   00007f8b6d99efc0 00007f8b6d8bfb70
+0x00007ffee2616ea0:   00007ffee2616fd0 00007fff48b03cb1
+0x00007ffee2616eb0:   0000000000000003 00007f8b644f29d0
+0x00007ffee2616ec0:   000000010d5fe080 000000010d5fe080
+0x00007ffee2616ed0:   00007ffee2616f60 00007fff72c7275a
+0x00007ffee2616ee0:   000000010d600a00 0000000100000002
+0x00007ffee2616ef0:   00007f8b6d9a2b80 00007f8b6d9fc080
+0x00007ffee2616f00:   00007ffee2616f60 0000000000000010
+0x00007ffee2616f10:   0000000000000001 00007f8b6d9a2b80
+0x00007ffee2616f20:   000000010d5fe080 00007f8b6d900000
+0x00007ffee2616f30:   000000010d601e00 0000000000000002
+0x00007ffee2616f40:   000000010d601e00 0000000000000003
+0x00007ffee2616f50:   000000010d5fe080 00007f8b6d900000
+0x00007ffee2616f60:   00007ffee2616fc0 00007fff72c73256
+0x00007ffee2616f70:   00007fffab488a80 00007f8b64600000
+0x00007ffee2616f80:   0000000000001400 0000000000000001
+0x00007ffee2616f90:   000000002b3100c5 00007f8b6d8bfb70
+0x00007ffee2616fa0:   7debe043e91500fd 00007f8b694bc200
+0x00007ffee2616fb0:   0000000000000002 00007f8b694bc208
+0x00007ffee2616fc0:   0000000000000000 00007fff4ac8f6d0
+0x00007ffee2616fd0:   00007ffee2616fe0 00007fff4ac8f417
+0x00007ffee2616fe0:   00007ffee26170b0 00007fff4ac8f33f
+0x00007ffee2616ff0:   00007f8b694bc200 00007f8b64600070
+0x00007ffee2617000:   00007fffa4e79f90 00007f8b64600200
+0x00007ffee2617010:   00007ffee26170b0 00007fff4ac8f19e
+0x00007ffee2617020:   0000000000000003 0000000500002d8a
+0x00007ffee2617030:   00007f8b64600200 00007f8b64600070
+0x00007ffee2617040:   00007ffee2617020 00007ffee2616ff0
+0x00007ffee2617050:   00007f8b64600210 00007f8b64600080
+0x00007ffee2617060:   00007f8b6d8bfb70 0000000000000002
+0x00007ffee2617070:   0000000000000001 00007ffee2616ff0
+0x00007ffee2617080:   7debe043e91500fd 00007f8b64600200 
+
+Instructions: (pc=0x00007fff48537454)
+0x00007fff48537434:   48 89 c7 ff 15 2b ad f4 5b 48 8b 35 4c b7 24 5c
+0x00007fff48537444:   48 89 c7 ff 15 1b ad f4 5b 48 89 05 cc 68 2c 5c
+0x00007fff48537454:   0f 0b 48 89 c7 e8 f0 3a 8a 00 31 ff 31 f6 31 c0
+0x00007fff48537464:   e8 28 89 e4 ff e8 04 3b 8a 00 48 89 c3 e8 f0 3a 
+
+Register to memory mapping:
+
+RAX=0x00007f8b65737200 is an unknown value
+RBX=0x00007f8b697977f0 is an unknown value
+RCX=0x0000000000000000 is an unknown value
+RDX=0x0000000000000ead is an unknown value
+RSP=0x00007ffee2616e90 is pointing into the stack for thread: 0x00007f8b6587a000
+RBP=0x00007ffee2616ea0 is pointing into the stack for thread: 0x00007f8b6587a000
+RSI=0x00007f8b6c266ea1 is an unknown value
+RDI=0x0000000008000101 is an unknown value
+R8 =0x0000000000000000 is an unknown value
+R9 =0x0000000000000000 is an unknown value
+R10=0x00007ffee2616998 is pointing into the stack for thread: 0x00007f8b6587a000
+R11=0xfffffffff94d11ff is an unknown value
+R12=0x00007f8b694bc200 is an unknown value
+R13=0x00007f8b65391068 is an unknown value
+R14=0x00007fff71e8ae80: objc_msgSend+0 in /usr/lib/libobjc.A.dylib at 0x00007fff71e84000
+R15=0x00007fff4ac8f6d0: _runLoopObserverWithBlockContext+0 in /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation at 0x00007fff4abec000
+
+
+Stack: [0x00007ffee1e1f000,0x00007ffee261f000],  sp=0x00007ffee2616e90,  free space=8159k
+Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
+C  [AppKit+0x36c454]  -[NSApplication _crashOnException:]+0x6d
+C  [AppKit+0x938cb1]  __65+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayRefresh]_block_invoke+0x35a
+C  [CoreFoundation+0xa3417]  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__+0x17
+C  [CoreFoundation+0xa333f]  __CFRunLoopDoObservers+0x20f
+C  [CoreFoundation+0x858b8]  __CFRunLoopRun+0x4d8
+C  [CoreFoundation+0x85153]  CFRunLoopRunSpecific+0x1e3
+C  [HIToolbox+0x2fd96]  RunCurrentEventLoopInMode+0x11e
+C  [HIToolbox+0x2fb06]  ReceiveNextEventCommon+0x265
+C  [HIToolbox+0x2f884]  _BlockUntilNextEventMatchingListInModeWithFilter+0x40
+C  [AppKit+0x41a73]  _DPSNextEvent+0x825
+C  [AppKit+0x7d7e34]  -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]+0xbe4
+C  [libosxapp.dylib+0x2328]  -[NSApplicationAWT nextEventMatchingMask:untilDate:inMode:dequeue:]+0x7c
+C  [AppKit+0x36885]  -[NSApplication run]+0x2fc
+C  [libosxapp.dylib+0x1f72]  +[NSApplicationAWT runAWTLoopWithApp:]+0x9c
+C  [libawt_lwawt.dylib+0x4711f]  -[AWTStarter starter:]+0x389
+C  [Foundation+0x682b5]  __NSThreadPerformPerform+0x14e
+C  [CoreFoundation+0xa3a11]  __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__+0x11
+C  [CoreFoundation+0x15d42c]  __CFRunLoopDoSource0+0x6c
+C  [CoreFoundation+0x86470]  __CFRunLoopDoSources0+0xd0
+C  [CoreFoundation+0x858ed]  __CFRunLoopRun+0x50d
+C  [CoreFoundation+0x85153]  CFRunLoopRunSpecific+0x1e3
+C  [java+0x6472]  CreateExecutionEnvironment+0x367
+C  [java+0x207c]  JLI_Launch+0x7a0
+C  [java+0x84cf]  main+0x65
+C  [java+0x18d4]  start+0x34
+C  0x0000000000000024
+
+
+---------------  P R O C E S S  ---------------
+
+Java Threads: ( => current thread )
+  0x00007f8b6cd1b800 JavaThread "SwingWorker-pool-2-thread-10" daemon [_thread_blocked, id=123403, stack(0x000070000818b000,0x000070000828b000)]
+  0x00007f8b6550b800 JavaThread "SwingWorker-pool-2-thread-9" daemon [_thread_blocked, id=95235, stack(0x0000700008088000,0x0000700008188000)]
+  0x00007f8b6b1a4000 JavaThread "SwingWorker-pool-2-thread-8" daemon [_thread_blocked, id=123927, stack(0x0000700007f85000,0x0000700008085000)]
+  0x00007f8b64f7f800 JavaThread "SwingWorker-pool-2-thread-7" daemon [_thread_blocked, id=124419, stack(0x0000700007e82000,0x0000700007f82000)]
+  0x00007f8b6550b000 JavaThread "SwingWorker-pool-2-thread-6" daemon [_thread_blocked, id=124939, stack(0x0000700007d7f000,0x0000700007e7f000)]
+  0x00007f8b6d22f000 JavaThread "SwingWorker-pool-2-thread-5" daemon [_thread_blocked, id=125463, stack(0x0000700007c7c000,0x0000700007d7c000)]
+  0x00007f8b6b1a6800 JavaThread "SwingWorker-pool-2-thread-4" daemon [_thread_blocked, id=125959, stack(0x0000700007b79000,0x0000700007c79000)]
+  0x00007f8b6d077000 JavaThread "SwingWorker-pool-2-thread-3" daemon [_thread_blocked, id=91927, stack(0x0000700007a76000,0x0000700007b76000)]
+  0x00007f8b6b1a6000 JavaThread "SwingWorker-pool-2-thread-2" daemon [_thread_blocked, id=128507, stack(0x0000700007973000,0x0000700007a73000)]
+  0x00007f8b6d076000 JavaThread "SwingWorker-pool-2-thread-1" daemon [_thread_blocked, id=126251, stack(0x0000700006fd2000,0x00007000070d2000)]
+  0x00007f8b6afc3000 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=127303, stack(0x00007000072db000,0x00007000073db000)]
+  0x00007f8b6d0d5800 JavaThread "Thread-13" [_thread_blocked, id=92939, stack(0x0000700007870000,0x0000700007970000)]
+  0x00007f8b650cc000 JavaThread "AppearanceColumnObserver" daemon [_thread_blocked, id=126735, stack(0x000070000776d000,0x000070000786d000)]
+  0x00007f8b6a1bf000 JavaThread "Context Refresh Thread" daemon [_thread_blocked, id=91175, stack(0x000070000766a000,0x000070000776a000)]
+  0x00007f8b6bb6c800 JavaThread "Project IO" [_thread_blocked, id=91395, stack(0x00007000073de000,0x00007000074de000)]
+  0x00007f8b650dd800 JavaThread "Keep-Alive-Timer" daemon [_thread_blocked, id=128851, stack(0x00007000071d8000,0x00007000072d8000)]
+  0x00007f8b64918800 JavaThread "Timer-0" daemon [_thread_blocked, id=88867, stack(0x00007000070d5000,0x00007000071d5000)]
+  0x00007f8b65d99800 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=77575, stack(0x0000700006228000,0x0000700006328000)]
+  0x00007f8b64946800 JavaThread "DestroyJavaVM" [_thread_blocked, id=9475, stack(0x0000700004e69000,0x0000700004f69000)]
+  0x00007f8b6561b000 JavaThread "Flushing caches" [_thread_blocked, id=130575, stack(0x0000700006e4c000,0x0000700006f4c000)]
+  0x00007f8b6a241800 JavaThread "Inactive RequestProcessor thread [Was:OpenIDE-request-processor-1/org.netbeans.core.startup.preferences.NbPreferences$1]" daemon [_thread_blocked, id=64515, stack(0x0000700006d49000,0x0000700006e49000)]
+  0x00007f8b6b01e800 JavaThread "TimerQueue" daemon [_thread_blocked, id=64259, stack(0x0000700006c46000,0x0000700006d46000)]
+  0x00007f8b64f19800 JavaThread "Thread-5" daemon [_thread_blocked, id=65035, stack(0x0000700006b43000,0x0000700006c43000)]
+  0x00007f8b65993000 JavaThread "Image Fetcher 0" daemon [_thread_blocked, id=63507, stack(0x0000700006a40000,0x0000700006b40000)]
+  0x00007f8b65aa4000 JavaThread "File Watcher" daemon [_thread_blocked, id=67595, stack(0x000070000693d000,0x0000700006a3d000)]
+  0x00007f8b65d50800 JavaThread "Thread-1" daemon [_thread_in_native, id=69151, stack(0x000070000683a000,0x000070000693a000)]
+  0x00007f8b66237000 JavaThread "Inactive RequestProcessor thread [Was:Folder recognizer/org.openide.loaders.FolderList$ListTask]" daemon [_thread_blocked, id=71531, stack(0x0000700006737000,0x0000700006837000)]
+  0x00007f8b6611a000 JavaThread "AWT-EventQueue-0" [_thread_in_native, id=74503, stack(0x0000700006634000,0x0000700006734000)]
+  0x00007f8b65445000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=53011, stack(0x0000700006531000,0x0000700006631000)]
+  0x00007f8b64ee0800 JavaThread "Java2D Queue Flusher" daemon [_thread_blocked, id=52487, stack(0x000070000642e000,0x000070000652e000)]
+  0x00007f8b66145800 JavaThread "RequestProcessor queue manager" daemon [_thread_blocked, id=77319, stack(0x000070000632b000,0x000070000642b000)]
+  0x00007f8b65903800 JavaThread "Inactive RequestProcessor thread [Was:Asynch children creator /org.openide.nodes.AsynchChildren]" daemon [_thread_blocked, id=82439, stack(0x0000700006125000,0x0000700006225000)]
+  0x00007f8b64e02800 JavaThread "AWT-Shutdown" [_thread_blocked, id=25387, stack(0x0000700005e99000,0x0000700005f99000)]
+=>0x00007f8b6587a000 JavaThread "AWT-AppKit" daemon [_thread_in_native, id=775, stack(0x00007ffee1e1f000,0x00007ffee261f000)]
+  0x00007f8b65361800 JavaThread "CLI Requests Server" daemon [_thread_in_native, id=16643, stack(0x0000700005d96000,0x0000700005e96000)]
+  0x00007f8b6535e800 JavaThread "Active Reference Queue Daemon" daemon [_thread_blocked, id=16899, stack(0x0000700005c93000,0x0000700005d93000)]
+  0x00007f8b65037000 JavaThread "Service Thread" daemon [_thread_blocked, id=14595, stack(0x0000700005a8d000,0x0000700005b8d000)]
+  0x00007f8b65036800 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=14083, stack(0x000070000598a000,0x0000700005a8a000)]
+  0x00007f8b65016800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=13571, stack(0x0000700005887000,0x0000700005987000)]
+  0x00007f8b64848800 JavaThread "C2 CompilerThread0" daemon [_thread_in_native, id=13059, stack(0x0000700005784000,0x0000700005884000)]
+  0x00007f8b64847800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=17927, stack(0x0000700005681000,0x0000700005781000)]
+  0x00007f8b64841000 JavaThread "Finalizer" daemon [_thread_blocked, id=20739, stack(0x000070000557e000,0x000070000567e000)]
+  0x00007f8b6580e800 JavaThread "Reference Handler" daemon [_thread_blocked, id=11779, stack(0x000070000547b000,0x000070000557b000)]
+
+Other Threads:
+  0x00007f8b6483c000 VMThread [stack: 0x0000700005378000,0x0000700005478000] [id=21251]
+  0x00007f8b65000000 WatcherThread [stack: 0x0000700005b90000,0x0000700005c90000] [id=17411]
+
+VM state:not at safepoint (normal execution)
+
+VM Mutex/Monitor currently owned by a thread: None
+
+Heap:
+ PSYoungGen      total 132096K, used 25330K [0x00000007b5580000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 112640K, 6% used [0x00000007b5580000,0x00000007b5c588f8,0x00000007bc380000)
+  from space 19456K, 94% used [0x00000007bc380000,0x00000007bd563f30,0x00000007bd680000)
+  to   space 22016K, 0% used [0x00000007bea80000,0x00000007bea80000,0x00000007c0000000)
+ ParOldGen       total 110080K, used 59392K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
+  object space 110080K, 53% used [0x00000007a0000000,0x00000007a3a00398,0x00000007a6b80000)
+ Metaspace       used 54664K, capacity 59482K, committed 59816K, reserved 1101824K
+  class space    used 6797K, capacity 8247K, committed 8360K, reserved 1048576K
+
+Card table byte_map: [0x000000010d6b1000,0x000000010d7b2000] byte_map_base: 0x00000001099b1000
+
+Marking Bits: (ParMarkBitMap*) 0x000000010e8f76e0
+ Begin Bits: [0x000000010f419000, 0x000000010fc19000)
+ End Bits:   [0x000000010fc19000, 0x0000000110419000)
+
+Polling page: 0x000000010d65e000
+
+CodeCache: size=245760Kb used=18815Kb max_used=19035Kb free=226945Kb
+ bounds [0x000000011a969000, 0x000000011bc29000, 0x0000000129969000]
+ total_blobs=7232 nmethods=6116 adapters=1022
+ compilation: enabled
+
+Compilation events (10 events):
+Event: 13.777 Thread 0x00007f8b65036800 7258       1       org.netbeans.core.windows.ModeStructureSnapshot$ModeSnapshot::getBounds (5 bytes)
+Event: 13.777 Thread 0x00007f8b65036800 nmethod 7258 0x000000011b42e6d0 code [0x000000011b42e820, 0x000000011b42e930]
+Event: 13.777 Thread 0x00007f8b65036800 7259       1       org.netbeans.core.windows.view.ModeStructureAccessorImpl$SlidingAccessorImpl::getSlideInSizes (5 bytes)
+Event: 13.777 Thread 0x00007f8b65036800 nmethod 7259 0x000000011b42e410 code [0x000000011b42e560, 0x000000011b42e670]
+Event: 13.778 Thread 0x00007f8b64848800 nmethod 7256 0x000000011b099890 code [0x000000011b0999e0, 0x000000011b099a88]
+Event: 13.780 Thread 0x00007f8b65036800 7260       1       org.netbeans.swing.tabcontrol.TabbedContainer::getType (5 bytes)
+Event: 13.780 Thread 0x00007f8b65036800 nmethod 7260 0x000000011ae69410 code [0x000000011ae69560, 0x000000011ae69670]
+Event: 13.782 Thread 0x00007f8b65036800 7261       3       com.apple.laf.AquaButtonUI$AquaButtonListener::updateDefaultButton (60 bytes)
+Event: 13.783 Thread 0x00007f8b65036800 nmethod 7261 0x000000011b3089d0 code [0x000000011b308bc0, 0x000000011b3096a8]
+Event: 13.785 Thread 0x00007f8b64848800 7262       4       java.awt.Component::getHWPeerAboveMe (90 bytes)
+
+GC Heap History (10 events):
+Event: 7.914 GC heap before
+{Heap before GC invocations=12 (full 2):
+ PSYoungGen      total 76800K, used 75482K [0x00000007b5580000, 0x00000007bbe80000, 0x00000007c0000000)
+  eden space 70144K, 100% used [0x00000007b5580000,0x00000007b9a00000,0x00000007b9a00000)
+  from space 6656K, 80% used [0x00000007b9a00000,0x00000007b9f36a30,0x00000007ba080000)
+  to   space 6656K, 0% used [0x00000007bb800000,0x00000007bb800000,0x00000007bbe80000)
+ ParOldGen       total 51712K, used 12901K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
+  object space 51712K, 24% used [0x00000007a0000000,0x00000007a0c99768,0x00000007a3280000)
+ Metaspace       used 48041K, capacity 51778K, committed 52008K, reserved 1093632K
+  class space    used 5858K, capacity 6918K, committed 6952K, reserved 1048576K
+Event: 7.935 GC heap after
+Heap after GC invocations=12 (full 2):
+ PSYoungGen      total 95232K, used 6652K [0x00000007b5580000, 0x00000007bc780000, 0x00000007c0000000)
+  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
+  from space 6656K, 99% used [0x00000007bb800000,0x00000007bbe7f328,0x00000007bbe80000)
+  to   space 12288K, 0% used [0x00000007bac00000,0x00000007bac00000,0x00000007bb800000)
+ ParOldGen       total 51712K, used 25758K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
+  object space 51712K, 49% used [0x00000007a0000000,0x00000007a1927a30,0x00000007a3280000)
+ Metaspace       used 48041K, capacity 51778K, committed 52008K, reserved 1093632K
+  class space    used 5858K, capacity 6918K, committed 6952K, reserved 1048576K
+}
+Event: 8.392 GC heap before
+{Heap before GC invocations=13 (full 2):
+ PSYoungGen      total 95232K, used 95228K [0x00000007b5580000, 0x00000007bc780000, 0x00000007c0000000)
+  eden space 88576K, 100% used [0x00000007b5580000,0x00000007bac00000,0x00000007bac00000)
+  from space 6656K, 99% used [0x00000007bb800000,0x00000007bbe7f328,0x00000007bbe80000)
+  to   space 12288K, 0% used [0x00000007bac00000,0x00000007bac00000,0x00000007bb800000)
+ ParOldGen       total 51712K, used 25758K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
+  object space 51712K, 49% used [0x00000007a0000000,0x00000007a1927a30,0x00000007a3280000)
+ Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
+  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
+Event: 8.420 GC heap after
+Heap after GC invocations=13 (full 2):
+ PSYoungGen      total 100864K, used 12266K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
+  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
+  from space 12288K, 99% used [0x00000007bac00000,0x00000007bb7fa810,0x00000007bb800000)
+  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
+ ParOldGen       total 51712K, used 42401K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
+  object space 51712K, 81% used [0x00000007a0000000,0x00000007a29686f0,0x00000007a3280000)
+ Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
+  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
+}
+Event: 8.421 GC heap before
+{Heap before GC invocations=14 (full 3):
+ PSYoungGen      total 100864K, used 12266K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
+  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
+  from space 12288K, 99% used [0x00000007bac00000,0x00000007bb7fa810,0x00000007bb800000)
+  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
+ ParOldGen       total 51712K, used 42401K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
+  object space 51712K, 81% used [0x00000007a0000000,0x00000007a29686f0,0x00000007a3280000)
+ Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
+  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
+Event: 8.673 GC heap after
+Heap after GC invocations=14 (full 3):
+ PSYoungGen      total 100864K, used 989K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
+  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
+  from space 12288K, 8% used [0x00000007bac00000,0x00000007bacf7618,0x00000007bb800000)
+  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
+ ParOldGen       total 110080K, used 51241K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
+  object space 110080K, 46% used [0x00000007a0000000,0x00000007a320a5b8,0x00000007a6b80000)
+ Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
+  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
+}
+Event: 9.523 GC heap before
+{Heap before GC invocations=15 (full 3):
+ PSYoungGen      total 100864K, used 89565K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
+  eden space 88576K, 100% used [0x00000007b5580000,0x00000007bac00000,0x00000007bac00000)
+  from space 12288K, 8% used [0x00000007bac00000,0x00000007bacf7618,0x00000007bb800000)
+  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
+ ParOldGen       total 110080K, used 51241K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
+  object space 110080K, 46% used [0x00000007a0000000,0x00000007a320a5b8,0x00000007a6b80000)
+ Metaspace       used 50999K, capacity 55474K, committed 55848K, reserved 1097728K
+  class space    used 6291K, capacity 7599K, committed 7720K, reserved 1048576K
+Event: 9.538 GC heap after
+Heap after GC invocations=15 (full 3):
+ PSYoungGen      total 125952K, used 5892K [0x00000007b5580000, 0x00000007be980000, 0x00000007c0000000)
+  eden space 112640K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bc380000)
+  from space 13312K, 44% used [0x00000007bdc80000,0x00000007be241160,0x00000007be980000)
+  to   space 19456K, 0% used [0x00000007bc380000,0x00000007bc380000,0x00000007bd680000)
+ ParOldGen       total 110080K, used 51265K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
+  object space 110080K, 46% used [0x00000007a0000000,0x00000007a32105b8,0x00000007a6b80000)
+ Metaspace       used 50999K, capacity 55474K, committed 55848K, reserved 1097728K
+  class space    used 6291K, capacity 7599K, committed 7720K, reserved 1048576K
+}
+Event: 13.662 GC heap before
+{Heap before GC invocations=16 (full 3):
+ PSYoungGen      total 125952K, used 118532K [0x00000007b5580000, 0x00000007be980000, 0x00000007c0000000)
+  eden space 112640K, 100% used [0x00000007b5580000,0x00000007bc380000,0x00000007bc380000)
+  from space 13312K, 44% used [0x00000007bdc80000,0x00000007be241160,0x00000007be980000)
+  to   space 19456K, 0% used [0x00000007bc380000,0x00000007bc380000,0x00000007bd680000)
+ ParOldGen       total 110080K, used 51265K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
+  object space 110080K, 46% used [0x00000007a0000000,0x00000007a32105b8,0x00000007a6b80000)
+ Metaspace       used 54598K, capacity 59322K, committed 59432K, reserved 1099776K
+  class space    used 6795K, capacity 8215K, committed 8232K, reserved 1048576K
+Event: 13.687 GC heap after
+Heap after GC invocations=16 (full 3):
+ PSYoungGen      total 132096K, used 18319K [0x00000007b5580000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 112640K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bc380000)
+  from space 19456K, 94% used [0x00000007bc380000,0x00000007bd563f30,0x00000007bd680000)
+  to   space 22016K, 0% used [0x00000007bea80000,0x00000007bea80000,0x00000007c0000000)
+ ParOldGen       total 110080K, used 59392K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
+  object space 110080K, 53% used [0x00000007a0000000,0x00000007a3a00398,0x00000007a6b80000)
+ Metaspace       used 54598K, capacity 59322K, committed 59432K, reserved 1099776K
+  class space    used 6795K, capacity 8215K, committed 8232K, reserved 1048576K
+}
+
+Deoptimization events (10 events):
+Event: 11.972 Thread 0x00007f8b6611a000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000011b690030 method=java.io.DataInputStream.readUnsignedByte()I @ 4
+Event: 12.085 Thread 0x00007f8b6611a000 Uncommon trap: reason=predicate action=maybe_recompile pc=0x000000011b33e0d4 method=java.lang.String.regionMatches(ZILjava/lang/String;II)Z @ 63
+Event: 12.085 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b66598c method=sun.java2d.pipe.RegionSpanIterator.nextSpan([I)Z @ 13
+Event: 13.451 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b858edc method=com.apple.laf.AquaUtils$IconImageFilter.grayTransform(II)I @ 5
+Event: 13.451 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b2bd818 method=com.apple.laf.AquaUtils$IconImageFilter.grayTransform(II)I @ 5
+Event: 13.458 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b45b10c method=java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Ljava/awt/AWTEvent;)V @ 195
+Event: 13.721 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b1b7af8 method=java.lang.ThreadLocal$ThreadLocalMap.set(Ljava/lang/ThreadLocal;Ljava/lang/Object;)V @ 119
+Event: 13.760 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b8dae00 method=org.openide.util.lookup.InheritanceTree.registerInterface(Lorg/openide/util/lookup/AbstractLookup$Pair;Ljava/util/Collection;)Z @ 62
+Event: 13.761 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b792998 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 19
+Event: 13.766 Thread 0x00007f8b6a241800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011bbf5c64 method=org.openide.util.WeakListenerImpl.get(Ljava/util/EventObject;)Ljava/util/EventListener; @ 9
+
+Classes redefined (0 events):
+No events
+
+Internal exceptions (10 events):
+Event: 9.540 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x00000007b5581cc8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 9.542 Thread 0x00007f8b6611a000 Implicit null exception at 0x000000011acf4b0c to 0x000000011acf4b89
+Event: 9.549 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x00000007b560a398) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 11.001 Thread 0x00007f8b66644800 Implicit null exception at 0x000000011b82fe94 to 0x000000011b83215d
+Event: 11.178 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b84b9478) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 11.190 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b84fb130) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 11.199 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/awt/FontEditor> (0x00000007b851e038) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 11.208 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b8561c30) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 11.210 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b857b770) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 13.766 Thread 0x00007f8b6a241800 Implicit null exception at 0x000000011bbf5996 to 0x000000011bbf5c41
+
+Events (10 events):
+Event: 13.766 Executing VM operation: RevokeBias
+Event: 13.766 Executing VM operation: RevokeBias done
+Event: 13.770 Executing VM operation: RevokeBias
+Event: 13.770 Executing VM operation: RevokeBias done
+Event: 13.771 Executing VM operation: RevokeBias
+Event: 13.771 Executing VM operation: RevokeBias done
+Event: 13.771 Executing VM operation: RevokeBias
+Event: 13.771 Executing VM operation: RevokeBias done
+Event: 13.772 Executing VM operation: RevokeBias
+Event: 13.772 Executing VM operation: RevokeBias done
+
+
+Dynamic libraries:
+0x00000000230d2000 	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
+0x00000000230d2000 	/System/Library/Frameworks/Security.framework/Versions/A/Security
+0x00000000230d2000 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
+0x00000000230d2000 	/usr/lib/libz.1.dylib
+0x00000000230d2000 	/usr/lib/libSystem.B.dylib
+0x00000000230d2000 	/usr/lib/libobjc.A.dylib
+0x00000000230d2000 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
+0x00000000230d2000 	/System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
+0x00000000230d2000 	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
+0x00000000230d2000 	/System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
+0x00000000230d2000 	/System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
+0x00000000230d2000 	/System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
+0x00000000230d2000 	/System/Library/PrivateFrameworks/DFRFoundation.framework/Versions/A/DFRFoundation
+0x00000000230d2000 	/System/Library/Frameworks/Metal.framework/Versions/A/Metal
+0x00000000230d2000 	/System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
+0x00000000230d2000 	/usr/lib/libenergytrace.dylib
+0x00000000230d2000 	/System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
+0x00000000230d2000 	/System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
+0x00000000230d2000 	/usr/lib/libScreenReader.dylib
+0x00000000230d2000 	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
+0x00000000230d2000 	/System/Library/Frameworks/IOSurface.framework/Versions/A/IOSurface
+0x00000000230d2000 	/System/Library/Frameworks/AudioToolbox.framework/Versions/A/AudioToolbox
+0x00000000230d2000 	/System/Library/Frameworks/AudioUnit.framework/Versions/A/AudioUnit
+0x00000000230d2000 	/System/Library/PrivateFrameworks/DataDetectorsCore.framework/Versions/A/DataDetectorsCore
+0x00000000230d2000 	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.framework/Versions/A/HIToolbox
+0x00000000230d2000 	/usr/lib/libicucore.A.dylib
+0x00000000230d2000 	/System/Library/Frameworks/QuartzCore.framework/Versions/A/QuartzCore
+0x00000000230d2000 	/System/Library/PrivateFrameworks/SignpostNotification.framework/Versions/A/SignpostNotification
+0x00000000230d2000 	/System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/SpeechRecognition.framework/Versions/A/SpeechRecognition
+0x00000000230d2000 	/usr/lib/libauto.dylib
+0x00000000230d2000 	/usr/lib/libxml2.2.dylib
+0x00000000230d2000 	/System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/CoreUI
+0x00000000230d2000 	/System/Library/Frameworks/CoreAudio.framework/Versions/A/CoreAudio
+0x00000000230d2000 	/System/Library/Frameworks/DiskArbitration.framework/Versions/A/DiskArbitration
+0x00000000230d2000 	/usr/lib/liblangid.dylib
+0x00000000230d2000 	/System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
+0x00000000230d2000 	/System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
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+0x00000000230d2000 	/System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
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+0x000000012a3b4000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln399623017371000138/jln8259570056051360089/natives/macosx-universal/libnativewindow_awt.jnilib
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+0x0000000159a6a000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln399623017371000138/jln8259570056051360089/natives/macosx-universal/libjogl_desktop.jnilib
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+0x000000012b14c000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/liblcms.dylib
+
+VM Arguments:
+jvm_args: -Djdk.home=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home -Dnetbeans.dirs=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/gephi::/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/plugins_clusters/plugins -Dnetbeans.home=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform -Xms64m -Xmx512m -Xverify:none -Dsun.java2d.noddraw=true -Dsun.awt.noerasebackground=true -Dnetbeans.indexing.noFileRefresh=true -Dplugin.manager.check.interval=EVERY_DAY -Dnetbeans.logger.console=true -ea -DaddExports:java.desktop/com.apple.eawt=ALL-UNNAMED -DaddExports:java.desktop/sun.awt=ALL-UNNAMED -DaddExports:java.base/jdk.internal.jrtfs=ALL-UNNAMED -DaddExports:java.desktop/apple.laf=ALL-UNNAMED -DaddExports:java.desktop/java.awt.peer=ALL-UNNAMED -DaddExports:java.desktop/com.sun.beans.editors=ALL-UNNAMED -DaddExports:java.desktop/sun.awt.im=ALL-UNNAMED -DaddExports:java.management/sun.management=ALL-UNNAMED -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/log/heapdump.hprof 
+java_command: org.netbeans.Main --cachedir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/cache --userdir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir --branding gephi --branding gephi
+java_class_path (initial): /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/boot.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-modules.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-lookup.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-ui.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ar_SA.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_bg.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ca.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_cs.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_de.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_es.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_fr.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_gl_ES.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_in_ID.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_it.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ja.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/li
+Launcher Type: SUN_STANDARD
+
+Environment Variables:
+JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home
+PATH=./bin:/usr/local/opt/rbenv/shims:/usr/local/opt/rbenv/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/amd64:/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/i386:
+SHELL=/bin/zsh
+
+Signal Handlers:
+SIGSEGV: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
+SIGBUS: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGFPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGPIPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGXFSZ: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGILL: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART
+SIGUSR2: [libjvm.dylib+0x48a5ae], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
+SIGHUP: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGINT: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
+SIGTERM: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGQUIT: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+
+
+---------------  S Y S T E M  ---------------
+
+OS:Bsduname:Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
+rlimit: STACK 8192k, CORE 0k, NPROC 1418, NOFILE 10240, AS infinity
+load average:6.54 5.20 4.83
+
+CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx
+
+Memory: 4k page, physical 16777216k(2131984k free)
+
+/proc/meminfo:
+
+
+vm_info: Java HotSpot(TM) 64-Bit Server VM (25.171-b11) for bsd-amd64 JRE (1.8.0_171-b11), built on Mar 28 2018 12:50:57 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
+
+time: Tue Aug 21 20:41:13 2018
+elapsed time: 13 seconds (0d 0h 0m 13s)
+
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
index f62f9fd..efb0841 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
@@ -22,3 +22,8 @@ Done:
 
     i. Resolve use of weight vs weight_dynamic
   Check if weight is dynamic; check if dynamic_weight is dynamic; use whichever one exists
+
+
+
+
+verifying weight column contains doubles in the initAlgo method
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index ddf5e03..b45cdea 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -43,6 +43,7 @@ Development and Distribution License("CDDL") (collectively, the
 // org.gephi.layout.plugins.layout.NodeWeight
 
 import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Element;
 import org.gephi.graph.api.Graph;
 import org.gephi.graph.api.GraphModel;
 import org.gephi.graph.api.Node;
@@ -51,6 +52,7 @@ Development and Distribution License("CDDL") (collectively, the
 import org.gephi.graph.api.types.IntervalMap;
 import org.gephi.graph.api.types.TimeMap;
 import org.gephi.graph.api.types.TimestampMap;
+import org.gephi.graph.api.types.TimestampDoubleMap;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
 // import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
 import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
@@ -66,7 +68,12 @@ Development and Distribution License("CDDL") (collectively, the
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
 import java.util.concurrent.Future;
+import java.util.Comparator;
+import java.util.Map;
+
+
 import org.gephi.graph.api.Interval;
+
 // import org.gephi.layout.plugin.AbstractLayout;
 import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
 
@@ -208,36 +215,161 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
+// public <T> T min(Collection<T> c, Comparator<T> comp) {
+// if ((c == null) || (comp == null)) {
+//      throw new IllegalArgumentException();
+//   }
+
+//   if (c.isEmpty() == true) {
+//      throw new NoSuchElementException();
+//   }
+
+
+ // Iterator itr = c.iterator();
+ // T min = (T)itr.next();
+ // T value;
+ // while (itr.hasNext()) {
+ //      value=(T)itr.next();
+ //      if (comp.compare(min, value) < 0) {
+ //         min = value;
+ //      }
+ // }
+//   return min;
+      private double weightMin(Node[] nodes, String column_name) {
+        Double[] minima;
+        Double min;
+
+        // seed min value from data
+        TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
+        double[] seed_weights = seed_map.toDoubleArray();
+        min = seed_weights[0];
+
+        for (Node n: nodes) {
+          TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(column_name);
+          double[] weights = map.toDoubleArray();
+
+          for (Double wt: weights) {
+            if (wt < min) {
+              min = wt;
+            }
+
+          }
+        }
+        return min;
+      }
+  //   private void weightMin(String column_name) {
+  //     Table nodeTable = graphModel.getNodeTable();
+  //     Float value;
+  //     ArrayList<Float> local_minima = new ArrayList<Float>();
+
+  //     if (nodeTable.hasColumn("weight")) {
+  //       // Iterable<Map.Entry> weight_list = getAttributes(nodeTable.getColumn("weight"));
+  //       for () {
+  //         Iterable<Map.Entry> weight_list = n.getAttributes(nodeTable.getColumn("weight"));
+  //         Iterator<Map.Entry> iter = weight_list.iterator();
+
+  //         Map.Entry next = (Map.Entry) iter.next();
+  //         float min = (float) next.getValue();
+
+  //         while (iter.hasNext()) {
+  //           value = (float) iter.next().getValue();
+  //           if (value.compareTo(min) < 0) {
+  //             local_minima.add(value);
+  //           }
+  //           // if (comp.compare(min, value) < 0) {
+  //           //   min = value;
+  //           // }
+  //         }
+  //     }
+
+  //   }
+
+  //   return Collections.min(local_minima);
+  // }
+
+    // private void weightMin(String column_name) {
+    //   Table nodeTable = graphModel.getNodeTable();
+    //   Float value;
+    //   if (nodeTable.hasColumn("weight")) {
+    //     // Iterable<Map.Entry> weight_list = getAttributes(nodeTable.getColumn("weight"));
+    //     for Nodes: n {
+
+    //     }
+    //     Iterable<Map.Entry> weight_list = nodeTable.getAttributes(nodeTable.getColumn("weight"));
+
+    //     Iterator<Map.Entry> iter = weight_list.iterator();
+
+    //     Map.Entry next = (Map.Entry) iter.next();
+    //     float min = (float) next.getValue();
+
+    //     while (iter.hasNext()) {
+    //       value = (float) iter.next().getValue();
+    //       if (value.compareTo(min) < 0) {
+    //         min = value;
+    //       }
+    //       // if (comp.compare(min, value) < 0) {
+    //       //   min = value;
+    //       // }
+    //     }
+    //   return min;
+    //   } else {
+    //     return 0;
+    //   }
+    // }
+
+    // private void weightMax(String column_name){
 
-    private float normalizeNodeWeight(Node node, Double weight) {
-      double d_weight = weight;
-      double d_max = getMaxWeight();
-      double d_min = getMinWeight();
-      float maxWeight = (float) d_max;
-      float minWeight = (float) d_min;
-      float f_weight = (float) d_weight;
-      Float normalized = (f_weight-minWeight)/(maxWeight-minWeight);
+    // }
 
-      return normalized;
-      // /**
-      // * 1. find the max and min in the column
-      // * 2. add to make all numbers positive
-      // * 3. divide by ten's place of the new max
-      // * 3b. functionality to choose desired max?
-      // */
-    }
 
-    private void adjustNodeTransparency(Node node, Double weight) {
-      Float normalized_weight = normalizeNodeWeight(node, weight);
-      node.setAlpha(normalized_weight);
-      // System.out.println("\"TESTING\"" + String.valueOf(getMinWeight()));
-      // /**
-      // * DO: Adjust transparency based on weight normalization
-      // * void  setAlpha(float a)
-      // * Sets the alpha (transparency) color component.
-      // ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/ElementProperties.html#alpha--
-      // */
-    }
+
+    // }
+    // private void getColumnMin(Column column) {
+
+    // }
+
+    // private void getColumnMax(Column column) {
+
+    // }
+
+
+    // private float normalizeNodeWeight(Node node, Double weight) {
+    //   double d_weight = weight;
+    //   double d_max = getMaxWeight();
+    //   double d_min = getMinWeight();
+    //   float maxWeight = (float) d_max;
+    //   float minWeight = (float) d_min;
+    //   float f_weight = (float) d_weight;
+    //   Float normalized = (f_weight-minWeight)/(maxWeight-minWeight);
+
+    //   return normalized;
+    //   // /**
+    //   // * 1. find the max and min in the column
+    //   // * 2. add to make all numbers positive
+    //   // * 3. divide by ten's place of the new max
+    //   // * 3b. functionality to choose desired max?
+    //   // */
+    // }
+
+    // private void adjustNodeTransparency(Node node, Double weight) {
+    //   Float normalized_weight = normalizeNodeWeight(node, weight);
+    //   node.setAlpha(normalized_weight);
+    //   // System.out.println("\"TESTING\"" + String.valueOf(getMinWeight()));
+    //   // /**
+    //   // * DO: Adjust transparency based on weight normalization
+    //   // * void  setAlpha(float a)
+    //   // * Sets the alpha (transparency) color component.
+    //   // ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/ElementProperties.html#alpha--
+    //   // */
+    // }
+
+
+
+    // private void heatMapNodeWeight(Node node, Double weight) {
+    //   getColumn
+
+    //   float hue = (float) ((weight-0)/(0.66-0))
+    // }
 
 
     // public void addWeightCol(graph){
@@ -376,9 +508,6 @@ public void goAlgo() {
 
                 }
 
-                adjustNodeTransparency(node_a, wt_a);
-                adjustNodeTransparency(node_b, wt_b);
-
                 NodeAttraction.apply(node_a, node_b, ((wt_a + wt_b)/2));
 
             }

From 62c20f4c1998c01f6a2bea0a66f0ae7981653d93 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Wed, 22 Aug 2018 17:19:44 +0100
Subject: [PATCH 14/32] have fn for min and max of weights

---
 .../layout/NodeWeight/ForceAtlas2.java        | 24 ++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index b45cdea..65f5495 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -236,7 +236,6 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
  // }
 //   return min;
       private double weightMin(Node[] nodes, String column_name) {
-        Double[] minima;
         Double min;
 
         // seed min value from data
@@ -257,6 +256,29 @@ private double weightMin(Node[] nodes, String column_name) {
         }
         return min;
       }
+
+      private double weightMax(Node[] nodes, String column_name) {
+        Double max;
+
+        // seed min value from data
+        TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
+        double[] seed_weights = seed_map.toDoubleArray();
+        max = seed_weights[0];
+
+        for (Node n: nodes) {
+          TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(column_name);
+          double[] weights = map.toDoubleArray();
+
+          for (Double wt: weights) {
+            if (wt > max) {
+              max = wt;
+            }
+
+          }
+        }
+        return max;
+      }
+
   //   private void weightMin(String column_name) {
   //     Table nodeTable = graphModel.getNodeTable();
   //     Float value;

From c9bc8971395b50be62969d3eb311fcdeb1a69250 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Thu, 23 Aug 2018 12:28:35 +0100
Subject: [PATCH 15/32] messing around with histogram

---
 .../layout/NodeWeight/ForceAtlas2.java        | 342 ++++++++----------
 1 file changed, 146 insertions(+), 196 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 0ac4414..53f86e3 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -40,6 +40,7 @@ Development and Distribution License("CDDL") (collectively, the
  Portions Copyrighted 2011 Gephi Consortium.
  */
 package org.gephi.layout.plugins.layout.NodeWeight;
+import java.awt.Color;
 // org.gephi.layout.plugins.layout.NodeWeight
 
 import org.gephi.graph.api.Edge;
@@ -77,20 +78,21 @@ Development and Distribution License("CDDL") (collectively, the
 import java.util.Map;
 
 
+
 import org.gephi.graph.api.Interval;
 
 // import org.gephi.layout.plugin.AbstractLayout;
 import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
-=======
 
 
->>>>>>> 32ef5fb6b2f878598a4894a4849029b11e9e1a36
 
 
 import org.openide.util.Exceptions;
 import org.openide.util.NbBundle;
 
 
+
+
 /**
  * ForceAtlas 2 Layout, manages each step of the computations.
  *
@@ -120,6 +122,21 @@ public class ForceAtlas2 implements Layout {
     private ExecutorService pool;
     private double minWeight;
     private double maxWeight;
+    private String nodeWeightColumnName;
+
+
+
+    private void setNodeWeightColumnName(Table table) {
+      if (table.hasColumn("weight")) {
+        this.nodeWeightColumnName = "weight";
+      }
+      // weight_dynamic
+      if (table.hasColumn("weight_dynamic")) {
+        this.nodeWeightColumnName = "weight_dynamic";
+      }
+    }
+
+
 
     public ForceAtlas2(ForceAtlas2Builder layoutBuilder) {
         this.layoutBuilder = layoutBuilder;
@@ -135,11 +152,23 @@ public void initAlgo() {
 
         Table table = graphModel.getNodeTable();
 
-        if (!(table.hasColumn("weight"))) {
+
+        if (!(table.hasColumn("weight") || table.hasColumn("weight_dynamic"))) {
           table.addColumn("weight", Double.class);
         }
-        // table.addColumn("weight", "weight", Double.class, (Double) 0.0);
-        // table.addColumn("weight", Double.class);
+
+        setNodeWeightColumnName(table);
+
+        if (!(table.getColumn(nodeWeightColumnName).getTypeClass()==Double.class || (table.getColumn(nodeWeightColumnName).getTypeClass()==TimestampDoubleMap.class))) {
+          // try {
+          //           future.get();
+          //       } catch (Exception e) {
+          //           throw new RuntimeException("Unable to layout " + this.getClass().getSimpleName() + ".", e);
+          //       }
+
+
+          //alert the user that need type double and abort algorithm
+        }
 
 
 
@@ -171,6 +200,23 @@ public void initAlgo() {
         }
     }
 
+    public static int[] calcHistogram(double[] data, double min, double max, int numBins) {
+      final int[] result = new int[numBins];
+      final double binSize = (max - min)/numBins;
+
+      for (double d : data) {
+        int bin = (int) ((d - min) / binSize);
+        if (bin < 0) { /* this data is smaller than min */ }
+        else if (bin >= numBins) { /* this data point is bigger than max */ }
+        else {
+          result[bin] += 1;
+        }
+      }
+      return result;
+    }
+
+
+
     private double getEdgeWeight(Edge edge, boolean isDynamicWeight, Interval interval) {
         if (isDynamicWeight) {
             return edge.getWeight(interval);
@@ -210,7 +256,7 @@ private boolean hasNodeWeight(Node node) {
     private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
         if (isDynamicNodeWeight) {
             // node_weight = (Double) n.getAttribute("gravity_x");
-            TimestampMap map = (TimestampMap) node.getAttribute("weight");
+            TimestampMap map = (TimestampMap) node.getAttribute(this.nodeWeightColumnName);
             // Estimator estimator = (Estimator) AVERAGE;
             Double prev_value = 0.0;
             Double value = (Double) map.get(interval, Estimator.AVERAGE);
@@ -222,55 +268,41 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
             }
 
         } else {
-          return (Double) node.getAttribute(column_name);
+          return (Double) node.getAttribute(this.nodeWeightColumnName);
         }
     }
 
-// public <T> T min(Collection<T> c, Comparator<T> comp) {
-// if ((c == null) || (comp == null)) {
-//      throw new IllegalArgumentException();
-//   }
-
-//   if (c.isEmpty() == true) {
-//      throw new NoSuchElementException();
-//   }
-
 
- // Iterator itr = c.iterator();
- // T min = (T)itr.next();
- // T value;
- // while (itr.hasNext()) {
- //      value=(T)itr.next();
- //      if (comp.compare(min, value) < 0) {
- //         min = value;
- //      }
- // }
-//   return min;
-      private double weightMin(Node[] nodes, String column_name) {
-        Double min;
-
-        // seed min value from data
-        TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
-        double[] seed_weights = seed_map.toDoubleArray();
-        min = seed_weights[0];
+    private void setterMinWeight(Node[] nodes) {
+      Double min;
 
-        for (Node n: nodes) {
-          TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(column_name);
-          double[] weights = map.toDoubleArray();
+      // seed min value from data
+      TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(this.nodeWeightColumnName);
+      double[] seed_weights = seed_map.toDoubleArray();
+      min = seed_weights[0];
 
-          for (Double wt: weights) {
-            if (wt < min) {
-              min = wt;
-            }
+      for (Node n: nodes) {
+        TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
+        double[] weights = map.toDoubleArray();
 
+        for (Double wt: weights) {
+          if (wt < min) {
+            min = wt;
           }
+
         }
-        return min;
       }
+      // System.out.println("");
+      // System.out.println("----------------------------");
+      // System.out.println("MIN: " +  min );
+      // System.out.println("----------------------------");
+      // System.out.println("");
+      this.minWeight = min;
+    }
 
-      private double weightMax(Node[] nodes, String column_name) {
+    private void setterMaxWeight(Node[] nodes) {
         Double max;
-
+        String column_name = this.nodeWeightColumnName;
         // seed min value from data
         TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
         double[] seed_weights = seed_map.toDoubleArray();
@@ -287,131 +319,43 @@ private double weightMax(Node[] nodes, String column_name) {
 
           }
         }
-        return max;
-      }
-
-  //   private void weightMin(String column_name) {
-  //     Table nodeTable = graphModel.getNodeTable();
-  //     Float value;
-  //     ArrayList<Float> local_minima = new ArrayList<Float>();
-
-  //     if (nodeTable.hasColumn("weight")) {
-  //       // Iterable<Map.Entry> weight_list = getAttributes(nodeTable.getColumn("weight"));
-  //       for () {
-  //         Iterable<Map.Entry> weight_list = n.getAttributes(nodeTable.getColumn("weight"));
-  //         Iterator<Map.Entry> iter = weight_list.iterator();
-
-  //         Map.Entry next = (Map.Entry) iter.next();
-  //         float min = (float) next.getValue();
-
-  //         while (iter.hasNext()) {
-  //           value = (float) iter.next().getValue();
-  //           if (value.compareTo(min) < 0) {
-  //             local_minima.add(value);
-  //           }
-  //           // if (comp.compare(min, value) < 0) {
-  //           //   min = value;
-  //           // }
-  //         }
-  //     }
-
-  //   }
-
-  //   return Collections.min(local_minima);
-  // }
-
-    // private void weightMin(String column_name) {
-    //   Table nodeTable = graphModel.getNodeTable();
-    //   Float value;
-    //   if (nodeTable.hasColumn("weight")) {
-    //     // Iterable<Map.Entry> weight_list = getAttributes(nodeTable.getColumn("weight"));
-    //     for Nodes: n {
-
-    //     }
-    //     Iterable<Map.Entry> weight_list = nodeTable.getAttributes(nodeTable.getColumn("weight"));
-
-    //     Iterator<Map.Entry> iter = weight_list.iterator();
-
-    //     Map.Entry next = (Map.Entry) iter.next();
-    //     float min = (float) next.getValue();
-
-    //     while (iter.hasNext()) {
-    //       value = (float) iter.next().getValue();
-    //       if (value.compareTo(min) < 0) {
-    //         min = value;
-    //       }
-    //       // if (comp.compare(min, value) < 0) {
-    //       //   min = value;
-    //       // }
-    //     }
-    //   return min;
-    //   } else {
-    //     return 0;
-    //   }
-    // }
-
-    // private void weightMax(String column_name){
-
-    // }
-
-
-
-    // }
-    // private void getColumnMin(Column column) {
-
-    // }
-
-    // private void getColumnMax(Column column) {
-
-    // }
-
-
-    // private float normalizeNodeWeight(Node node, Double weight) {
-    //   double d_weight = weight;
-    //   double d_max = getMaxWeight();
-    //   double d_min = getMinWeight();
-    //   float maxWeight = (float) d_max;
-    //   float minWeight = (float) d_min;
-    //   float f_weight = (float) d_weight;
-    //   Float normalized = (f_weight-minWeight)/(maxWeight-minWeight);
-
-    //   return normalized;
-    //   // /**
-    //   // * 1. find the max and min in the column
-    //   // * 2. add to make all numbers positive
-    //   // * 3. divide by ten's place of the new max
-    //   // * 3b. functionality to choose desired max?
-    //   // */
-    // }
-
-    // private void adjustNodeTransparency(Node node, Double weight) {
-    //   Float normalized_weight = normalizeNodeWeight(node, weight);
-    //   node.setAlpha(normalized_weight);
-    //   // System.out.println("\"TESTING\"" + String.valueOf(getMinWeight()));
-    //   // /**
-    //   // * DO: Adjust transparency based on weight normalization
-    //   // * void  setAlpha(float a)
-    //   // * Sets the alpha (transparency) color component.
-    //   // ** https://gephi.org/gephi/0.9.2/apidocs/org/gephi/graph/api/ElementProperties.html#alpha--
-    //   // */
-    // }
-
-
-
-    // private void heatMapNodeWeight(Node node, Double weight) {
-    //   getColumn
-
-    //   float hue = (float) ((weight-0)/(0.66-0))
-    // }
-
+        // System.out.println("");
+        // System.out.println("----------------------------");
+        // System.out.println("MAX: " +  max );
+        // System.out.println("----------------------------");
+        // System.out.println("");
+        this.maxWeight = max;
+    }
+
+    private void adjustHue(Node[] nodes, Node node, Double weight){
+        // Double min = getMinWeight(nodes);
+        // Double max = getMaxWeight(nodes);
+
+        Double min = this.minWeight;
+        System.out.println("");
+        System.out.println("----------------------------");
+        System.out.println("MIN: " +  min );
+        System.out.println("----------------------------");
+        System.out.println("");
+        Double max = this.maxWeight;
+        System.out.println("");
+        System.out.println("----------------------------");
+        System.out.println("MAX: " +  max );
+        System.out.println("----------------------------");
+        System.out.println("");
+
+        // scale weights to lie between 0 and 0.66
+        double hue_double = (double)(((weight - min)/(max - min))*(0.66-0.0) + 0.0);
+        //node.getNodeData().setColor(float r, float g, float b)
+        float hue_float = (float) hue_double;
+        float s = 1.0f;
+        float b = 1.0f;
+        Color new_color = Color.getHSBColor(hue_float, s, b);
+        node.setColor(new_color);
+//Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
+    }
 
-    // public void addWeightCol(graph){
-    //   graph.addColumn();
-    // }
 
-    // public void switchToDynamic(col){
-    //   return 0;
-    // }
 
     @Override
     public void goAlgo() {
@@ -420,27 +364,13 @@ public void goAlgo() {
             return;
         }
 
-        // Table table = graphModel.getNodeTable();
-        // table.addColumn("weight", Double.class);
-
-
         graph = graphModel.getGraphVisible();
 
         graph.readLock();
         boolean isDynamicWeight = graphModel.getEdgeTable().getColumn("weight").isDynamic();
         // to-do: make compatible with weight_dynamic
         // provide exception catch otherwise
-        // boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn("weight").isDynamic();
-        boolean isDynamicNodeWeight = false;
-
-        Table node_table = graphModel.getNodeTable();
-        if (node_table.hasColumn("weight") && node_table.getColumn("weight").isDynamic()){
-          isDynamicNodeWeight = true;
-        } else if (node_table.hasColumn("weight_dynamic") && node_table.getColumn("weight_dynamic").isDynamic()){
-          isDynamicNodeWeight = true;
-        }
-
-
+        boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn(this.nodeWeightColumnName).isDynamic();
 
 
 
@@ -449,6 +379,30 @@ public void goAlgo() {
         try {
             Node[] nodes = graph.getNodes().toArray();
             Edge[] edges = graph.getEdges().toArray();
+            setterMinWeight(nodes);
+            setterMaxWeight(nodes);
+            List<Double> all_weights = new ArrayList<Double>();
+
+            for (Node n: nodes) {
+              TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
+              double[] weights = map.toDoubleArray();
+
+              for (Double wt: weights) {
+                if (wt != null) {
+                all_weights.add(wt);
+                }
+
+              }
+            }
+            Double[] all_weights_array = new Double[all_weights.size()];
+            all_weights_array = all_weights.toArray(all_weights_array);
+            // double[] weights_double_ary = Stream.of(all_weights_array).mapToDouble(Double::doubleValue).toArray();
+
+
+            // int[] histogram = calcHistogram(all_weights_array, this.minWeight, this.maxWeight, 20);
+
+            // System.out.println(histogram);
+            // This is a histogram with 4 bins, 0-2.5, 2.5-5, 5-7.5, 7.5-10.
 
             // Initialise layout data
             for (Node n : nodes) {
@@ -517,9 +471,13 @@ public void goAlgo() {
                     Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
                 }
             }
-            // Node Weight
 
+            // Node Weight
             AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
+
+            // setterMinWeight(nodes);
+            // setterMaxWeight(nodes);
+
             for (Edge e : edges) {
               Node node_a = e.getSource();
               Node node_b = e.getTarget();
@@ -527,20 +485,12 @@ public void goAlgo() {
               if (hasNodeWeight(node_a) && hasNodeWeight(node_b)) {
                 Double wt_a = 0.0;
                 Double wt_b = 0.0;
-                if (hasNodeWeightStop(node_a) && hasNodeWeightStop(node_b)) {
-
-                  wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval, "weight");
-                  wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval, "weight");
-
-                }
-
-                if (hasNodeWeightDynamic(node_a) && hasNodeWeightDynamic(node_b)) {
-
-                  wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval, "weight_dynamic");
-                  wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval, "weight_dynamic");
-
-                }
-
+                wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
+                wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
+                // setterMinWeight();
+                // setterMaxWeight();
+                // adjustHue(nodes, node_a, wt_a);
+                // adjustHue(nodes, node_b, wt_b);
                 NodeAttraction.apply(node_a, node_b, ((wt_a + wt_b)/2));
 
             }

From 7dc2b6101ad8e159b2759d78304afd4238a190bc Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Sat, 25 Aug 2018 19:33:41 +0100
Subject: [PATCH 16/32] toggle of heat map and heat map implemented

---
 .../layout/NodeWeight/ForceAtlas2.java        | 281 +++++++++++-------
 .../layout/NodeWeight/Bundle.properties       |  10 +-
 2 files changed, 184 insertions(+), 107 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 53f86e3..a3bd581 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -115,6 +115,7 @@ public class ForceAtlas2 implements Layout {
     private double barnesHutTheta;
     private boolean linLogMode;
     private boolean strongGravityMode;
+    private boolean heatMapMode;
     private int threadCount;
     private int currentThreadCount;
     private Region rootRegion;
@@ -200,20 +201,20 @@ public void initAlgo() {
         }
     }
 
-    public static int[] calcHistogram(double[] data, double min, double max, int numBins) {
-      final int[] result = new int[numBins];
-      final double binSize = (max - min)/numBins;
+    // public static int[] calcHistogram(double[] data, double min, double max, int numBins) {
+    //   final int[] result = new int[numBins];
+    //   final double binSize = (max - min)/numBins;
 
-      for (double d : data) {
-        int bin = (int) ((d - min) / binSize);
-        if (bin < 0) { /* this data is smaller than min */ }
-        else if (bin >= numBins) { /* this data point is bigger than max */ }
-        else {
-          result[bin] += 1;
-        }
-      }
-      return result;
-    }
+    //   for (double d : data) {
+    //     int bin = (int) ((d - min) / binSize);
+    //     if (bin < 0) { /* this data is smaller than min */ }
+    //     else if (bin >= numBins) { /* this data point is bigger than max */ }
+    //     else {
+    //       result[bin] += 1;
+    //     }
+    //   }
+    //   return result;
+    // }
 
 
 
@@ -273,87 +274,130 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
     }
 
 
-    private void setterMinWeight(Node[] nodes) {
-      Double min;
-
-      // seed min value from data
-      TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(this.nodeWeightColumnName);
-      double[] seed_weights = seed_map.toDoubleArray();
-      min = seed_weights[0];
+    // private void setterMinWeight(Node[] nodes) {
+    //   Double min;
+
+    //   // seed min value from data
+    //   TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(this.nodeWeightColumnName);
+    //   double[] seed_weights = seed_map.toDoubleArray();
+    //   min = seed_weights[0];
+
+    //   for (Node n: nodes) {
+    //     TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
+    //     double[] weights = map.toDoubleArray();
+
+    //     for (Double wt: weights) {
+    //       if (wt < min) {
+    //         min = wt;
+    //       }
+
+    //     }
+    //   }
+    //   // System.out.println("");
+    //   // System.out.println("----------------------------");
+    //   // System.out.println("MIN: " +  min );
+    //   // System.out.println("----------------------------");
+    //   // System.out.println("");
+    //   this.minWeight = min;
+    // }
+
+    // private void setterMaxWeight(Node[] nodes) {
+    //     Double max;
+    //     String column_name = this.nodeWeightColumnName;
+    //     // seed min value from data
+    //     TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
+    //     double[] seed_weights = seed_map.toDoubleArray();
+    //     max = seed_weights[0];
+
+    //     for (Node n: nodes) {
+    //       TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(column_name);
+    //       double[] weights = map.toDoubleArray();
+
+    //       for (Double wt: weights) {
+    //         if (wt > max) {
+    //           max = wt;
+    //         }
+
+    //       }
+    //     }
+    //     // System.out.println("");
+    //     // System.out.println("----------------------------");
+    //     // System.out.println("MAX: " +  max );
+    //     // System.out.println("----------------------------");
+    //     // System.out.println("");
+    //     this.maxWeight = max;
+    // }
 
-      for (Node n: nodes) {
-        TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
-        double[] weights = map.toDoubleArray();
-
-        for (Double wt: weights) {
-          if (wt < min) {
-            min = wt;
-          }
-
-        }
-      }
-      // System.out.println("");
-      // System.out.println("----------------------------");
-      // System.out.println("MIN: " +  min );
-      // System.out.println("----------------------------");
-      // System.out.println("");
-      this.minWeight = min;
-    }
-
-    private void setterMaxWeight(Node[] nodes) {
-        Double max;
-        String column_name = this.nodeWeightColumnName;
-        // seed min value from data
-        TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
-        double[] seed_weights = seed_map.toDoubleArray();
-        max = seed_weights[0];
-
-        for (Node n: nodes) {
-          TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(column_name);
-          double[] weights = map.toDoubleArray();
-
-          for (Double wt: weights) {
-            if (wt > max) {
-              max = wt;
-            }
+    private void adjustHue(Node[] nodes, Node node, Double weight){
+        // Double min = getMinWeight(nodes);
+        // Double max = getMaxWeight(nodes);
 
-          }
-        }
+        // Double min = this.minWeight;
+        // System.out.println("");
+        // System.out.println("----------------------------");
+        // System.out.println("MIN: " +  min );
+        // System.out.println("----------------------------");
+        // System.out.println("");
+        // Double max = this.maxWeight;
         // System.out.println("");
         // System.out.println("----------------------------");
         // System.out.println("MAX: " +  max );
         // System.out.println("----------------------------");
         // System.out.println("");
-        this.maxWeight = max;
-    }
 
-    private void adjustHue(Node[] nodes, Node node, Double weight){
-        // Double min = getMinWeight(nodes);
-        // Double max = getMaxWeight(nodes);
+        // scale weights to lie between 0 and 0.66
+        // if (weight > -3 || weight < 3) {
+        //   double hue_double = (double)(((weight - (-3))/(3 - (-3)))*(0.66-0.0) + 0.0);
+        //   //node.getNodeData().setColor(float r, float g, float b)
+        //   float hue_float = (float) hue_double;
+        //   float s = 1.0f;
+        //   float b = 1.0f;
+        //   Color new_color = Color.getHSBColor(hue_float, s, b);
+        //   node.setColor(new_color);
+        // }
+
+      float s = 1.0f;
+      float b = 1.0f;
+      float hue_float = 0f;
+      if (weight >= -3.0 && weight < -2.5) {
+        hue_float = (0)*(0.055f);
+      } if (weight >= -2.5 && weight < -2.0) {
+        hue_float = (1)*(0.055f);
+      } if (weight >= -2.0 && weight < -1.5) {
+        hue_float = (2)*(0.055f);
+      } if (weight >= -1.5 && weight < -1.0) {
+        hue_float = (3)*(0.055f);
+      } if (weight >= -1.0 && weight < -0.5) {
+        hue_float = (4)*(0.055f);
+      } if (weight >= -0.5 && weight < 0) {
+        hue_float = (5)*(0.055f);
+      } if (weight >= 0.0 && weight < 0.5) {
+        hue_float = (6)*(0.055f);
+      } if (weight >= 0.5 && weight < 1.0) {
+        hue_float = (7)*(0.055f);
+      } if (weight >= 1.0 && weight < 1.5) {
+        hue_float = (8)*(0.055f);
+      } if (weight >= 1.5 && weight < 2.0) {
+        hue_float = (9)*(0.055f);
+      } if (weight >= 2.0 && weight < 2.5) {
+        hue_float = (10)*(0.055f);
+      } if (weight >= 2.5 && weight <= 3) {
+        hue_float = (11)*(0.055f);
+      }
+      Color new_color = Color.getHSBColor(hue_float, s, b);
+      node.setColor(new_color);
 
-        Double min = this.minWeight;
-        System.out.println("");
-        System.out.println("----------------------------");
-        System.out.println("MIN: " +  min );
-        System.out.println("----------------------------");
-        System.out.println("");
-        Double max = this.maxWeight;
-        System.out.println("");
-        System.out.println("----------------------------");
-        System.out.println("MAX: " +  max );
-        System.out.println("----------------------------");
-        System.out.println("");
 
-        // scale weights to lie between 0 and 0.66
-        double hue_double = (double)(((weight - min)/(max - min))*(0.66-0.0) + 0.0);
-        //node.getNodeData().setColor(float r, float g, float b)
-        float hue_float = (float) hue_double;
-        float s = 1.0f;
-        float b = 1.0f;
-        Color new_color = Color.getHSBColor(hue_float, s, b);
-        node.setColor(new_color);
-//Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
+      if (weight < -3.0) {
+        node.setColor(Color.gray);
+      } if (weight > 3.0) {
+        node.setColor(Color.black);
+      }
     }
+//Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
+
+
+
 
 
 
@@ -379,29 +423,40 @@ public void goAlgo() {
         try {
             Node[] nodes = graph.getNodes().toArray();
             Edge[] edges = graph.getEdges().toArray();
-            setterMinWeight(nodes);
-            setterMaxWeight(nodes);
-            List<Double> all_weights = new ArrayList<Double>();
+            // setterMinWeight(nodes);
+            // setterMaxWeight(nodes);
+            // List<Double> all_weights = new ArrayList<Double>();
 
-            for (Node n: nodes) {
-              TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
-              double[] weights = map.toDoubleArray();
+            // for (Node n: nodes) {
+            //   TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
+            //   double[] weights = map.toDoubleArray();
 
-              for (Double wt: weights) {
-                if (wt != null) {
-                all_weights.add(wt);
-                }
+            //   for (Double wt: weights) {
+            //     if (wt != null) {
+            //     all_weights.add(wt);
+            //     }
+
+            //   }
+            // }
+            // // Double[] all_weights_array = new Double[all_weights.size()];
+            // // all_weights_array = all_weights.toArray(all_weights_array);
 
-              }
-            }
-            Double[] all_weights_array = new Double[all_weights.size()];
-            all_weights_array = all_weights.toArray(all_weights_array);
-            // double[] weights_double_ary = Stream.of(all_weights_array).mapToDouble(Double::doubleValue).toArray();
+
+            // double[] tempArray = new double[all_weights.size()];
+            // int i = 0;
+            // for(Double d : all_weights) {
+            //   tempArray[i] = (double) d;
+            //   i++;
+            // }
 
 
-            // int[] histogram = calcHistogram(all_weights_array, this.minWeight, this.maxWeight, 20);
+            // int[] histogram = calcHistogram(tempArray, -3.0, 3.0, 12);
+            // Double bin_diff = 0.5;
+            // for (int j=0; j<12 ; j++ ) {
+            //   System.out.println(String.valueOf(-3 + ((j)*(bin_diff))) + "-" + String.valueOf(-3 + ((j+1)*(bin_diff))) + ": " + String.valueOf(histogram[j]));
+            //   // System.out.println(histogram[j]);
+            // }
 
-            // System.out.println(histogram);
             // This is a histogram with 4 bins, 0-2.5, 2.5-5, 5-7.5, 7.5-10.
 
             // Initialise layout data
@@ -473,7 +528,8 @@ public void goAlgo() {
             }
 
             // Node Weight
-            AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
+            AttractionForce NodeAttraction = \
+            ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
 
             // setterMinWeight(nodes);
             // setterMaxWeight(nodes);
@@ -489,8 +545,10 @@ public void goAlgo() {
                 wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
                 // setterMinWeight();
                 // setterMaxWeight();
-                // adjustHue(nodes, node_a, wt_a);
-                // adjustHue(nodes, node_b, wt_b);
+                if (isHeatMapMode()) {
+                  adjustHue(nodes, node_a, wt_a);
+                  adjustHue(nodes, node_b, wt_b);
+                }
                 NodeAttraction.apply(node_a, node_b, ((wt_a + wt_b)/2));
 
             }
@@ -665,7 +723,13 @@ public LayoutProperty[] getProperties() {
                     "ForceAtlas2.strongGravityMode.name",
                     NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.desc"),
                     "isStrongGravityMode", "setStrongGravityMode"));
-
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapMode.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.heatMapMode.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapMode.desc"),
+                    "isHeatMapMode", "setHeatMapMode"));
             properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.gravity.name"),
@@ -760,6 +824,7 @@ public void resetPropertiesValues() {
             setScalingRatio(10.0);
         }
         setStrongGravityMode(false);
+        setHeatMapMode(false);
         setGravity(1.);
 
         // Behavior
@@ -855,6 +920,14 @@ public void setStrongGravityMode(Boolean strongGravityMode) {
         this.strongGravityMode = strongGravityMode;
     }
 
+    public Boolean isHeatMapMode() {
+        return heatMapMode;
+    }
+
+    public void setHeatMapMode(Boolean heatMapMode) {
+        this.heatMapMode = heatMapMode;
+    }
+
     public Double getGravity() {
         return gravity;
     }
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index b4ea3eb..2fbbb07 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -19,10 +19,13 @@ ForceAtlas2.behavior=Behavior Alternatives
 ForceAtlas2.performance=Performance
 ForceAtlas2.threads=Threads
 
-ForceAtlas2.minWeight.name=Minimum Weight
-ForceAtlas2.minWeight.desc=Minimum weight possible in your data
 ForceAtlas2.maxWeight.name=Maximum Weight
-ForceAtlas2.maxWeight.desc=Maxium weight possible in your data
+ForceAtlas2.maxWeight.desc=maximum of node weights
+ForceAtlas2.minWeight.name=Minimum Weight
+ForceAtlas2.minWeight.desc=minimum of node weights
+
+ForceAtlas2.heatMapMode.name=Heat Map
+ForceAtlas2.heatMapMode.desc=Turn on heat map based on normalized node weights
 
 
 
@@ -33,6 +36,7 @@ ForceAtlas2.gravity.name=Gravity
 ForceAtlas2.gravity.desc=Attracts nodes to the center. Prevents islands from drifting away.
 ForceAtlas2.strongGravityMode.name=Stronger Gravity
 ForceAtlas2.strongGravityMode.desc=A stronger gravity law
+
 ForceAtlas2.distributedAttraction.name=Dissuade Hubs
 ForceAtlas2.distributedAttraction.desc=Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
 ForceAtlas2.linLogMode.name=LinLog mode

From 80a597c237ee712a50da33175626569ae681958b Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Sat, 25 Aug 2018 20:11:36 +0100
Subject: [PATCH 17/32] changed color scheme on heat map

---
 .../layout/NodeWeight/ForceAtlas2.java        | 114 +++++++++++++++---
 1 file changed, 96 insertions(+), 18 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index a3bd581..1a997e1 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -127,6 +127,7 @@ public class ForceAtlas2 implements Layout {
 
 
 
+
     private void setNodeWeightColumnName(Table table) {
       if (table.hasColumn("weight")) {
         this.nodeWeightColumnName = "weight";
@@ -356,35 +357,113 @@ private void adjustHue(Node[] nodes, Node node, Double weight){
         //   node.setColor(new_color);
         // }
 
-      float s = 1.0f;
-      float b = 1.0f;
-      float hue_float = 0f;
+      // float s = 1.0f;
+      // float b = 1.0f;
+      // float r = 0f;
+      // if (weight >= -3.0 && weight < -2.5) {
+      //   hue_float = (0)*(0.055f);
+      // } if (weight >= -2.5 && weight < -2.0) {
+      //   hue_float = (1)*(0.055f);
+      // } if (weight >= -2.0 && weight < -1.5) {
+      //   hue_float = (2)*(0.055f);
+      // } if (weight >= -1.5 && weight < -1.0) {
+      //   hue_float = (3)*(0.055f);
+      // } if (weight >= -1.0 && weight < -0.5) {
+      //   hue_float = (4)*(0.055f);
+      // } if (weight >= -0.5 && weight < 0) {
+      //   hue_float = (5)*(0.055f);
+      // } if (weight >= 0.0 && weight < 0.5) {
+      //   hue_float = (6)*(0.055f);
+      // } if (weight >= 0.5 && weight < 1.0) {
+      //   hue_float = (7)*(0.055f);
+      // } if (weight >= 1.0 && weight < 1.5) {
+      //   hue_float = (8)*(0.055f);
+      // } if (weight >= 1.5 && weight < 2.0) {
+      //   hue_float = (9)*(0.055f);
+      // } if (weight >= 2.0 && weight < 2.5) {
+      //   hue_float = (10)*(0.055f);
+      // } if (weight >= 2.5 && weight <= 3) {
+      //   hue_float = (11)*(0.055f);
+      // }
+    //         Color new_color = Color.getHSBColor(hue_float, s, b);
+    //   node.setColor(new_color);
+
+
+    //   if (weight < -3.0) {
+    //     node.setColor(Color.gray);
+    //   } if (weight > 3.0) {
+    //     node.setColor(Color.black);
+    //   }
+    // }
+
+      float r = 0.0f;
+      float g = 0.0f;
+      float b = 0.0f;
+
+
       if (weight >= -3.0 && weight < -2.5) {
-        hue_float = (0)*(0.055f);
+        // rgb(0,51,153)
+        r = 0f;
+        g = 51/255f;
+        b = 153/255f;
       } if (weight >= -2.5 && weight < -2.0) {
-        hue_float = (1)*(0.055f);
+// rgb(51,92,173)
+        r = 51/255f;
+        g = 92/255f;
+        b = 173/255f;
       } if (weight >= -2.0 && weight < -1.5) {
-        hue_float = (2)*(0.055f);
+// rgb(102,133,194)
+        r = 102/255f;
+        g = 133/255f;
+        b = 194/255f;
+
       } if (weight >= -1.5 && weight < -1.0) {
-        hue_float = (3)*(0.055f);
+// rgb(153,173,214)
+        r = 153/255f;
+        g = 173/255f;
+        b = 214/255f;
       } if (weight >= -1.0 && weight < -0.5) {
-        hue_float = (4)*(0.055f);
+// rgb(204,214,235)
+        r = 204/255f;
+        g = 214/255f;
+        b = 235/255f;
       } if (weight >= -0.5 && weight < 0) {
-        hue_float = (5)*(0.055f);
+// rgb(255,255,255)
+        r = 255/255f;
+        g = 255/255f;
+        b = 255/255f;
       } if (weight >= 0.0 && weight < 0.5) {
-        hue_float = (6)*(0.055f);
+// rgb(238,213,213)
+        r = 238/255f;
+        g = 213/255f;
+        b = 213/255f;
       } if (weight >= 0.5 && weight < 1.0) {
-        hue_float = (7)*(0.055f);
+// rgb(221,170,170)
+        r = 221/255f;
+        g = 170/255f;
+        b = 170/255f;
       } if (weight >= 1.0 && weight < 1.5) {
-        hue_float = (8)*(0.055f);
+// rgb(204,128,128)
+        r = 204/255f;
+        g = 128/255f;
+        b = 128/255f;
       } if (weight >= 1.5 && weight < 2.0) {
-        hue_float = (9)*(0.055f);
+// rgb(187,85,85)
+        r = 187/255f;
+        g = 85/255f;
+        b = 85/255f;
       } if (weight >= 2.0 && weight < 2.5) {
-        hue_float = (10)*(0.055f);
+// rgb(170,43,43)
+        r = 170/255f;
+        g = 43/255f;
+        b = 43/255f;
       } if (weight >= 2.5 && weight <= 3) {
-        hue_float = (11)*(0.055f);
+// rgb(153,0,0)
+        r = 153/255f;
+        g = 0f;
+        b = 0f;
       }
-      Color new_color = Color.getHSBColor(hue_float, s, b);
+      Color new_color = new Color(r, g, b);
       node.setColor(new_color);
 
 
@@ -528,8 +607,7 @@ public void goAlgo() {
             }
 
             // Node Weight
-            AttractionForce NodeAttraction = \
-            ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
+            AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
 
             // setterMinWeight(nodes);
             // setterMaxWeight(nodes);

From 5675b9546916572693c3740bb4c15e4bb666ae59 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 28 Aug 2018 17:27:07 +0100
Subject: [PATCH 18/32] node weight given scaling factor; error with previous
 node weight being reset fixed

---
 hs_err_pid39777.log                           | 706 ++++++++++++++++++
 hs_err_pid43526.log                           | 705 +++++++++++++++++
 .../layout/NodeWeight/ForceAtlas2.java        |  94 ++-
 .../layout/NodeWeight/Bundle.properties       |  12 +-
 4 files changed, 1479 insertions(+), 38 deletions(-)
 create mode 100644 hs_err_pid39777.log
 create mode 100644 hs_err_pid43526.log

diff --git a/hs_err_pid39777.log b/hs_err_pid39777.log
new file mode 100644
index 0000000..0b92034
--- /dev/null
+++ b/hs_err_pid39777.log
@@ -0,0 +1,706 @@
+#
+# A fatal error has been detected by the Java Runtime Environment:
+#
+#  SIGSEGV (0xb) at pc=0x0000000110fe8734, pid=39777, tid=0x000000000001d90f
+#
+# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
+# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode bsd-amd64 compressed oops)
+# Problematic frame:
+# j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
+#
+# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
+#
+# If you would like to submit a bug report, please visit:
+#   http://bugreport.java.com/bugreport/crash.jsp
+#
+
+---------------  T H R E A D  ---------------
+
+Current thread (0x00007fb91f19f800):  JavaThread "Timer-519" [_thread_in_Java, id=121103, stack(0x00007000061ab000,0x00007000062ab000)]
+
+siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x000000000001d90f
+
+Registers:
+RAX=0x000000000001d90f, RBX=0x0000000136bdbeb0, RCX=0x00007fb91f2e9038, RDX=0x00000000000aacc0
+RSP=0x00007000062aa5d0, RBP=0x00007000062aa650, RSI=0x000000010209a800, RDI=0x0000000000000001
+R8 =0x0000000000000005, R9 =0x00007fb928450550, R10=0x0000000000000000, R11=0x0000000110fe1d1b
+R12=0x0000000000000000, R13=0x0000000136bdbeb0, R14=0x00007000062aa690, R15=0x00007fb91f19f800
+RIP=0x0000000110fe8734, EFLAGS=0x0000000000010206, ERR=0x0000000000000004
+  TRAPNO=0x000000000000000e
+
+Top of Stack: (sp=0x00007000062aa5d0)
+0x00007000062aa5d0:   0000000000000000 0000000110fe8667
+0x00007000062aa5e0:   000000000000006b 00000000000000f2
+0x00007000062aa5f0:   00000007309aeb90 00000007309aeb90
+0x00007000062aa600:   00007000062aa600 000000017b13aaa4
+0x00007000062aa610:   00007000062aa610 0000000000000000
+0x00007000062aa620:   00007000062aa690 0000000136bdd758
+0x00007000062aa630:   0000000000000000 0000000136bdbeb0
+0x00007000062aa640:   0000000000000000 00007000062aa670
+0x00007000062aa650:   00007000062aa6d8 0000000110fd8040
+0x00007000062aa660:   0000000000000000 0000000110fe1d1b
+0x00007000062aa670:   00000000000002ed 00000000000001cc
+0x00007000062aa680:   00000007309a0028 00000004f60d89b8
+0x00007000062aa690:   00000004f3782518 00007000062aa698
+0x00007000062aa6a0:   0000000136bdbf63 00007000062aa720
+0x00007000062aa6b0:   0000000136bdd758 0000000000000000
+0x00007000062aa6c0:   0000000136bdc010 00007000062aa670
+0x00007000062aa6d0:   00007000062aa700 00007000062aa770
+0x00007000062aa6e0:   0000000110fd8040 0000000000000000
+0x00007000062aa6f0:   0000000000000000 0000000000000000
+0x00007000062aa700:   00000000000002ed 00000000000001cc
+0x00007000062aa710:   00000007309a0028 00000004f60d89b8
+0x00007000062aa720:   00000004f3782518 000000073099f898
+0x00007000062aa730:   00007000062aa730 00000001677b9cbe
+0x00007000062aa740:   00007000062aa7c8 000000017b136730
+0x00007000062aa750:   0000000000000000 00000001677b9d70
+0x00007000062aa760:   00007000062aa700 00007000062aa7b8
+0x00007000062aa770:   00007000062aa810 0000000110fd82bd
+0x00007000062aa780:   00000004f3782518 00000007309a0028
+0x00007000062aa790:   00000007309a0008 000000073099ffe8
+0x00007000062aa7a0:   00000004f3863dc8 000000073099ffa0
+0x00007000062aa7b0:   00000007309aeba8 00000007276610f0
+0x00007000062aa7c0:   00000004f60d89b8 000000073099f898 
+
+Instructions: (pc=0x0000000110fe8734)
+0x0000000110fe8714:   10 01 00 00 00 4c 3b 5d 18 0f 85 20 00 00 00 48
+0x0000000110fe8724:   8b 04 24 48 83 c4 10 48 85 c0 0f 84 03 00 00 00
+0x0000000110fe8734:   48 8b 00 48 89 45 10 48 83 ec 10 48 89 04 24 41
+0x0000000110fe8744:   81 bf 9c 02 00 00 01 00 00 00 0f 85 bd 00 00 00 
+
+Register to memory mapping:
+
+RAX=0x000000000001d90f is an unknown value
+RBX={method} {0x0000000136bdbeb0} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
+RCX=0x00007fb91f2e9038 is an unknown value
+RDX=0x00000000000aacc0 is an unknown value
+RSP=0x00007000062aa5d0 is pointing into the stack for thread: 0x00007fb91f19f800
+RBP=0x00007000062aa650 is pointing into the stack for thread: 0x00007fb91f19f800
+RSI=0x000000010209a800 is an unknown value
+RDI=0x0000000000000001 is an unknown value
+R8 =0x0000000000000005 is an unknown value
+R9 =0x00007fb928450550 is an unknown value
+R10=0x0000000000000000 is an unknown value
+R11=0x0000000110fe1d1b is at code_begin+27 in an Interpreter codelet
+result handlers for native calls  [0x0000000110fe1d00, 0x0000000110fe1d20]  32 bytes
+R12=0x0000000000000000 is an unknown value
+R13={method} {0x0000000136bdbeb0} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
+R14=0x00007000062aa690 is pointing into the stack for thread: 0x00007fb91f19f800
+R15=0x00007fb91f19f800 is a thread
+
+
+Stack: [0x00007000061ab000,0x00007000062ab000],  sp=0x00007000062aa5d0,  free space=1021k
+Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
+j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
+j  com.apple.laf.ScreenPopupFactory.getPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+27
+j  org.gephi.ui.components.richtooltip.RichTooltip.showTooltip(Ljavax/swing/JComponent;Ljava/awt/Point;)V+294
+j  org.gephi.desktop.timeline.TimelineTooltip$1.run()V+73
+J 12023 C1 java.util.TimerThread.mainLoop()V (232 bytes) @ 0x0000000112cffba4 [0x0000000112cfef20+0xc84]
+J 12257 C1 java.util.TimerThread.run()V (74 bytes) @ 0x0000000112daa024 [0x0000000112da9fa0+0x84]
+v  ~StubRoutines::call_stub
+V  [libjvm.dylib+0x2ef1f6]  JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*)+0x6ae
+V  [libjvm.dylib+0x2ef99a]  JavaCalls::call_virtual(JavaValue*, KlassHandle, Symbol*, Symbol*, JavaCallArguments*, Thread*)+0x164
+V  [libjvm.dylib+0x2efb46]  JavaCalls::call_virtual(JavaValue*, Handle, KlassHandle, Symbol*, Symbol*, Thread*)+0x4a
+V  [libjvm.dylib+0x34a46d]  thread_entry(JavaThread*, Thread*)+0x7c
+V  [libjvm.dylib+0x56eb0f]  JavaThread::thread_main_inner()+0x9b
+V  [libjvm.dylib+0x57020a]  JavaThread::run()+0x1c2
+V  [libjvm.dylib+0x48d4a6]  java_start(Thread*)+0xf6
+C  [libsystem_pthread.dylib+0x3661]  _pthread_body+0x154
+C  [libsystem_pthread.dylib+0x350d]  _pthread_body+0x0
+C  [libsystem_pthread.dylib+0x2bf9]  thread_start+0xd
+C  0x0000000000000000
+
+
+---------------  P R O C E S S  ---------------
+
+Java Threads: ( => current thread )
+=>0x00007fb91f19f800 JavaThread "Timer-519" [_thread_in_Java, id=121103, stack(0x00007000061ab000,0x00007000062ab000)]
+  0x00007fb91ef38800 JavaThread "pool-7-thread-3" [_thread_blocked, id=77463, stack(0x00007000064b4000,0x00007000065b4000)]
+  0x00007fb91f4c4000 JavaThread "pool-7-thread-2" [_thread_blocked, id=96083, stack(0x00007000063b1000,0x00007000064b1000)]
+  0x00007fb9256a3000 JavaThread "pool-7-thread-1" [_thread_blocked, id=69963, stack(0x00007000062ae000,0x00007000063ae000)]
+  0x00007fb927e27800 JavaThread "layout" [_thread_in_Java, id=59695, stack(0x0000700005fa5000,0x00007000060a5000)]
+  0x00007fb9275df800 JavaThread "Filter Auto-Refresh - Workspace 1" daemon [_thread_blocked, id=98719, stack(0x00007000060a8000,0x00007000061a8000)]
+  0x00007fb929212000 JavaThread "Filter Thread - Workspace 1" daemon [_thread_blocked, id=92527, stack(0x000070000568a000,0x000070000578a000)]
+  0x00007fb9205c0800 JavaThread "UpdateAnimator" daemon [_thread_blocked, id=123419, stack(0x0000700005481000,0x0000700005581000)]
+  0x00007fb9294cc000 JavaThread "DisplayAnimator" daemon [_thread_blocked, id=98107, stack(0x0000700004148000,0x0000700004248000)]
+  0x00007fb91f64a800 JavaThread "GraphChangeObserver" daemon [_thread_blocked, id=47847, stack(0x00007000046d7000,0x00007000047d7000)]
+  0x00007fb91ffe0000 JavaThread "KeyTipManager processing thread" daemon [_thread_blocked, id=95759, stack(0x0000700003eb9000,0x0000700003fb9000)]
+  0x00007fb9253d1800 JavaThread "SwingWorker-pool-2-thread-10" daemon [_thread_blocked, id=57175, stack(0x0000700005ea2000,0x0000700005fa2000)]
+  0x00007fb925a64800 JavaThread "SwingWorker-pool-2-thread-9" daemon [_thread_blocked, id=126735, stack(0x0000700005d9f000,0x0000700005e9f000)]
+  0x00007fb92538c800 JavaThread "SwingWorker-pool-2-thread-8" daemon [_thread_blocked, id=89391, stack(0x0000700005c9c000,0x0000700005d9c000)]
+  0x00007fb927853800 JavaThread "SwingWorker-pool-2-thread-7" daemon [_thread_blocked, id=49435, stack(0x0000700005b99000,0x0000700005c99000)]
+  0x00007fb9269c9000 JavaThread "SwingWorker-pool-2-thread-6" daemon [_thread_blocked, id=63519, stack(0x0000700005a96000,0x0000700005b96000)]
+  0x00007fb92754e000 JavaThread "SwingWorker-pool-2-thread-5" daemon [_thread_blocked, id=53791, stack(0x0000700005993000,0x0000700005a93000)]
+  0x00007fb9240d5000 JavaThread "SwingWorker-pool-2-thread-4" daemon [_thread_blocked, id=57723, stack(0x0000700005890000,0x0000700005990000)]
+  0x00007fb9259a8000 JavaThread "SwingWorker-pool-2-thread-3" daemon [_thread_blocked, id=128523, stack(0x000070000578d000,0x000070000588d000)]
+  0x00007fb920541000 JavaThread "SwingWorker-pool-2-thread-2" daemon [_thread_blocked, id=129323, stack(0x00007000051f8000,0x00007000052f8000)]
+  0x00007fb91fd13000 JavaThread "SwingWorker-pool-2-thread-1" daemon [_thread_blocked, id=92175, stack(0x00007000050f5000,0x00007000051f5000)]
+  0x00007fb9252c3000 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=69683, stack(0x000070000537e000,0x000070000547e000)]
+  0x00007fb927822000 JavaThread "Thread-15" [_thread_blocked, id=19467, stack(0x0000700005587000,0x0000700005687000)]
+  0x00007fb926a54800 JavaThread "Context Refresh Thread" daemon [_thread_blocked, id=128939, stack(0x0000700004dec000,0x0000700004eec000)]
+  0x00007fb927787800 JavaThread "AppearanceColumnObserver" daemon [_thread_blocked, id=88963, stack(0x00007000049e0000,0x0000700004ae0000)]
+  0x00007fb92536f000 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=91407, stack(0x0000700004ff2000,0x00007000050f2000)]
+  0x00007fb925082000 JavaThread "Timer-0" daemon [_thread_blocked, id=90387, stack(0x0000700004eef000,0x0000700004fef000)]
+  0x00007fb9206f2000 JavaThread "DestroyJavaVM" [_thread_blocked, id=9987, stack(0x0000700002d86000,0x0000700002e86000)]
+  0x00007fb9242c5000 JavaThread "Inactive RequestProcessor thread [Was:TimedSoftReference/org.openide.util.TimedSoftReference]" daemon [_thread_blocked, id=130307, stack(0x0000700004ce9000,0x0000700004de9000)]
+  0x00007fb9242b6800 JavaThread "TimerQueue" daemon [_thread_blocked, id=88067, stack(0x0000700004be6000,0x0000700004ce6000)]
+  0x00007fb91e833800 JavaThread "Thread-5" daemon [_thread_blocked, id=63019, stack(0x0000700004ae3000,0x0000700004be3000)]
+  0x00007fb91f603800 JavaThread "File Watcher" daemon [_thread_blocked, id=61443, stack(0x00007000048dd000,0x00007000049dd000)]
+  0x00007fb920434000 JavaThread "Thread-1" daemon [_thread_in_native, id=66083, stack(0x00007000047da000,0x00007000048da000)]
+  0x00007fb920368000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=53511, stack(0x00007000045d4000,0x00007000046d4000)]
+  0x00007fb91eda2000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=76043, stack(0x00007000044d1000,0x00007000045d1000)]
+  0x00007fb920371800 JavaThread "Java2D Queue Flusher" daemon [_thread_blocked, id=76807, stack(0x00007000043ce000,0x00007000044ce000)]
+  0x00007fb91faac800 JavaThread "RequestProcessor queue manager" daemon [_thread_blocked, id=77059, stack(0x00007000042cb000,0x00007000043cb000)]
+  0x00007fb9202ac800 JavaThread "AWT-Shutdown" [_thread_blocked, id=26667, stack(0x0000700003db6000,0x0000700003eb6000)]
+  0x00007fb91ecca000 JavaThread "AWT-AppKit" daemon [_thread_in_native, id=775, stack(0x00007ffeed387000,0x00007ffeedb87000)]
+  0x00007fb920217000 JavaThread "CLI Requests Server" daemon [_thread_in_native, id=15875, stack(0x0000700003cb3000,0x0000700003db3000)]
+  0x00007fb920232800 JavaThread "Active Reference Queue Daemon" daemon [_thread_blocked, id=14339, stack(0x0000700003bb0000,0x0000700003cb0000)]
+  0x00007fb91f80a800 JavaThread "Service Thread" daemon [_thread_blocked, id=16643, stack(0x00007000039aa000,0x0000700003aaa000)]
+  0x00007fb91f800000 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=16899, stack(0x00007000038a7000,0x00007000039a7000)]
+  0x00007fb91f02b800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=17411, stack(0x00007000037a4000,0x00007000038a4000)]
+  0x00007fb920038800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=13315, stack(0x00007000036a1000,0x00007000037a1000)]
+  0x00007fb920037800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18179, stack(0x000070000359e000,0x000070000369e000)]
+  0x00007fb91e813000 JavaThread "Finalizer" daemon [_thread_blocked, id=11523, stack(0x000070000349b000,0x000070000359b000)]
+  0x00007fb92002c000 JavaThread "Reference Handler" daemon [_thread_blocked, id=20483, stack(0x0000700003398000,0x0000700003498000)]
+
+Other Threads:
+  0x00007fb920027800 VMThread [stack: 0x0000700003295000,0x0000700003395000] [id=11267]
+  0x00007fb92006a000 WatcherThread [stack: 0x0000700003aad000,0x0000700003bad000] [id=13827]
+
+VM state:not at safepoint (normal execution)
+
+VM Mutex/Monitor currently owned by a thread: None
+
+Heap:
+ PSYoungGen      total 3765248K, used 1662426K [0x00000006d1180000, 0x00000007b8800000, 0x00000007c0000000)
+  eden space 3739648K, 43% used [0x00000006d1180000,0x00000007356b4068,0x00000007b5580000)
+  from space 25600K, 73% used [0x00000007b6e00000,0x00000007b8042a50,0x00000007b8700000)
+  to   space 25088K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007b6e00000)
+ ParOldGen       total 658432K, used 596142K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a2b9f0,0x000000051b700000)
+ Metaspace       used 60414K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+
+Card table byte_map: [0x0000000103d6e000,0x00000001053d5000] byte_map_base: 0x00000001015d4000
+
+Marking Bits: (ParMarkBitMap*) 0x00000001032f76e0
+ Begin Bits: [0x000000011ffd0000, 0x000000012b300000)
+ End Bits:   [0x000000012b300000, 0x0000000136630000)
+
+Polling page: 0x00000001020f6000
+
+CodeCache: size=245760Kb used=30938Kb max_used=31074Kb free=214821Kb
+ bounds [0x0000000110fd0000, 0x0000000112e70000, 0x000000011ffd0000]
+ total_blobs=10361 nmethods=9202 adapters=1067
+ compilation: enabled
+
+Compilation events (10 events):
+Event: 698.765 Thread 0x00007fb91f800000 12318 %s!   3       sun.java2d.opengl.OGLRenderQueue$QueueFlusher::run @ 2 (234 bytes)
+Event: 698.768 Thread 0x00007fb91f800000 nmethod 12318% 0x0000000112ad5f10 code [0x0000000112ad6280, 0x0000000112ad86d8]
+Event: 703.864 Thread 0x00007fb91f800000 12319  s!   3       sun.java2d.opengl.OGLRenderQueue$QueueFlusher::run (234 bytes)
+Event: 703.868 Thread 0x00007fb91f800000 nmethod 12319 0x0000000112d7c390 code [0x0000000112d7c700, 0x0000000112d7ea58]
+Event: 704.373 Thread 0x00007fb91f800000 12320       3       java.lang.reflect.ReflectAccess::copyMethod (5 bytes)
+Event: 704.373 Thread 0x00007fb91f800000 nmethod 12320 0x0000000112805a90 code [0x0000000112805c00, 0x0000000112805e08]
+Event: 707.706 Thread 0x00007fb91f800000 12321       1       java.text.AttributedString$AttributedStringIterator::getEndIndex (5 bytes)
+Event: 707.706 Thread 0x00007fb91f800000 nmethod 12321 0x0000000111e0dfd0 code [0x0000000111e0e120, 0x0000000111e0e230]
+Event: 707.706 Thread 0x00007fb91f800000 12322       3       sun.util.locale.provider.RuleBasedBreakIterator::getNextIndex (34 bytes)
+Event: 707.707 Thread 0x00007fb91f800000 nmethod 12322 0x00000001124e5c50 code [0x00000001124e5de0, 0x00000001124e6168]
+
+GC Heap History (10 events):
+Event: 666.008 GC heap before
+{Heap before GC invocations=459 (full 7):
+ PSYoungGen      total 3725824K, used 3715828K [0x00000006d1180000, 0x00000007b7300000, 0x00000007c0000000)
+  eden space 3697152K, 100% used [0x00000006d1180000,0x00000007b2c00000,0x00000007b2c00000)
+  from space 28672K, 65% used [0x00000007b2c00000,0x00000007b3e3d110,0x00000007b4800000)
+  to   space 27648K, 0% used [0x00000007b5800000,0x00000007b5800000,0x00000007b7300000)
+ ParOldGen       total 658432K, used 596022K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a0db60,0x000000051b700000)
+ Metaspace       used 60363K, capacity 65236K, committed 65448K, reserved 1105920K
+  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
+Event: 666.023 GC heap after
+Heap after GC invocations=459 (full 7):
+ PSYoungGen      total 3740160K, used 18711K [0x00000006d1180000, 0x00000007b7180000, 0x00000007c0000000)
+  eden space 3714048K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b3c80000)
+  from space 26112K, 71% used [0x00000007b5800000,0x00000007b6a45df0,0x00000007b7180000)
+  to   space 27136K, 0% used [0x00000007b3c80000,0x00000007b3c80000,0x00000007b5700000)
+ ParOldGen       total 658432K, used 596086K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a1d9f0,0x000000051b700000)
+ Metaspace       used 60363K, capacity 65236K, committed 65448K, reserved 1105920K
+  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
+}
+Event: 671.856 GC heap before
+{Heap before GC invocations=460 (full 7):
+ PSYoungGen      total 3740160K, used 3732759K [0x00000006d1180000, 0x00000007b7180000, 0x00000007c0000000)
+  eden space 3714048K, 100% used [0x00000006d1180000,0x00000007b3c80000,0x00000007b3c80000)
+  from space 26112K, 71% used [0x00000007b5800000,0x00000007b6a45df0,0x00000007b7180000)
+  to   space 27136K, 0% used [0x00000007b3c80000,0x00000007b3c80000,0x00000007b5700000)
+ ParOldGen       total 658432K, used 596086K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a1d9f0,0x000000051b700000)
+ Metaspace       used 60386K, capacity 65236K, committed 65448K, reserved 1105920K
+  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
+Event: 671.870 GC heap after
+Heap after GC invocations=460 (full 7):
+ PSYoungGen      total 3741184K, used 18768K [0x00000006d1180000, 0x00000007b8000000, 0x00000007c0000000)
+  eden space 3714048K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b3c80000)
+  from space 27136K, 69% used [0x00000007b3c80000,0x00000007b4ed41e0,0x00000007b5700000)
+  to   space 26624K, 0% used [0x00000007b6600000,0x00000007b6600000,0x00000007b8000000)
+ ParOldGen       total 658432K, used 596110K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a239f0,0x000000051b700000)
+ Metaspace       used 60386K, capacity 65236K, committed 65448K, reserved 1105920K
+  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
+}
+Event: 682.048 GC heap before
+{Heap before GC invocations=461 (full 7):
+ PSYoungGen      total 3741184K, used 3732816K [0x00000006d1180000, 0x00000007b8000000, 0x00000007c0000000)
+  eden space 3714048K, 100% used [0x00000006d1180000,0x00000007b3c80000,0x00000007b3c80000)
+  from space 27136K, 69% used [0x00000007b3c80000,0x00000007b4ed41e0,0x00000007b5700000)
+  to   space 26624K, 0% used [0x00000007b6600000,0x00000007b6600000,0x00000007b8000000)
+ ParOldGen       total 658432K, used 596110K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a239f0,0x000000051b700000)
+ Metaspace       used 60391K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+Event: 682.065 GC heap after
+Heap after GC invocations=461 (full 7):
+ PSYoungGen      total 3751424K, used 20008K [0x00000006d1180000, 0x00000007b7d00000, 0x00000007c0000000)
+  eden space 3727872K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b4a00000)
+  from space 23552K, 84% used [0x00000007b6600000,0x00000007b798a2c8,0x00000007b7d00000)
+  to   space 26112K, 0% used [0x00000007b4a00000,0x00000007b4a00000,0x00000007b6380000)
+ ParOldGen       total 658432K, used 596118K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a259f0,0x000000051b700000)
+ Metaspace       used 60391K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+}
+Event: 702.204 GC heap before
+{Heap before GC invocations=462 (full 7):
+ PSYoungGen      total 3751424K, used 3747880K [0x00000006d1180000, 0x00000007b7d00000, 0x00000007c0000000)
+  eden space 3727872K, 100% used [0x00000006d1180000,0x00000007b4a00000,0x00000007b4a00000)
+  from space 23552K, 84% used [0x00000007b6600000,0x00000007b798a2c8,0x00000007b7d00000)
+  to   space 26112K, 0% used [0x00000007b4a00000,0x00000007b4a00000,0x00000007b6380000)
+ ParOldGen       total 658432K, used 596118K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a259f0,0x000000051b700000)
+ Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+Event: 702.219 GC heap after
+Heap after GC invocations=462 (full 7):
+ PSYoungGen      total 3753984K, used 18756K [0x00000006d1180000, 0x00000007b8700000, 0x00000007c0000000)
+  eden space 3727872K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b4a00000)
+  from space 26112K, 71% used [0x00000007b4a00000,0x00000007b5c512c8,0x00000007b6380000)
+  to   space 25600K, 0% used [0x00000007b6e00000,0x00000007b6e00000,0x00000007b8700000)
+ ParOldGen       total 658432K, used 596126K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a279f0,0x000000051b700000)
+ Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+}
+Event: 705.321 GC heap before
+{Heap before GC invocations=463 (full 7):
+ PSYoungGen      total 3753984K, used 3746628K [0x00000006d1180000, 0x00000007b8700000, 0x00000007c0000000)
+  eden space 3727872K, 100% used [0x00000006d1180000,0x00000007b4a00000,0x00000007b4a00000)
+  from space 26112K, 71% used [0x00000007b4a00000,0x00000007b5c512c8,0x00000007b6380000)
+  to   space 25600K, 0% used [0x00000007b6e00000,0x00000007b6e00000,0x00000007b8700000)
+ ParOldGen       total 658432K, used 596126K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a279f0,0x000000051b700000)
+ Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+Event: 705.334 GC heap after
+Heap after GC invocations=463 (full 7):
+ PSYoungGen      total 3765248K, used 18698K [0x00000006d1180000, 0x00000007b8800000, 0x00000007c0000000)
+  eden space 3739648K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b5580000)
+  from space 25600K, 73% used [0x00000007b6e00000,0x00000007b8042a50,0x00000007b8700000)
+  to   space 25088K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007b6e00000)
+ ParOldGen       total 658432K, used 596142K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
+  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a2b9f0,0x000000051b700000)
+ Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
+  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
+}
+
+Deoptimization events (10 events):
+Event: 613.034 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001119b85ec method=java.math.MutableBigInteger.divideMagnitude(Ljava/math/MutableBigInteger;Ljava/math/MutableBigInteger;Z)Ljava/math/MutableBigInteger; @ 549
+Event: 613.075 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112da7448 method=org.gephi.layout.plugins.layout.NodeWeight.ForceAtlas2.adjustHue([Lorg/gephi/graph/api/Node;Lorg/gephi/graph/api/Node;Ljava/lang/Double;)V @ 17
+Event: 613.087 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011259c388 method=java.math.MutableBigInteger.getMagnitudeArray()[I @ 16
+Event: 613.305 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d6e610 method=java.math.MutableBigInteger.compare(Ljava/math/MutableBigInteger;)I @ 90
+Event: 639.803 Thread 0x00007fb9205c0800 Uncommon trap: reason=range_check action=make_not_entrant pc=0x0000000112d8f090 method=it.unimi.dsi.fastutil.ints.IntRBTreeSet.add(I)Z @ 759
+Event: 675.550 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112e242e8 method=org.gephi.graph.api.types.TimestampMap.getAverageBigDecimal(Lorg/gephi/graph/api/Interval;)Ljava/math/BigDecimal; @ 24
+Event: 675.550 Thread 0x00007fb927e27800 Uncommon trap: reason=null_check action=make_not_entrant pc=0x0000000111ccbc3c method=org.gephi.layout.plugins.layout.NodeWeight.ForceAtlas2.getNodeWeight(Lorg/gephi/graph/api/Node;ZLorg/gephi/graph/api/Interval;)D @ 34
+Event: 675.551 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001127ff49c method=org.gephi.graph.api.types.TimestampMap.getAverageBigDecimal(Lorg/gephi/graph/api/Interval;)Ljava/math/BigDecimal; @ 24
+Event: 684.173 Thread 0x00007fb9205c0800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d9784c method=it.unimi.dsi.fastutil.ints.IntRBTreeSet.add(I)Z @ 380
+Event: 698.013 Thread 0x00007fb926a54800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001119ab564 method=java.util.concurrent.locks.ReentrantReadWriteLock$Sync.tryAcquire(I)Z @ 80
+
+Classes redefined (0 events):
+No events
+
+Internal exceptions (10 events):
+Event: 258.466 Thread 0x00007fb9242c5000 Implicit null exception at 0x00000001124ec0ae to 0x00000001124ed1b5
+Event: 443.159 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000703ed9a78) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 443.160 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000703ef2ba8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 443.160 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000703f092d8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 520.545 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000713ff23f8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 520.546 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x000000071400b580) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 520.546 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000714021c20) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 527.209 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x00000006d423dfa8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
+Event: 707.710 Thread 0x00007fb91f19f800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': -1> (0x00000007309b7800) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
+Event: 707.710 Thread 0x00007fb91f19f800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException'> (0x00000007309b7800) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/prims/jni.cpp, line 709]
+
+Events (10 events):
+Event: 707.182 Thread 0x00007fb929c4c000 Thread exited: 0x00007fb929c4c000
+Event: 707.183 Thread 0x00007fb92712c000 Thread added: 0x00007fb92712c000
+Event: 707.187 Thread 0x00007fb91f19f800 Thread added: 0x00007fb91f19f800
+Event: 707.187 Thread 0x00007fb92712c000 Thread exited: 0x00007fb92712c000
+Event: 707.192 Thread 0x00007fb91f19f800 Thread exited: 0x00007fb91f19f800
+Event: 707.192 Thread 0x00007fb929c4c000 Thread added: 0x00007fb929c4c000
+Event: 707.193 Thread 0x00007fb929c4c000 Thread exited: 0x00007fb929c4c000
+Event: 707.194 Thread 0x00007fb92044a000 Thread added: 0x00007fb92044a000
+Event: 707.200 Thread 0x00007fb92044a000 Thread exited: 0x00007fb92044a000
+Event: 707.200 Thread 0x00007fb91f19f800 Thread added: 0x00007fb91f19f800
+
+
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+0x000000010f41e000 	/System/Library/Extensions/AppleIntelSKLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelSKLGraphicsGLDriver
+0x000000000f6fa000 	/System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
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+0x000000000f6fa000 	/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
+0x0000000136a89000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libsplashscreen.dylib
+0x0000000136ce1000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libfontmanager.dylib
+0x0000000110f24000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libosxui.dylib
+0x000000000f6fa000 	/System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
+0x0000000139538000 	/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/modules/lib/libjnidispatch-422.jnilib
+0x000000010e397000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libgluegen-rt.jnilib
+0x000000010e59c000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libnativewindow_awt.jnilib
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+0x000000010e18a000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libjogl_mobile.jnilib
+0x000000010e1f1000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libmanagement.dylib
+0x000000010d489000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libdcpr.dylib
+0x0000000138fc7000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libsunec.dylib
+0x000000010e1ff000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libosx.dylib
+0x000000013974e000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/liblcms.dylib
+0x000000000f6fa000 	/System/Library/PrivateFrameworks/login.framework/Versions/A/login
+0x000000000f6fa000 	/System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
+0x000000000f6fa000 	/System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
+
+VM Arguments:
+jvm_args: -Djdk.home=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home -Dnetbeans.dirs=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/gephi::/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/plugins_clusters/plugins -Dnetbeans.home=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform -Xms64m -Xmx11468m -Xverify:none -Dsun.java2d.noddraw=true -Dsun.awt.noerasebackground=true -Dnetbeans.indexing.noFileRefresh=true -Dplugin.manager.check.interval=EVERY_DAY -Dnetbeans.logger.console=true -ea -DaddExports:java.desktop/com.apple.eawt=ALL-UNNAMED -DaddExports:java.desktop/sun.awt=ALL-UNNAMED -DaddExports:java.base/jdk.internal.jrtfs=ALL-UNNAMED -DaddExports:java.desktop/apple.laf=ALL-UNNAMED -DaddExports:java.desktop/java.awt.peer=ALL-UNNAMED -DaddExports:java.desktop/com.sun.beans.editors=ALL-UNNAMED -DaddExports:java.desktop/sun.awt.im=ALL-UNNAMED -DaddExports:java.management/sun.management=ALL-UNNAMED -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/log/heapdump.hprof 
+java_command: org.netbeans.Main --cachedir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/cache --userdir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir --branding gephi --branding gephi
+java_class_path (initial): /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/boot.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-modules.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-lookup.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-ui.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ar_SA.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_bg.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ca.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_cs.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_de.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_es.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_fr.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_gl_ES.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_in_ID.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_it.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ja.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/li
+Launcher Type: SUN_STANDARD
+
+Environment Variables:
+JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home
+PATH=./bin:/usr/local/opt/rbenv/shims:/usr/local/opt/rbenv/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/amd64:/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/i386:
+SHELL=/bin/zsh
+
+Signal Handlers:
+SIGSEGV: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
+SIGBUS: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGFPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGPIPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGXFSZ: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGILL: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART
+SIGUSR2: [libjvm.dylib+0x48a5ae], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
+SIGHUP: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGINT: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
+SIGTERM: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGQUIT: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+
+
+---------------  S Y S T E M  ---------------
+
+OS:Bsduname:Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
+rlimit: STACK 8192k, CORE 0k, NPROC 1418, NOFILE 10240, AS infinity
+load average:2.42 2.32 2.78
+
+CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx
+
+Memory: 4k page, physical 16777216k(884572k free)
+
+/proc/meminfo:
+
+
+vm_info: Java HotSpot(TM) 64-Bit Server VM (25.171-b11) for bsd-amd64 JRE (1.8.0_171-b11), built on Mar 28 2018 12:50:57 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
+
+time: Tue Aug 28 14:23:15 2018
+elapsed time: 707 seconds (0d 0h 11m 47s)
+
diff --git a/hs_err_pid43526.log b/hs_err_pid43526.log
new file mode 100644
index 0000000..db4a570
--- /dev/null
+++ b/hs_err_pid43526.log
@@ -0,0 +1,705 @@
+#
+# A fatal error has been detected by the Java Runtime Environment:
+#
+#  SIGSEGV (0xb) at pc=0x0000000111d4a734, pid=43526, tid=0x0000000000015c57
+#
+# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
+# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode bsd-amd64 compressed oops)
+# Problematic frame:
+# j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
+#
+# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
+#
+# If you would like to submit a bug report, please visit:
+#   http://bugreport.java.com/bugreport/crash.jsp
+#
+
+---------------  T H R E A D  ---------------
+
+Current thread (0x00007fc2427cb800):  JavaThread "Timer-371" [_thread_in_Java, id=89175, stack(0x000070000fd45000,0x000070000fe45000)]
+
+siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000015c57
+
+Registers:
+RAX=0x0000000000015c57, RBX=0x00000001415d8338, RCX=0x00007fc242c1c038, RDX=0x000000000009d460
+RSP=0x000070000fe445d0, RBP=0x000070000fe44650, RSI=0x000000010cafa400, RDI=0x00007fc242c1c038
+R8 =0x0000000000000005, R9 =0x00007fc241441ba0, R10=0x0000000000000000, R11=0x0000000111d43d1b
+R12=0x0000000000000000, R13=0x00000001415d8338, R14=0x000070000fe44690, R15=0x00007fc2427cb800
+RIP=0x0000000111d4a734, EFLAGS=0x0000000000010202, ERR=0x0000000000000004
+  TRAPNO=0x000000000000000e
+
+Top of Stack: (sp=0x000070000fe445d0)
+0x000070000fe445d0:   0000000000000000 0000000111d4a667
+0x000070000fe445e0:   00007fc2427cb800 00007fc2427cb800
+0x000070000fe445f0:   0000000172f64d70 00007fc2427cb800
+0x000070000fe44600:   000070000fe44700 0000000111d56523
+0x000070000fe44610:   000070000fe44610 0000000000000000
+0x000070000fe44620:   000070000fe44690 00000001415d9be0
+0x000070000fe44630:   0000000000000000 00000001415d8338
+0x000070000fe44640:   0000000000000000 000070000fe44670
+0x000070000fe44650:   000070000fe446d8 0000000111d3a040
+0x000070000fe44660:   0000000000000000 0000000111d43d1b
+0x000070000fe44670:   00000000000002b7 0000000000000188
+0x000070000fe44680:   00000007131b6658 00000004f4a6bb30
+0x000070000fe44690:   00000004f38cd3d0 000070000fe44698
+0x000070000fe446a0:   00000001415d83eb 000070000fe44720
+0x000070000fe446b0:   00000001415d9be0 0000000000000000
+0x000070000fe446c0:   00000001415d8498 000070000fe44670
+0x000070000fe446d0:   000070000fe44700 000070000fe44770
+0x000070000fe446e0:   0000000111d3a040 0000000000000000
+0x000070000fe446f0:   0000000000000000 0000000000000000
+0x000070000fe44700:   00000000000002b7 0000000000000188
+0x000070000fe44710:   00000007131b6658 00000004f4a6bb30
+0x000070000fe44720:   00000004f38cd3d0 0000000713190248
+0x000070000fe44730:   000070000fe44730 0000000172f64cbe
+0x000070000fe44740:   000070000fe447c8 00000001899317e8
+0x000070000fe44750:   0000000000000000 0000000172f64d70
+0x000070000fe44760:   000070000fe44700 000070000fe447b8
+0x000070000fe44770:   000070000fe44810 0000000111d3a2bd
+0x000070000fe44780:   00000004f38cd3d0 00000007131b6658
+0x000070000fe44790:   00000007131b2920 00000007131b1610
+0x000070000fe447a0:   00000004f3824268 00000007131b0278
+0x000070000fe447b0:   0000000713270f38 0000000704bb7e10
+0x000070000fe447c0:   00000004f4a6bb30 0000000713190248 
+
+Instructions: (pc=0x0000000111d4a734)
+0x0000000111d4a714:   11 01 00 00 00 4c 3b 5d 18 0f 85 20 00 00 00 48
+0x0000000111d4a724:   8b 04 24 48 83 c4 10 48 85 c0 0f 84 03 00 00 00
+0x0000000111d4a734:   48 8b 00 48 89 45 10 48 83 ec 10 48 89 04 24 41
+0x0000000111d4a744:   81 bf 9c 02 00 00 01 00 00 00 0f 85 bd 00 00 00 
+
+Register to memory mapping:
+
+RAX=0x0000000000015c57 is an unknown value
+RBX={method} {0x00000001415d8338} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
+RCX=0x00007fc242c1c038 is an unknown value
+RDX=0x000000000009d460 is an unknown value
+RSP=0x000070000fe445d0 is pointing into the stack for thread: 0x00007fc2427cb800
+RBP=0x000070000fe44650 is pointing into the stack for thread: 0x00007fc2427cb800
+RSI=0x000000010cafa400 is an unknown value
+RDI=0x00007fc242c1c038 is an unknown value
+R8 =0x0000000000000005 is an unknown value
+R9 =0x00007fc241441ba0 is an unknown value
+R10=0x0000000000000000 is an unknown value
+R11=0x0000000111d43d1b is at code_begin+27 in an Interpreter codelet
+result handlers for native calls  [0x0000000111d43d00, 0x0000000111d43d20]  32 bytes
+R12=0x0000000000000000 is an unknown value
+R13={method} {0x00000001415d8338} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
+R14=0x000070000fe44690 is pointing into the stack for thread: 0x00007fc2427cb800
+R15=0x00007fc2427cb800 is a thread
+
+
+Stack: [0x000070000fd45000,0x000070000fe45000],  sp=0x000070000fe445d0,  free space=1021k
+Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
+j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
+j  com.apple.laf.ScreenPopupFactory.getPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+27
+j  org.gephi.ui.components.richtooltip.RichTooltip.showTooltip(Ljavax/swing/JComponent;Ljava/awt/Point;)V+294
+j  org.gephi.desktop.timeline.TimelineTooltip$1.run()V+73
+J 8640 C1 java.util.TimerThread.mainLoop()V (232 bytes) @ 0x00000001131d6164 [0x00000001131d54e0+0xc84]
+J 9989 C1 java.util.TimerThread.run()V (74 bytes) @ 0x00000001127c6164 [0x00000001127c60e0+0x84]
+v  ~StubRoutines::call_stub
+V  [libjvm.dylib+0x2ef1f6]
+V  [libjvm.dylib+0x2ef99a]
+V  [libjvm.dylib+0x2efb46]
+V  [libjvm.dylib+0x34a46d]
+V  [libjvm.dylib+0x56eb0f]
+V  [libjvm.dylib+0x57020a]
+V  [libjvm.dylib+0x48d4a6]
+C  [libsystem_pthread.dylib+0x3661]  _pthread_body+0x154
+C  [libsystem_pthread.dylib+0x350d]  _pthread_body+0x0
+C  [libsystem_pthread.dylib+0x2bf9]  thread_start+0xd
+C  0x0000000000000000
+
+
+---------------  P R O C E S S  ---------------
+
+Java Threads: ( => current thread )
+  0x00007fc2428bb000 JavaThread "sampler-awt" daemon [_thread_blocked, id=93371, stack(0x0000700011593000,0x0000700011693000)]
+=>0x00007fc2427cb800 JavaThread "Timer-371" [_thread_in_Java, id=89175, stack(0x000070000fd45000,0x000070000fe45000)]
+  0x00007fc2426ed800 JavaThread "UpdateAnimator" daemon [_thread_blocked, id=78659, stack(0x0000700011490000,0x0000700011590000)]
+  0x00007fc241c06800 JavaThread "DisplayAnimator" daemon [_thread_blocked, id=129379, stack(0x0000700010e7e000,0x0000700010f7e000)]
+  0x00007fc23f207800 JavaThread "Inactive RequestProcessor thread [Was:Timeable Event Queue Watch Dog/org.netbeans.core.TimableEventQueue]" daemon [_thread_blocked, id=125227, stack(0x0000700010560000,0x0000700010660000)]
+  0x00007fc2409f1800 JavaThread "SwingWorker-pool-3-thread-10" daemon [_thread_blocked, id=36871, stack(0x000070001138d000,0x000070001148d000)]
+  0x00007fc23a285000 JavaThread "SwingWorker-pool-3-thread-9" daemon [_thread_blocked, id=66315, stack(0x000070001128a000,0x000070001138a000)]
+  0x00007fc240e0a000 JavaThread "SwingWorker-pool-3-thread-8" daemon [_thread_blocked, id=59163, stack(0x0000700011187000,0x0000700011287000)]
+  0x00007fc2390a2000 JavaThread "SwingWorker-pool-3-thread-7" daemon [_thread_blocked, id=89383, stack(0x0000700011084000,0x0000700011184000)]
+  0x00007fc23f80e000 JavaThread "SwingWorker-pool-3-thread-6" daemon [_thread_blocked, id=69407, stack(0x0000700010f81000,0x0000700011081000)]
+  0x00007fc242995800 JavaThread "SwingWorker-pool-3-thread-5" daemon [_thread_blocked, id=89703, stack(0x0000700010d7b000,0x0000700010e7b000)]
+  0x00007fc2429e2000 JavaThread "SwingWorker-pool-3-thread-4" daemon [_thread_blocked, id=91179, stack(0x0000700010b75000,0x0000700010c75000)]
+  0x00007fc240e16000 JavaThread "SwingWorker-pool-3-thread-3" daemon [_thread_blocked, id=88603, stack(0x000070001045d000,0x000070001055d000)]
+  0x00007fc242bba800 JavaThread "SwingWorker-pool-3-thread-2" daemon [_thread_blocked, id=91887, stack(0x000070001035a000,0x000070001045a000)]
+  0x00007fc23f8ab000 JavaThread "SwingWorker-pool-3-thread-1" daemon [_thread_blocked, id=47991, stack(0x000070000ffce000,0x00007000100ce000)]
+  0x00007fc2397f6800 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=129579, stack(0x0000700010c78000,0x0000700010d78000)]
+  0x00007fc24247b800 JavaThread "pool-2-thread-3" [_thread_blocked, id=26887, stack(0x0000700010a72000,0x0000700010b72000)]
+  0x00007fc239320800 JavaThread "pool-2-thread-2" [_thread_blocked, id=130635, stack(0x000070001096f000,0x0000700010a6f000)]
+  0x00007fc24243a000 JavaThread "pool-2-thread-1" [_thread_blocked, id=55639, stack(0x000070001086c000,0x000070001096c000)]
+  0x00007fc242492000 JavaThread "layout" [_thread_in_Java, id=70647, stack(0x0000700010663000,0x0000700010763000)]
+  0x00007fc242296000 JavaThread "Filter Auto-Refresh - Workspace 1" daemon [_thread_blocked, id=94019, stack(0x000070000fe48000,0x000070000ff48000)]
+  0x00007fc23f2fd800 JavaThread "Filter Thread - Workspace 1" daemon [_thread_blocked, id=69959, stack(0x000070000dcdc000,0x000070000dddc000)]
+  0x00007fc242391800 JavaThread "Thread-13" [_thread_blocked, id=95243, stack(0x0000700010769000,0x0000700010869000)]
+  0x00007fc242883000 JavaThread "AppearanceColumnObserver" daemon [_thread_blocked, id=126739, stack(0x00007000100d1000,0x00007000101d1000)]
+  0x00007fc2422ba800 JavaThread "Context Refresh Thread" daemon [_thread_blocked, id=62495, stack(0x000070000fa3c000,0x000070000fb3c000)]
+  0x00007fc241acb800 JavaThread "Timer-0" daemon [_thread_blocked, id=90375, stack(0x00007000101d4000,0x00007000102d4000)]
+  0x00007fc23ad79800 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=76039, stack(0x000070000f224000,0x000070000f324000)]
+  0x00007fc23a1b6000 JavaThread "DestroyJavaVM" [_thread_blocked, id=10243, stack(0x000070000de65000,0x000070000df65000)]
+  0x00007fc23f81e800 JavaThread "TimerQueue" daemon [_thread_blocked, id=61443, stack(0x000070000fc42000,0x000070000fd42000)]
+  0x00007fc239cc0800 JavaThread "Thread-5" daemon [_thread_blocked, id=60947, stack(0x000070000fb3f000,0x000070000fc3f000)]
+  0x00007fc23a7f7800 JavaThread "File Watcher" daemon [_thread_blocked, id=58119, stack(0x000070000f939000,0x000070000fa39000)]
+  0x00007fc23a7f6800 JavaThread "Thread-1" daemon [_thread_in_native, id=65571, stack(0x000070000f836000,0x000070000f936000)]
+  0x00007fc23a2e9000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=55047, stack(0x000070000f630000,0x000070000f730000)]
+  0x00007fc239470000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=74771, stack(0x000070000f52d000,0x000070000f62d000)]
+  0x00007fc23ad06800 JavaThread "Java2D Queue Flusher" daemon [_thread_blocked, id=75271, stack(0x000070000f42a000,0x000070000f52a000)]
+  0x00007fc23acfb800 JavaThread "RequestProcessor queue manager" daemon [_thread_blocked, id=75783, stack(0x000070000f327000,0x000070000f427000)]
+  0x00007fc23937f800 JavaThread "AWT-Shutdown" [_thread_blocked, id=38699, stack(0x000070000ef18000,0x000070000f018000)]
+  0x00007fc23abb6000 JavaThread "AWT-AppKit" daemon [_thread_blocked, id=775, stack(0x00007ffee2926000,0x00007ffee3126000)]
+  0x00007fc239264000 JavaThread "CLI Requests Server" daemon [_thread_in_native, id=17155, stack(0x000070000ed92000,0x000070000ee92000)]
+  0x00007fc239171800 JavaThread "Active Reference Queue Daemon" daemon [_thread_blocked, id=15363, stack(0x000070000ec8f000,0x000070000ed8f000)]
+  0x00007fc239804000 JavaThread "Service Thread" daemon [_thread_blocked, id=17667, stack(0x000070000ea89000,0x000070000eb89000)]
+  0x00007fc23901c800 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=14595, stack(0x000070000e986000,0x000070000ea86000)]
+  0x00007fc23a85b000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=14339, stack(0x000070000e883000,0x000070000e983000)]
+  0x00007fc239803000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=13827, stack(0x000070000e780000,0x000070000e880000)]
+  0x00007fc239049800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18439, stack(0x000070000e67d000,0x000070000e77d000)]
+  0x00007fc23901b000 JavaThread "Finalizer" daemon [_thread_blocked, id=11779, stack(0x000070000e57a000,0x000070000e67a000)]
+  0x00007fc23a825800 JavaThread "Reference Handler" daemon [_thread_blocked, id=20739, stack(0x000070000e477000,0x000070000e577000)]
+
+Other Threads:
+  0x00007fc239802800 VMThread [stack: 0x000070000e374000,0x000070000e474000] [id=20995]
+  0x00007fc23a831800 WatcherThread [stack: 0x000070000eb8c000,0x000070000ec8c000] [id=15107]
+
+VM state:synchronizing (normal execution)
+
+VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
+[0x00007fc238f03ef0] Safepoint_lock - owner thread: 0x00007fc239802800
+[0x00007fc238f03f70] Threads_lock - owner thread: 0x00007fc239802800
+
+Heap:
+ PSYoungGen      total 3900416K, used 1104675K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3887616K, 28% used [0x00000006d1180000,0x0000000713c4d308,0x00000007be600000)
+  from space 12800K, 95% used [0x00000007bf380000,0x00000007bff7ba00,0x00000007c0000000)
+  to   space 13312K, 0% used [0x00000007be600000,0x00000007be600000,0x00000007bf300000)
+ ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
+ Metaspace       used 58216K, capacity 63110K, committed 63384K, reserved 1103872K
+  class space    used 7038K, capacity 8514K, committed 8616K, reserved 1048576K
+
+Card table byte_map: [0x000000010e76e000,0x000000010fdd5000] byte_map_base: 0x000000010bfd4000
+
+Marking Bits: (ParMarkBitMap*) 0x000000010dcf76e0
+ Begin Bits: [0x0000000120d32000, 0x000000012c062000)
+ End Bits:   [0x000000012c062000, 0x0000000137392000)
+
+Polling page: 0x000000010cb57000
+
+CodeCache: size=245760Kb used=27912Kb max_used=28443Kb free=217847Kb
+ bounds [0x0000000111d32000, 0x0000000113932000, 0x0000000120d32000]
+ total_blobs=9480 nmethods=8321 adapters=1069
+ compilation: enabled
+
+Compilation events (10 events):
+Event: 1194.342 Thread 0x00007fc239803000 nmethod 10548 0x0000000113695710 code [0x0000000113695860, 0x00000001136958d8]
+Event: 1194.343 Thread 0x00007fc23a85b000 10550       4       sun.font.SunFontManager::getInstance (9 bytes)
+Event: 1194.345 Thread 0x00007fc23901c800 10551       1       sun.font.GlyphLayout::access$000 (5 bytes)
+Event: 1194.345 Thread 0x00007fc23901c800 nmethod 10551 0x0000000113576910 code [0x0000000113576a60, 0x0000000113576b50]
+Event: 1194.346 Thread 0x00007fc23a85b000 nmethod 10550 0x00000001128980d0 code [0x0000000112898240, 0x00000001128984b8]
+Event: 1194.346 Thread 0x00007fc23a85b000 10553       4       sun.font.StandardGlyphVector::setFRCTX (26 bytes)
+Event: 1194.347 Thread 0x00007fc23901c800 10552       3       sun.font.StandardGlyphVector::getGlyphOutlineBounds (41 bytes)
+Event: 1194.348 Thread 0x00007fc239803000 10558       4       java.awt.geom.RectangularShape::getMinX (5 bytes)
+Event: 1194.348 Thread 0x00007fc23a85b000 nmethod 10553 0x0000000112e5b110 code [0x0000000112e5b260, 0x0000000112e5b438]
+Event: 1194.348 Thread 0x00007fc23a85b000 10559       4       java.awt.geom.RectangularShape::getMinY (5 bytes)
+
+GC Heap History (10 events):
+Event: 1169.280 GC heap before
+{Heap before GC invocations=387 (full 5):
+ PSYoungGen      total 3903488K, used 3902650K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3892736K, 100% used [0x00000006d1180000,0x00000007beb00000,0x00000007beb00000)
+  from space 10752K, 92% used [0x00000007beb00000,0x00000007bf4ae810,0x00000007bf580000)
+  to   space 10752K, 0% used [0x00000007bf580000,0x00000007bf580000,0x00000007c0000000)
+ ParOldGen       total 162304K, used 46355K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 28% used [0x00000004f3400000,0x00000004f6144d50,0x00000004fd280000)
+ Metaspace       used 57831K, capacity 62756K, committed 63000K, reserved 1103872K
+  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
+Event: 1169.293 GC heap after
+Heap after GC invocations=387 (full 5):
+ PSYoungGen      total 3902464K, used 10743K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3891712K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007bea00000)
+  from space 10752K, 99% used [0x00000007bf580000,0x00000007bfffddd0,0x00000007c0000000)
+  to   space 11264K, 0% used [0x00000007bea00000,0x00000007bea00000,0x00000007bf500000)
+ ParOldGen       total 162304K, used 47833K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 29% used [0x00000004f3400000,0x00000004f62b6470,0x00000004fd280000)
+ Metaspace       used 57831K, capacity 62756K, committed 63000K, reserved 1103872K
+  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
+}
+Event: 1174.467 GC heap before
+{Heap before GC invocations=388 (full 5):
+ PSYoungGen      total 3902464K, used 3902455K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3891712K, 100% used [0x00000006d1180000,0x00000007bea00000,0x00000007bea00000)
+  from space 10752K, 99% used [0x00000007bf580000,0x00000007bfffddd0,0x00000007c0000000)
+  to   space 11264K, 0% used [0x00000007bea00000,0x00000007bea00000,0x00000007bf500000)
+ ParOldGen       total 162304K, used 47833K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 29% used [0x00000004f3400000,0x00000004f62b6470,0x00000004fd280000)
+ Metaspace       used 57854K, capacity 62756K, committed 63000K, reserved 1103872K
+  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
+Event: 1174.477 GC heap after
+Heap after GC invocations=388 (full 5):
+ PSYoungGen      total 3902976K, used 11249K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3891712K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007bea00000)
+  from space 11264K, 99% used [0x00000007bea00000,0x00000007bf4fc770,0x00000007bf500000)
+  to   space 11264K, 0% used [0x00000007bf500000,0x00000007bf500000,0x00000007c0000000)
+ ParOldGen       total 162304K, used 49069K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f63eb6f8,0x00000004fd280000)
+ Metaspace       used 57854K, capacity 62756K, committed 63000K, reserved 1103872K
+  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
+}
+Event: 1181.149 GC heap before
+{Heap before GC invocations=389 (full 5):
+ PSYoungGen      total 3902976K, used 3902961K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3891712K, 100% used [0x00000006d1180000,0x00000007bea00000,0x00000007bea00000)
+  from space 11264K, 99% used [0x00000007bea00000,0x00000007bf4fc770,0x00000007bf500000)
+  to   space 11264K, 0% used [0x00000007bf500000,0x00000007bf500000,0x00000007c0000000)
+ ParOldGen       total 162304K, used 49069K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f63eb6f8,0x00000004fd280000)
+ Metaspace       used 57866K, capacity 62758K, committed 63000K, reserved 1103872K
+  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
+Event: 1181.166 GC heap after
+Heap after GC invocations=389 (full 5):
+ PSYoungGen      total 3899904K, used 11246K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3888640K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007be700000)
+  from space 11264K, 99% used [0x00000007bf500000,0x00000007bfffba60,0x00000007c0000000)
+  to   space 12800K, 0% used [0x00000007be700000,0x00000007be700000,0x00000007bf380000)
+ ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
+ Metaspace       used 57866K, capacity 62758K, committed 63000K, reserved 1103872K
+  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
+}
+Event: 1186.598 GC heap before
+{Heap before GC invocations=390 (full 5):
+ PSYoungGen      total 3899904K, used 3899886K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3888640K, 100% used [0x00000006d1180000,0x00000007be700000,0x00000007be700000)
+  from space 11264K, 99% used [0x00000007bf500000,0x00000007bfffba60,0x00000007c0000000)
+  to   space 12800K, 0% used [0x00000007be700000,0x00000007be700000,0x00000007bf380000)
+ ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
+ Metaspace       used 57868K, capacity 62758K, committed 63000K, reserved 1103872K
+  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
+Event: 1186.609 GC heap after
+Heap after GC invocations=390 (full 5):
+ PSYoungGen      total 3901440K, used 11786K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3888640K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007be700000)
+  from space 12800K, 92% used [0x00000007be700000,0x00000007bf2829e8,0x00000007bf380000)
+  to   space 12800K, 0% used [0x00000007bf380000,0x00000007bf380000,0x00000007c0000000)
+ ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
+ Metaspace       used 57868K, capacity 62758K, committed 63000K, reserved 1103872K
+  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
+}
+Event: 1192.735 GC heap before
+{Heap before GC invocations=391 (full 5):
+ PSYoungGen      total 3901440K, used 3900426K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3888640K, 100% used [0x00000006d1180000,0x00000007be700000,0x00000007be700000)
+  from space 12800K, 92% used [0x00000007be700000,0x00000007bf2829e8,0x00000007bf380000)
+  to   space 12800K, 0% used [0x00000007bf380000,0x00000007bf380000,0x00000007c0000000)
+ ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
+ Metaspace       used 57869K, capacity 62758K, committed 63000K, reserved 1103872K
+  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
+Event: 1192.742 GC heap after
+Heap after GC invocations=391 (full 5):
+ PSYoungGen      total 3900416K, used 12270K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
+  eden space 3887616K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007be600000)
+  from space 12800K, 95% used [0x00000007bf380000,0x00000007bff7ba00,0x00000007c0000000)
+  to   space 13312K, 0% used [0x00000007be600000,0x00000007be600000,0x00000007bf300000)
+ ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
+  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
+ Metaspace       used 57869K, capacity 62758K, committed 63000K, reserved 1103872K
+  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
+}
+
+Deoptimization events (10 events):
+Event: 1178.582 Thread 0x00007fc241c06800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x0000000112f573c0 method=java.awt.EventQueue.coalesceEvent(Ljava/awt/AWTEvent;I)Z @ 77
+Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
+Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
+Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
+Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
+Event: 1194.330 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001122b2474 method=java.awt.geom.AffineTransform.updateState()V @ 24
+Event: 1194.340 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d6e5c8 method=java.awt.geom.Path2D$Float.getBounds2D()Ljava/awt/geom/Rectangle2D; @ 8
+Event: 1194.340 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d26e24 method=java.awt.geom.Rectangle2D$Float.isEmpty()Z @ 6
+Event: 1194.344 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d711f0 method=java.awt.geom.Path2D$Float.getBounds2D()Ljava/awt/geom/Rectangle2D; @ 8
+Event: 1194.348 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d7bbdc method=java.awt.geom.Path2D$Float.getBounds2D()Ljava/awt/geom/Rectangle2D; @ 8
+
+Classes redefined (0 events):
+No events
+
+Internal exceptions (10 events):
+Event: 261.644 Thread 0x00007fc23a2e9000 Implicit null exception at 0x00000001132d0dd4 to 0x00000001132d1bf5
+Event: 261.943 Thread 0x00007fc23a2e9000 Implicit null exception at 0x000000011341f050 to 0x000000011341fe11
+Event: 261.943 Thread 0x00007fc23a2e9000 Implicit null exception at 0x00000001128a2414 to 0x00000001128a245e
+Event: 263.222 Thread 0x00007fc23a2e9000 Implicit null exception at 0x000000011266b76c to 0x000000011266d1a5
+Event: 1163.695 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000113654cfb to 0x000000011365962d
+Event: 1164.825 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000112e5b170 to 0x0000000112e5b2b1
+Event: 1165.479 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000112d3a255 to 0x0000000112d3a2c5
+Event: 1165.525 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000112e12031 to 0x0000000112e120e9
+Event: 1194.348 Thread 0x00007fc2427cb800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': -1> (0x0000000713279c58) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
+Event: 1194.349 Thread 0x00007fc2427cb800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException'> (0x0000000713279c58) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/prims/jni.cpp, line 709]
+
+Events (10 events):
+Event: 1194.346 Executing VM operation: RevokeBias done
+Event: 1194.346 Executing VM operation: RevokeBias
+Event: 1194.346 Executing VM operation: RevokeBias done
+Event: 1194.347 Executing VM operation: RevokeBias
+Event: 1194.347 Executing VM operation: RevokeBias done
+Event: 1194.348 Thread 0x00007fc2427cb800 Uncommon trap: trap_request=0xffffff65 fr.pc=0x0000000112d7bbdc
+Event: 1194.348 Executing VM operation: RevokeBias
+Event: 1194.348 Executing VM operation: RevokeBias done
+Event: 1194.348 Thread 0x00007fc2427cb800 DEOPT PACKING pc=0x0000000112d7bbdc sp=0x000070000fe43250
+Event: 1194.348 Thread 0x00007fc2427cb800 DEOPT UNPACKING pc=0x0000000111d7773a sp=0x000070000fe43090 mode 2
+
+
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+jvm_args: -Djdk.home=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home -Dnetbeans.dirs=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/gephi::/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/plugins_clusters/plugins -Dnetbeans.home=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform -Xms64m -Xmx11468m -Xverify:none -Dsun.java2d.noddraw=true -Dsun.awt.noerasebackground=true -Dnetbeans.indexing.noFileRefresh=true -Dplugin.manager.check.interval=EVERY_DAY -Dnetbeans.logger.console=true -ea -DaddExports:java.desktop/com.apple.eawt=ALL-UNNAMED -DaddExports:java.desktop/sun.awt=ALL-UNNAMED -DaddExports:java.base/jdk.internal.jrtfs=ALL-UNNAMED -DaddExports:java.desktop/apple.laf=ALL-UNNAMED -DaddExports:java.desktop/java.awt.peer=ALL-UNNAMED -DaddExports:java.desktop/com.sun.beans.editors=ALL-UNNAMED -DaddExports:java.desktop/sun.awt.im=ALL-UNNAMED -DaddExports:java.management/sun.management=ALL-UNNAMED -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/log/heapdump.hprof 
+java_command: org.netbeans.Main --cachedir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/cache --userdir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir --branding gephi --branding gephi
+java_class_path (initial): /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/boot.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-modules.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-lookup.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-ui.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ar_SA.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_bg.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ca.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_cs.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_de.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_es.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_fr.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_gl_ES.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_in_ID.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_it.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ja.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/li
+Launcher Type: SUN_STANDARD
+
+Environment Variables:
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+PATH=./bin:/usr/local/opt/rbenv/shims:/usr/local/opt/rbenv/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
+LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/amd64:/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/i386:
+SHELL=/bin/zsh
+
+Signal Handlers:
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+SIGBUS: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
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+SIGILL: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART
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+SIGQUIT: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
+
+
+---------------  S Y S T E M  ---------------
+
+OS:Bsduname:Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
+rlimit: STACK 8192k, CORE 0k, NPROC 1418, NOFILE 10240, AS infinity
+load average:5.89 6.97 5.79
+
+CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx
+
+Memory: 4k page, physical 16777216k(15852k free)
+
+/proc/meminfo:
+
+
+vm_info: Java HotSpot(TM) 64-Bit Server VM (25.171-b11) for bsd-amd64 JRE (1.8.0_171-b11), built on Mar 28 2018 12:50:57 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
+
+time: Tue Aug 28 16:30:35 2018
+elapsed time: 1194 seconds (0d 0h 19m 54s)
+
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 1a997e1..70bfe1d 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -124,6 +124,7 @@ public class ForceAtlas2 implements Layout {
     private double minWeight;
     private double maxWeight;
     private String nodeWeightColumnName;
+    private double nodeWeightScaling;
 
 
 
@@ -256,19 +257,21 @@ private boolean hasNodeWeight(Node node) {
 
 
     private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
+
         if (isDynamicNodeWeight) {
             // node_weight = (Double) n.getAttribute("gravity_x");
             TimestampMap map = (TimestampMap) node.getAttribute(this.nodeWeightColumnName);
             // Estimator estimator = (Estimator) AVERAGE;
-            Double prev_value = 0.0;
+
             Double value = (Double) map.get(interval, Estimator.AVERAGE);
-            if (value != null) {
-              prev_value = value;
-              return value;
-            } else {
-              return prev_value;
+            if (value == null) {
+              Interval prev_interval = new Interval (Interval.INFINITY_INTERVAL.getLow(), interval.getLow());
+              value = (Double) map.get(prev_interval, Estimator.LAST);
+              if (value == null) {
+                value = 0.0;
+              }
             }
-
+            return value;
         } else {
           return (Double) node.getAttribute(this.nodeWeightColumnName);
         }
@@ -407,32 +410,38 @@ private void adjustHue(Node[] nodes, Node node, Double weight){
         g = 51/255f;
         b = 153/255f;
       } if (weight >= -2.5 && weight < -2.0) {
-// rgb(51,92,173)
-        r = 51/255f;
-        g = 92/255f;
-        b = 173/255f;
+// rgb(43,85,170)
+        r = 43/255f;
+        g = 85/255f;
+        b = 170/255f;
       } if (weight >= -2.0 && weight < -1.5) {
-// rgb(102,133,194)
-        r = 102/255f;
-        g = 133/255f;
-        b = 194/255f;
+// rgb(85,119,187)
+        r = 85/255f;
+        g = 119/255f;
+        b = 187/255f;
 
       } if (weight >= -1.5 && weight < -1.0) {
-// rgb(153,173,214)
+// rgb(128,153,204)
         r = 153/255f;
         g = 173/255f;
         b = 214/255f;
       } if (weight >= -1.0 && weight < -0.5) {
-// rgb(204,214,235)
+// rgb(170,187,221)
         r = 204/255f;
         g = 214/255f;
         b = 235/255f;
       } if (weight >= -0.5 && weight < 0) {
+// rgb(213,221,238)
+        r = 213/255f;
+        g = 221/255f;
+        b = 238/255f;
+      }
+      if (weight == 0) {
 // rgb(255,255,255)
         r = 255/255f;
         g = 255/255f;
         b = 255/255f;
-      } if (weight >= 0.0 && weight < 0.5) {
+      } if (weight > 0.0 && weight < 0.5) {
 // rgb(238,213,213)
         r = 238/255f;
         g = 213/255f;
@@ -627,7 +636,7 @@ public void goAlgo() {
                   adjustHue(nodes, node_a, wt_a);
                   adjustHue(nodes, node_b, wt_b);
                 }
-                NodeAttraction.apply(node_a, node_b, ((wt_a + wt_b)/2));
+                NodeAttraction.apply(node_a, node_b, (getNodeWeightScaling()*(wt_a + wt_b)/2));
 
             }
 
@@ -772,20 +781,20 @@ public LayoutProperty[] getProperties() {
         final String FORCEATLAS2_THREADS = NbBundle.getMessage(getClass(), "ForceAtlas2.threads");
 
         try {
-            properties.add(LayoutProperty.createProperty(
-                    this, Double.class,
-                    NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.name"),
-                    FORCEATLAS2_TUNING,
-                    "ForceAtlas2.maxWeight.name",
-                    NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.desc"),
-                    "getMaxWeight", "setMaxWeight"));
-            properties.add(LayoutProperty.createProperty(
-                    this, Double.class,
-                    NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.name"),
-                    FORCEATLAS2_TUNING,
-                    "ForceAtlas2.minWeight.name",
-                    NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.desc"),
-                    "getMinWeight", "setMinWeight"));
+            // properties.add(LayoutProperty.createProperty(
+            //         this, Double.class,
+            //         NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.name"),
+            //         FORCEATLAS2_TUNING,
+            //         "ForceAtlas2.maxWeight.name",
+            //         NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.desc"),
+            //         "getMaxWeight", "setMaxWeight"));
+            // properties.add(LayoutProperty.createProperty(
+            //         this, Double.class,
+            //         NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.name"),
+            //         FORCEATLAS2_TUNING,
+            //         "ForceAtlas2.minWeight.name",
+            //         NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.desc"),
+            //         "getMinWeight", "setMinWeight"));
             properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.scalingRatio.name"),
@@ -793,7 +802,13 @@ public LayoutProperty[] getProperties() {
                     "ForceAtlas2.scalingRatio.name",
                     NbBundle.getMessage(getClass(), "ForceAtlas2.scalingRatio.desc"),
                     "getScalingRatio", "setScalingRatio"));
-
+            properties.add(LayoutProperty.createProperty(
+                    this, Double.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.nodeWeightScaling.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.nodeWeightScaling.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.nodeWeightScaling.desc"),
+                    "getNodeWeightScaling", "setNodeWeightScaling"));
             properties.add(LayoutProperty.createProperty(
                     this, Boolean.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.name"),
@@ -902,6 +917,8 @@ public void resetPropertiesValues() {
             setScalingRatio(10.0);
         }
         setStrongGravityMode(false);
+        // setNodeWeightAttraction(false);
+        setNodeWeightScaling(1.);
         setHeatMapMode(false);
         setGravity(1.);
 
@@ -1014,6 +1031,15 @@ public void setGravity(Double gravity) {
         this.gravity = gravity;
     }
 
+    public Double getNodeWeightScaling() {
+      return nodeWeightScaling;
+    }
+
+    public void setNodeWeightScaling(Double factor) {
+      this.nodeWeightScaling = factor;
+    }
+
+
     public Integer getThreadsCount() {
         return threadCount;
     }
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index 2fbbb07..ca6c0a0 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -19,15 +19,19 @@ ForceAtlas2.behavior=Behavior Alternatives
 ForceAtlas2.performance=Performance
 ForceAtlas2.threads=Threads
 
-ForceAtlas2.maxWeight.name=Maximum Weight
-ForceAtlas2.maxWeight.desc=maximum of node weights
-ForceAtlas2.minWeight.name=Minimum Weight
-ForceAtlas2.minWeight.desc=minimum of node weights
+# ForceAtlas2.maxWeight.name=Maximum Weight
+# ForceAtlas2.maxWeight.desc=maximum of node weights
+# ForceAtlas2.minWeight.name=Minimum Weight
+# ForceAtlas2.minWeight.desc=minimum of node weights
 
 ForceAtlas2.heatMapMode.name=Heat Map
 ForceAtlas2.heatMapMode.desc=Turn on heat map based on normalized node weights
 
 
+ForceAtlas2.nodeWeightScaling.name=Node Weight Scaling
+ForceAtlas2.nodeWeightScaling.desc=Adjust scaling on node weight attraction. More creates larger distance between nodes.
+
+
 
 ForceAtlas2.scalingRatio.name=Scaling
 ForceAtlas2.scalingRatio.desc=How much repulsion you want. More makes a more sparse graph.

From b6433e7d48abcf180592eacc8db8cc06dc9171e4 Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Tue, 28 Aug 2018 17:28:08 +0100
Subject: [PATCH 19/32] Delete hs_err_pid39777.log

---
 hs_err_pid39777.log | 706 --------------------------------------------
 1 file changed, 706 deletions(-)
 delete mode 100644 hs_err_pid39777.log

diff --git a/hs_err_pid39777.log b/hs_err_pid39777.log
deleted file mode 100644
index 0b92034..0000000
--- a/hs_err_pid39777.log
+++ /dev/null
@@ -1,706 +0,0 @@
-#
-# A fatal error has been detected by the Java Runtime Environment:
-#
-#  SIGSEGV (0xb) at pc=0x0000000110fe8734, pid=39777, tid=0x000000000001d90f
-#
-# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
-# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode bsd-amd64 compressed oops)
-# Problematic frame:
-# j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
-#
-# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
-#
-# If you would like to submit a bug report, please visit:
-#   http://bugreport.java.com/bugreport/crash.jsp
-#
-
----------------  T H R E A D  ---------------
-
-Current thread (0x00007fb91f19f800):  JavaThread "Timer-519" [_thread_in_Java, id=121103, stack(0x00007000061ab000,0x00007000062ab000)]
-
-siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x000000000001d90f
-
-Registers:
-RAX=0x000000000001d90f, RBX=0x0000000136bdbeb0, RCX=0x00007fb91f2e9038, RDX=0x00000000000aacc0
-RSP=0x00007000062aa5d0, RBP=0x00007000062aa650, RSI=0x000000010209a800, RDI=0x0000000000000001
-R8 =0x0000000000000005, R9 =0x00007fb928450550, R10=0x0000000000000000, R11=0x0000000110fe1d1b
-R12=0x0000000000000000, R13=0x0000000136bdbeb0, R14=0x00007000062aa690, R15=0x00007fb91f19f800
-RIP=0x0000000110fe8734, EFLAGS=0x0000000000010206, ERR=0x0000000000000004
-  TRAPNO=0x000000000000000e
-
-Top of Stack: (sp=0x00007000062aa5d0)
-0x00007000062aa5d0:   0000000000000000 0000000110fe8667
-0x00007000062aa5e0:   000000000000006b 00000000000000f2
-0x00007000062aa5f0:   00000007309aeb90 00000007309aeb90
-0x00007000062aa600:   00007000062aa600 000000017b13aaa4
-0x00007000062aa610:   00007000062aa610 0000000000000000
-0x00007000062aa620:   00007000062aa690 0000000136bdd758
-0x00007000062aa630:   0000000000000000 0000000136bdbeb0
-0x00007000062aa640:   0000000000000000 00007000062aa670
-0x00007000062aa650:   00007000062aa6d8 0000000110fd8040
-0x00007000062aa660:   0000000000000000 0000000110fe1d1b
-0x00007000062aa670:   00000000000002ed 00000000000001cc
-0x00007000062aa680:   00000007309a0028 00000004f60d89b8
-0x00007000062aa690:   00000004f3782518 00007000062aa698
-0x00007000062aa6a0:   0000000136bdbf63 00007000062aa720
-0x00007000062aa6b0:   0000000136bdd758 0000000000000000
-0x00007000062aa6c0:   0000000136bdc010 00007000062aa670
-0x00007000062aa6d0:   00007000062aa700 00007000062aa770
-0x00007000062aa6e0:   0000000110fd8040 0000000000000000
-0x00007000062aa6f0:   0000000000000000 0000000000000000
-0x00007000062aa700:   00000000000002ed 00000000000001cc
-0x00007000062aa710:   00000007309a0028 00000004f60d89b8
-0x00007000062aa720:   00000004f3782518 000000073099f898
-0x00007000062aa730:   00007000062aa730 00000001677b9cbe
-0x00007000062aa740:   00007000062aa7c8 000000017b136730
-0x00007000062aa750:   0000000000000000 00000001677b9d70
-0x00007000062aa760:   00007000062aa700 00007000062aa7b8
-0x00007000062aa770:   00007000062aa810 0000000110fd82bd
-0x00007000062aa780:   00000004f3782518 00000007309a0028
-0x00007000062aa790:   00000007309a0008 000000073099ffe8
-0x00007000062aa7a0:   00000004f3863dc8 000000073099ffa0
-0x00007000062aa7b0:   00000007309aeba8 00000007276610f0
-0x00007000062aa7c0:   00000004f60d89b8 000000073099f898 
-
-Instructions: (pc=0x0000000110fe8734)
-0x0000000110fe8714:   10 01 00 00 00 4c 3b 5d 18 0f 85 20 00 00 00 48
-0x0000000110fe8724:   8b 04 24 48 83 c4 10 48 85 c0 0f 84 03 00 00 00
-0x0000000110fe8734:   48 8b 00 48 89 45 10 48 83 ec 10 48 89 04 24 41
-0x0000000110fe8744:   81 bf 9c 02 00 00 01 00 00 00 0f 85 bd 00 00 00 
-
-Register to memory mapping:
-
-RAX=0x000000000001d90f is an unknown value
-RBX={method} {0x0000000136bdbeb0} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
-RCX=0x00007fb91f2e9038 is an unknown value
-RDX=0x00000000000aacc0 is an unknown value
-RSP=0x00007000062aa5d0 is pointing into the stack for thread: 0x00007fb91f19f800
-RBP=0x00007000062aa650 is pointing into the stack for thread: 0x00007fb91f19f800
-RSI=0x000000010209a800 is an unknown value
-RDI=0x0000000000000001 is an unknown value
-R8 =0x0000000000000005 is an unknown value
-R9 =0x00007fb928450550 is an unknown value
-R10=0x0000000000000000 is an unknown value
-R11=0x0000000110fe1d1b is at code_begin+27 in an Interpreter codelet
-result handlers for native calls  [0x0000000110fe1d00, 0x0000000110fe1d20]  32 bytes
-R12=0x0000000000000000 is an unknown value
-R13={method} {0x0000000136bdbeb0} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
-R14=0x00007000062aa690 is pointing into the stack for thread: 0x00007fb91f19f800
-R15=0x00007fb91f19f800 is a thread
-
-
-Stack: [0x00007000061ab000,0x00007000062ab000],  sp=0x00007000062aa5d0,  free space=1021k
-Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
-j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
-j  com.apple.laf.ScreenPopupFactory.getPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+27
-j  org.gephi.ui.components.richtooltip.RichTooltip.showTooltip(Ljavax/swing/JComponent;Ljava/awt/Point;)V+294
-j  org.gephi.desktop.timeline.TimelineTooltip$1.run()V+73
-J 12023 C1 java.util.TimerThread.mainLoop()V (232 bytes) @ 0x0000000112cffba4 [0x0000000112cfef20+0xc84]
-J 12257 C1 java.util.TimerThread.run()V (74 bytes) @ 0x0000000112daa024 [0x0000000112da9fa0+0x84]
-v  ~StubRoutines::call_stub
-V  [libjvm.dylib+0x2ef1f6]  JavaCalls::call_helper(JavaValue*, methodHandle*, JavaCallArguments*, Thread*)+0x6ae
-V  [libjvm.dylib+0x2ef99a]  JavaCalls::call_virtual(JavaValue*, KlassHandle, Symbol*, Symbol*, JavaCallArguments*, Thread*)+0x164
-V  [libjvm.dylib+0x2efb46]  JavaCalls::call_virtual(JavaValue*, Handle, KlassHandle, Symbol*, Symbol*, Thread*)+0x4a
-V  [libjvm.dylib+0x34a46d]  thread_entry(JavaThread*, Thread*)+0x7c
-V  [libjvm.dylib+0x56eb0f]  JavaThread::thread_main_inner()+0x9b
-V  [libjvm.dylib+0x57020a]  JavaThread::run()+0x1c2
-V  [libjvm.dylib+0x48d4a6]  java_start(Thread*)+0xf6
-C  [libsystem_pthread.dylib+0x3661]  _pthread_body+0x154
-C  [libsystem_pthread.dylib+0x350d]  _pthread_body+0x0
-C  [libsystem_pthread.dylib+0x2bf9]  thread_start+0xd
-C  0x0000000000000000
-
-
----------------  P R O C E S S  ---------------
-
-Java Threads: ( => current thread )
-=>0x00007fb91f19f800 JavaThread "Timer-519" [_thread_in_Java, id=121103, stack(0x00007000061ab000,0x00007000062ab000)]
-  0x00007fb91ef38800 JavaThread "pool-7-thread-3" [_thread_blocked, id=77463, stack(0x00007000064b4000,0x00007000065b4000)]
-  0x00007fb91f4c4000 JavaThread "pool-7-thread-2" [_thread_blocked, id=96083, stack(0x00007000063b1000,0x00007000064b1000)]
-  0x00007fb9256a3000 JavaThread "pool-7-thread-1" [_thread_blocked, id=69963, stack(0x00007000062ae000,0x00007000063ae000)]
-  0x00007fb927e27800 JavaThread "layout" [_thread_in_Java, id=59695, stack(0x0000700005fa5000,0x00007000060a5000)]
-  0x00007fb9275df800 JavaThread "Filter Auto-Refresh - Workspace 1" daemon [_thread_blocked, id=98719, stack(0x00007000060a8000,0x00007000061a8000)]
-  0x00007fb929212000 JavaThread "Filter Thread - Workspace 1" daemon [_thread_blocked, id=92527, stack(0x000070000568a000,0x000070000578a000)]
-  0x00007fb9205c0800 JavaThread "UpdateAnimator" daemon [_thread_blocked, id=123419, stack(0x0000700005481000,0x0000700005581000)]
-  0x00007fb9294cc000 JavaThread "DisplayAnimator" daemon [_thread_blocked, id=98107, stack(0x0000700004148000,0x0000700004248000)]
-  0x00007fb91f64a800 JavaThread "GraphChangeObserver" daemon [_thread_blocked, id=47847, stack(0x00007000046d7000,0x00007000047d7000)]
-  0x00007fb91ffe0000 JavaThread "KeyTipManager processing thread" daemon [_thread_blocked, id=95759, stack(0x0000700003eb9000,0x0000700003fb9000)]
-  0x00007fb9253d1800 JavaThread "SwingWorker-pool-2-thread-10" daemon [_thread_blocked, id=57175, stack(0x0000700005ea2000,0x0000700005fa2000)]
-  0x00007fb925a64800 JavaThread "SwingWorker-pool-2-thread-9" daemon [_thread_blocked, id=126735, stack(0x0000700005d9f000,0x0000700005e9f000)]
-  0x00007fb92538c800 JavaThread "SwingWorker-pool-2-thread-8" daemon [_thread_blocked, id=89391, stack(0x0000700005c9c000,0x0000700005d9c000)]
-  0x00007fb927853800 JavaThread "SwingWorker-pool-2-thread-7" daemon [_thread_blocked, id=49435, stack(0x0000700005b99000,0x0000700005c99000)]
-  0x00007fb9269c9000 JavaThread "SwingWorker-pool-2-thread-6" daemon [_thread_blocked, id=63519, stack(0x0000700005a96000,0x0000700005b96000)]
-  0x00007fb92754e000 JavaThread "SwingWorker-pool-2-thread-5" daemon [_thread_blocked, id=53791, stack(0x0000700005993000,0x0000700005a93000)]
-  0x00007fb9240d5000 JavaThread "SwingWorker-pool-2-thread-4" daemon [_thread_blocked, id=57723, stack(0x0000700005890000,0x0000700005990000)]
-  0x00007fb9259a8000 JavaThread "SwingWorker-pool-2-thread-3" daemon [_thread_blocked, id=128523, stack(0x000070000578d000,0x000070000588d000)]
-  0x00007fb920541000 JavaThread "SwingWorker-pool-2-thread-2" daemon [_thread_blocked, id=129323, stack(0x00007000051f8000,0x00007000052f8000)]
-  0x00007fb91fd13000 JavaThread "SwingWorker-pool-2-thread-1" daemon [_thread_blocked, id=92175, stack(0x00007000050f5000,0x00007000051f5000)]
-  0x00007fb9252c3000 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=69683, stack(0x000070000537e000,0x000070000547e000)]
-  0x00007fb927822000 JavaThread "Thread-15" [_thread_blocked, id=19467, stack(0x0000700005587000,0x0000700005687000)]
-  0x00007fb926a54800 JavaThread "Context Refresh Thread" daemon [_thread_blocked, id=128939, stack(0x0000700004dec000,0x0000700004eec000)]
-  0x00007fb927787800 JavaThread "AppearanceColumnObserver" daemon [_thread_blocked, id=88963, stack(0x00007000049e0000,0x0000700004ae0000)]
-  0x00007fb92536f000 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=91407, stack(0x0000700004ff2000,0x00007000050f2000)]
-  0x00007fb925082000 JavaThread "Timer-0" daemon [_thread_blocked, id=90387, stack(0x0000700004eef000,0x0000700004fef000)]
-  0x00007fb9206f2000 JavaThread "DestroyJavaVM" [_thread_blocked, id=9987, stack(0x0000700002d86000,0x0000700002e86000)]
-  0x00007fb9242c5000 JavaThread "Inactive RequestProcessor thread [Was:TimedSoftReference/org.openide.util.TimedSoftReference]" daemon [_thread_blocked, id=130307, stack(0x0000700004ce9000,0x0000700004de9000)]
-  0x00007fb9242b6800 JavaThread "TimerQueue" daemon [_thread_blocked, id=88067, stack(0x0000700004be6000,0x0000700004ce6000)]
-  0x00007fb91e833800 JavaThread "Thread-5" daemon [_thread_blocked, id=63019, stack(0x0000700004ae3000,0x0000700004be3000)]
-  0x00007fb91f603800 JavaThread "File Watcher" daemon [_thread_blocked, id=61443, stack(0x00007000048dd000,0x00007000049dd000)]
-  0x00007fb920434000 JavaThread "Thread-1" daemon [_thread_in_native, id=66083, stack(0x00007000047da000,0x00007000048da000)]
-  0x00007fb920368000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=53511, stack(0x00007000045d4000,0x00007000046d4000)]
-  0x00007fb91eda2000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=76043, stack(0x00007000044d1000,0x00007000045d1000)]
-  0x00007fb920371800 JavaThread "Java2D Queue Flusher" daemon [_thread_blocked, id=76807, stack(0x00007000043ce000,0x00007000044ce000)]
-  0x00007fb91faac800 JavaThread "RequestProcessor queue manager" daemon [_thread_blocked, id=77059, stack(0x00007000042cb000,0x00007000043cb000)]
-  0x00007fb9202ac800 JavaThread "AWT-Shutdown" [_thread_blocked, id=26667, stack(0x0000700003db6000,0x0000700003eb6000)]
-  0x00007fb91ecca000 JavaThread "AWT-AppKit" daemon [_thread_in_native, id=775, stack(0x00007ffeed387000,0x00007ffeedb87000)]
-  0x00007fb920217000 JavaThread "CLI Requests Server" daemon [_thread_in_native, id=15875, stack(0x0000700003cb3000,0x0000700003db3000)]
-  0x00007fb920232800 JavaThread "Active Reference Queue Daemon" daemon [_thread_blocked, id=14339, stack(0x0000700003bb0000,0x0000700003cb0000)]
-  0x00007fb91f80a800 JavaThread "Service Thread" daemon [_thread_blocked, id=16643, stack(0x00007000039aa000,0x0000700003aaa000)]
-  0x00007fb91f800000 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=16899, stack(0x00007000038a7000,0x00007000039a7000)]
-  0x00007fb91f02b800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=17411, stack(0x00007000037a4000,0x00007000038a4000)]
-  0x00007fb920038800 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=13315, stack(0x00007000036a1000,0x00007000037a1000)]
-  0x00007fb920037800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18179, stack(0x000070000359e000,0x000070000369e000)]
-  0x00007fb91e813000 JavaThread "Finalizer" daemon [_thread_blocked, id=11523, stack(0x000070000349b000,0x000070000359b000)]
-  0x00007fb92002c000 JavaThread "Reference Handler" daemon [_thread_blocked, id=20483, stack(0x0000700003398000,0x0000700003498000)]
-
-Other Threads:
-  0x00007fb920027800 VMThread [stack: 0x0000700003295000,0x0000700003395000] [id=11267]
-  0x00007fb92006a000 WatcherThread [stack: 0x0000700003aad000,0x0000700003bad000] [id=13827]
-
-VM state:not at safepoint (normal execution)
-
-VM Mutex/Monitor currently owned by a thread: None
-
-Heap:
- PSYoungGen      total 3765248K, used 1662426K [0x00000006d1180000, 0x00000007b8800000, 0x00000007c0000000)
-  eden space 3739648K, 43% used [0x00000006d1180000,0x00000007356b4068,0x00000007b5580000)
-  from space 25600K, 73% used [0x00000007b6e00000,0x00000007b8042a50,0x00000007b8700000)
-  to   space 25088K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007b6e00000)
- ParOldGen       total 658432K, used 596142K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a2b9f0,0x000000051b700000)
- Metaspace       used 60414K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-
-Card table byte_map: [0x0000000103d6e000,0x00000001053d5000] byte_map_base: 0x00000001015d4000
-
-Marking Bits: (ParMarkBitMap*) 0x00000001032f76e0
- Begin Bits: [0x000000011ffd0000, 0x000000012b300000)
- End Bits:   [0x000000012b300000, 0x0000000136630000)
-
-Polling page: 0x00000001020f6000
-
-CodeCache: size=245760Kb used=30938Kb max_used=31074Kb free=214821Kb
- bounds [0x0000000110fd0000, 0x0000000112e70000, 0x000000011ffd0000]
- total_blobs=10361 nmethods=9202 adapters=1067
- compilation: enabled
-
-Compilation events (10 events):
-Event: 698.765 Thread 0x00007fb91f800000 12318 %s!   3       sun.java2d.opengl.OGLRenderQueue$QueueFlusher::run @ 2 (234 bytes)
-Event: 698.768 Thread 0x00007fb91f800000 nmethod 12318% 0x0000000112ad5f10 code [0x0000000112ad6280, 0x0000000112ad86d8]
-Event: 703.864 Thread 0x00007fb91f800000 12319  s!   3       sun.java2d.opengl.OGLRenderQueue$QueueFlusher::run (234 bytes)
-Event: 703.868 Thread 0x00007fb91f800000 nmethod 12319 0x0000000112d7c390 code [0x0000000112d7c700, 0x0000000112d7ea58]
-Event: 704.373 Thread 0x00007fb91f800000 12320       3       java.lang.reflect.ReflectAccess::copyMethod (5 bytes)
-Event: 704.373 Thread 0x00007fb91f800000 nmethod 12320 0x0000000112805a90 code [0x0000000112805c00, 0x0000000112805e08]
-Event: 707.706 Thread 0x00007fb91f800000 12321       1       java.text.AttributedString$AttributedStringIterator::getEndIndex (5 bytes)
-Event: 707.706 Thread 0x00007fb91f800000 nmethod 12321 0x0000000111e0dfd0 code [0x0000000111e0e120, 0x0000000111e0e230]
-Event: 707.706 Thread 0x00007fb91f800000 12322       3       sun.util.locale.provider.RuleBasedBreakIterator::getNextIndex (34 bytes)
-Event: 707.707 Thread 0x00007fb91f800000 nmethod 12322 0x00000001124e5c50 code [0x00000001124e5de0, 0x00000001124e6168]
-
-GC Heap History (10 events):
-Event: 666.008 GC heap before
-{Heap before GC invocations=459 (full 7):
- PSYoungGen      total 3725824K, used 3715828K [0x00000006d1180000, 0x00000007b7300000, 0x00000007c0000000)
-  eden space 3697152K, 100% used [0x00000006d1180000,0x00000007b2c00000,0x00000007b2c00000)
-  from space 28672K, 65% used [0x00000007b2c00000,0x00000007b3e3d110,0x00000007b4800000)
-  to   space 27648K, 0% used [0x00000007b5800000,0x00000007b5800000,0x00000007b7300000)
- ParOldGen       total 658432K, used 596022K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a0db60,0x000000051b700000)
- Metaspace       used 60363K, capacity 65236K, committed 65448K, reserved 1105920K
-  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
-Event: 666.023 GC heap after
-Heap after GC invocations=459 (full 7):
- PSYoungGen      total 3740160K, used 18711K [0x00000006d1180000, 0x00000007b7180000, 0x00000007c0000000)
-  eden space 3714048K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b3c80000)
-  from space 26112K, 71% used [0x00000007b5800000,0x00000007b6a45df0,0x00000007b7180000)
-  to   space 27136K, 0% used [0x00000007b3c80000,0x00000007b3c80000,0x00000007b5700000)
- ParOldGen       total 658432K, used 596086K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a1d9f0,0x000000051b700000)
- Metaspace       used 60363K, capacity 65236K, committed 65448K, reserved 1105920K
-  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
-}
-Event: 671.856 GC heap before
-{Heap before GC invocations=460 (full 7):
- PSYoungGen      total 3740160K, used 3732759K [0x00000006d1180000, 0x00000007b7180000, 0x00000007c0000000)
-  eden space 3714048K, 100% used [0x00000006d1180000,0x00000007b3c80000,0x00000007b3c80000)
-  from space 26112K, 71% used [0x00000007b5800000,0x00000007b6a45df0,0x00000007b7180000)
-  to   space 27136K, 0% used [0x00000007b3c80000,0x00000007b3c80000,0x00000007b5700000)
- ParOldGen       total 658432K, used 596086K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a1d9f0,0x000000051b700000)
- Metaspace       used 60386K, capacity 65236K, committed 65448K, reserved 1105920K
-  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
-Event: 671.870 GC heap after
-Heap after GC invocations=460 (full 7):
- PSYoungGen      total 3741184K, used 18768K [0x00000006d1180000, 0x00000007b8000000, 0x00000007c0000000)
-  eden space 3714048K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b3c80000)
-  from space 27136K, 69% used [0x00000007b3c80000,0x00000007b4ed41e0,0x00000007b5700000)
-  to   space 26624K, 0% used [0x00000007b6600000,0x00000007b6600000,0x00000007b8000000)
- ParOldGen       total 658432K, used 596110K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a239f0,0x000000051b700000)
- Metaspace       used 60386K, capacity 65236K, committed 65448K, reserved 1105920K
-  class space    used 7368K, capacity 8849K, committed 8872K, reserved 1048576K
-}
-Event: 682.048 GC heap before
-{Heap before GC invocations=461 (full 7):
- PSYoungGen      total 3741184K, used 3732816K [0x00000006d1180000, 0x00000007b8000000, 0x00000007c0000000)
-  eden space 3714048K, 100% used [0x00000006d1180000,0x00000007b3c80000,0x00000007b3c80000)
-  from space 27136K, 69% used [0x00000007b3c80000,0x00000007b4ed41e0,0x00000007b5700000)
-  to   space 26624K, 0% used [0x00000007b6600000,0x00000007b6600000,0x00000007b8000000)
- ParOldGen       total 658432K, used 596110K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a239f0,0x000000051b700000)
- Metaspace       used 60391K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-Event: 682.065 GC heap after
-Heap after GC invocations=461 (full 7):
- PSYoungGen      total 3751424K, used 20008K [0x00000006d1180000, 0x00000007b7d00000, 0x00000007c0000000)
-  eden space 3727872K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b4a00000)
-  from space 23552K, 84% used [0x00000007b6600000,0x00000007b798a2c8,0x00000007b7d00000)
-  to   space 26112K, 0% used [0x00000007b4a00000,0x00000007b4a00000,0x00000007b6380000)
- ParOldGen       total 658432K, used 596118K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a259f0,0x000000051b700000)
- Metaspace       used 60391K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-}
-Event: 702.204 GC heap before
-{Heap before GC invocations=462 (full 7):
- PSYoungGen      total 3751424K, used 3747880K [0x00000006d1180000, 0x00000007b7d00000, 0x00000007c0000000)
-  eden space 3727872K, 100% used [0x00000006d1180000,0x00000007b4a00000,0x00000007b4a00000)
-  from space 23552K, 84% used [0x00000007b6600000,0x00000007b798a2c8,0x00000007b7d00000)
-  to   space 26112K, 0% used [0x00000007b4a00000,0x00000007b4a00000,0x00000007b6380000)
- ParOldGen       total 658432K, used 596118K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a259f0,0x000000051b700000)
- Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-Event: 702.219 GC heap after
-Heap after GC invocations=462 (full 7):
- PSYoungGen      total 3753984K, used 18756K [0x00000006d1180000, 0x00000007b8700000, 0x00000007c0000000)
-  eden space 3727872K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b4a00000)
-  from space 26112K, 71% used [0x00000007b4a00000,0x00000007b5c512c8,0x00000007b6380000)
-  to   space 25600K, 0% used [0x00000007b6e00000,0x00000007b6e00000,0x00000007b8700000)
- ParOldGen       total 658432K, used 596126K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a279f0,0x000000051b700000)
- Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-}
-Event: 705.321 GC heap before
-{Heap before GC invocations=463 (full 7):
- PSYoungGen      total 3753984K, used 3746628K [0x00000006d1180000, 0x00000007b8700000, 0x00000007c0000000)
-  eden space 3727872K, 100% used [0x00000006d1180000,0x00000007b4a00000,0x00000007b4a00000)
-  from space 26112K, 71% used [0x00000007b4a00000,0x00000007b5c512c8,0x00000007b6380000)
-  to   space 25600K, 0% used [0x00000007b6e00000,0x00000007b6e00000,0x00000007b8700000)
- ParOldGen       total 658432K, used 596126K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a279f0,0x000000051b700000)
- Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-Event: 705.334 GC heap after
-Heap after GC invocations=463 (full 7):
- PSYoungGen      total 3765248K, used 18698K [0x00000006d1180000, 0x00000007b8800000, 0x00000007c0000000)
-  eden space 3739648K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007b5580000)
-  from space 25600K, 73% used [0x00000007b6e00000,0x00000007b8042a50,0x00000007b8700000)
-  to   space 25088K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007b6e00000)
- ParOldGen       total 658432K, used 596142K [0x00000004f3400000, 0x000000051b700000, 0x00000006d1180000)
-  object space 658432K, 90% used [0x00000004f3400000,0x0000000517a2b9f0,0x000000051b700000)
- Metaspace       used 60412K, capacity 65242K, committed 65448K, reserved 1105920K
-  class space    used 7369K, capacity 8850K, committed 8872K, reserved 1048576K
-}
-
-Deoptimization events (10 events):
-Event: 613.034 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001119b85ec method=java.math.MutableBigInteger.divideMagnitude(Ljava/math/MutableBigInteger;Ljava/math/MutableBigInteger;Z)Ljava/math/MutableBigInteger; @ 549
-Event: 613.075 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112da7448 method=org.gephi.layout.plugins.layout.NodeWeight.ForceAtlas2.adjustHue([Lorg/gephi/graph/api/Node;Lorg/gephi/graph/api/Node;Ljava/lang/Double;)V @ 17
-Event: 613.087 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011259c388 method=java.math.MutableBigInteger.getMagnitudeArray()[I @ 16
-Event: 613.305 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d6e610 method=java.math.MutableBigInteger.compare(Ljava/math/MutableBigInteger;)I @ 90
-Event: 639.803 Thread 0x00007fb9205c0800 Uncommon trap: reason=range_check action=make_not_entrant pc=0x0000000112d8f090 method=it.unimi.dsi.fastutil.ints.IntRBTreeSet.add(I)Z @ 759
-Event: 675.550 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112e242e8 method=org.gephi.graph.api.types.TimestampMap.getAverageBigDecimal(Lorg/gephi/graph/api/Interval;)Ljava/math/BigDecimal; @ 24
-Event: 675.550 Thread 0x00007fb927e27800 Uncommon trap: reason=null_check action=make_not_entrant pc=0x0000000111ccbc3c method=org.gephi.layout.plugins.layout.NodeWeight.ForceAtlas2.getNodeWeight(Lorg/gephi/graph/api/Node;ZLorg/gephi/graph/api/Interval;)D @ 34
-Event: 675.551 Thread 0x00007fb927e27800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001127ff49c method=org.gephi.graph.api.types.TimestampMap.getAverageBigDecimal(Lorg/gephi/graph/api/Interval;)Ljava/math/BigDecimal; @ 24
-Event: 684.173 Thread 0x00007fb9205c0800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d9784c method=it.unimi.dsi.fastutil.ints.IntRBTreeSet.add(I)Z @ 380
-Event: 698.013 Thread 0x00007fb926a54800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001119ab564 method=java.util.concurrent.locks.ReentrantReadWriteLock$Sync.tryAcquire(I)Z @ 80
-
-Classes redefined (0 events):
-No events
-
-Internal exceptions (10 events):
-Event: 258.466 Thread 0x00007fb9242c5000 Implicit null exception at 0x00000001124ec0ae to 0x00000001124ed1b5
-Event: 443.159 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000703ed9a78) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 443.160 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000703ef2ba8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 443.160 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000703f092d8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 520.545 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000713ff23f8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 520.546 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x000000071400b580) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 520.546 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x0000000714021c20) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 527.209 Thread 0x00007fb920368000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x00000006d423dfa8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 707.710 Thread 0x00007fb91f19f800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': -1> (0x00000007309b7800) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
-Event: 707.710 Thread 0x00007fb91f19f800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException'> (0x00000007309b7800) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/prims/jni.cpp, line 709]
-
-Events (10 events):
-Event: 707.182 Thread 0x00007fb929c4c000 Thread exited: 0x00007fb929c4c000
-Event: 707.183 Thread 0x00007fb92712c000 Thread added: 0x00007fb92712c000
-Event: 707.187 Thread 0x00007fb91f19f800 Thread added: 0x00007fb91f19f800
-Event: 707.187 Thread 0x00007fb92712c000 Thread exited: 0x00007fb92712c000
-Event: 707.192 Thread 0x00007fb91f19f800 Thread exited: 0x00007fb91f19f800
-Event: 707.192 Thread 0x00007fb929c4c000 Thread added: 0x00007fb929c4c000
-Event: 707.193 Thread 0x00007fb929c4c000 Thread exited: 0x00007fb929c4c000
-Event: 707.194 Thread 0x00007fb92044a000 Thread added: 0x00007fb92044a000
-Event: 707.200 Thread 0x00007fb92044a000 Thread exited: 0x00007fb92044a000
-Event: 707.200 Thread 0x00007fb91f19f800 Thread added: 0x00007fb91f19f800
-
-
-Dynamic libraries:
-0x000000000f6fa000 	/System/Library/Frameworks/Cocoa.framework/Versions/A/Cocoa
-0x000000000f6fa000 	/System/Library/Frameworks/Security.framework/Versions/A/Security
-0x000000000f6fa000 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/ApplicationServices
-0x000000000f6fa000 	/usr/lib/libz.1.dylib
-0x000000000f6fa000 	/usr/lib/libSystem.B.dylib
-0x000000000f6fa000 	/usr/lib/libobjc.A.dylib
-0x000000000f6fa000 	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
-0x000000000f6fa000 	/System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
-0x000000000f6fa000 	/System/Library/Frameworks/AppKit.framework/Versions/C/AppKit
-0x000000000f6fa000 	/System/Library/Frameworks/CoreData.framework/Versions/A/CoreData
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/RemoteViewServices.framework/Versions/A/RemoteViewServices
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/DFRFoundation.framework/Versions/A/DFRFoundation
-0x000000000f6fa000 	/System/Library/Frameworks/Metal.framework/Versions/A/Metal
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/DesktopServicesPriv
-0x000000000f6fa000 	/usr/lib/libenergytrace.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/SkyLight.framework/Versions/A/SkyLight
-0x000000000f6fa000 	/System/Library/Frameworks/CoreGraphics.framework/Versions/A/CoreGraphics
-0x000000000f6fa000 	/usr/lib/libScreenReader.dylib
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-0x000000000f6fa000 	/System/Library/Frameworks/CoreMedia.framework/Versions/A/CoreMedia
-0x000000000f6fa000 	/System/Library/Frameworks/VideoToolbox.framework/Versions/A/VideoToolbox
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/CoreAUC.framework/Versions/A/CoreAUC
-0x000000000f6fa000 	/usr/lib/libspindump.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/AppleVA.framework/Versions/A/AppleVA
-0x000000000f6fa000 	/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
-0x000000000f6fa000 	/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libTrueTypeScaler.dylib
-0x000000000f6fa000 	/System/Library/Extensions/AppleIntelSKLGraphicsMTLDriver.bundle/Contents/MacOS/AppleIntelSKLGraphicsMTLDriver
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/GPUCompiler.framework/Versions/3802/Libraries/libmetal_timestamp.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyControls
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/CommerceCore.framework/Versions/A/CommerceCore
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/SystemAdministration.framework/Versions/A/SystemAdministration
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/AppContainer.framework/Versions/A/AppContainer
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/DiskManagement
-0x000000000f6fa000 	/System/Library/Frameworks/DirectoryService.framework/Versions/A/DirectoryService
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages
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-0x000000000f6fa000 	/usr/lib/libCoreStorage.dylib
-0x000000000f6fa000 	/usr/lib/libcsfde.dylib
-0x000000000f6fa000 	/usr/lib/libodfde.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/MediaKit.framework/Versions/A/MediaKit
-0x000000000f6fa000 	/System/Library/Frameworks/DiscRecording.framework/Versions/A/DiscRecording
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/EFILogin.framework/Versions/A/EFILogin
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
-0x000000000f6fa000 	/usr/lib/libcurl.4.dylib
-0x000000000f6fa000 	/usr/lib/libcrypto.35.dylib
-0x000000000f6fa000 	/usr/lib/libssl.35.dylib
-0x000000000f6fa000 	/System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
-0x000000000f6fa000 	/usr/lib/libsasl2.2.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
-0x000000000f6fa000 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
-0x000000000f6fa000 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
-0x000000010f41e000 	/System/Library/Extensions/AppleIntelSKLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelSKLGraphicsGLDriver
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
-0x000000000f6fa000 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
-0x000000000f6fa000 	/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
-0x0000000136a89000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libsplashscreen.dylib
-0x0000000136ce1000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libfontmanager.dylib
-0x0000000110f24000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libosxui.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
-0x0000000139538000 	/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/modules/lib/libjnidispatch-422.jnilib
-0x000000010e397000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libgluegen-rt.jnilib
-0x000000010e59c000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libnativewindow_awt.jnilib
-0x000000010e59f000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libjawt.dylib
-0x0000000166e66000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libnativewindow_macosx.jnilib
-0x00000001673ae000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libjogl_desktop.jnilib
-0x000000010e18a000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7141739527789646462/jln4577135066445807290/natives/macosx-universal/libjogl_mobile.jnilib
-0x000000010e1f1000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libmanagement.dylib
-0x000000010d489000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libdcpr.dylib
-0x0000000138fc7000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libsunec.dylib
-0x000000010e1ff000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libosx.dylib
-0x000000013974e000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/liblcms.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/login.framework/Versions/A/login
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/Shortcut.framework/Versions/A/Shortcut
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/HelpData.framework/Versions/A/HelpData
-
-VM Arguments:
-jvm_args: -Djdk.home=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home -Dnetbeans.dirs=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/gephi::/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/plugins_clusters/plugins -Dnetbeans.home=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform -Xms64m -Xmx11468m -Xverify:none -Dsun.java2d.noddraw=true -Dsun.awt.noerasebackground=true -Dnetbeans.indexing.noFileRefresh=true -Dplugin.manager.check.interval=EVERY_DAY -Dnetbeans.logger.console=true -ea -DaddExports:java.desktop/com.apple.eawt=ALL-UNNAMED -DaddExports:java.desktop/sun.awt=ALL-UNNAMED -DaddExports:java.base/jdk.internal.jrtfs=ALL-UNNAMED -DaddExports:java.desktop/apple.laf=ALL-UNNAMED -DaddExports:java.desktop/java.awt.peer=ALL-UNNAMED -DaddExports:java.desktop/com.sun.beans.editors=ALL-UNNAMED -DaddExports:java.desktop/sun.awt.im=ALL-UNNAMED -DaddExports:java.management/sun.management=ALL-UNNAMED -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/log/heapdump.hprof 
-java_command: org.netbeans.Main --cachedir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/cache --userdir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir --branding gephi --branding gephi
-java_class_path (initial): /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/boot.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-modules.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-lookup.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-ui.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ar_SA.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_bg.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ca.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_cs.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_de.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_es.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_fr.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_gl_ES.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_in_ID.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_it.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ja.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/li
-Launcher Type: SUN_STANDARD
-
-Environment Variables:
-JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home
-PATH=./bin:/usr/local/opt/rbenv/shims:/usr/local/opt/rbenv/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
-LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/amd64:/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/i386:
-SHELL=/bin/zsh
-
-Signal Handlers:
-SIGSEGV: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
-SIGBUS: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGFPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGPIPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGXFSZ: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGILL: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART
-SIGUSR2: [libjvm.dylib+0x48a5ae], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
-SIGHUP: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGINT: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
-SIGTERM: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGQUIT: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-
-
----------------  S Y S T E M  ---------------
-
-OS:Bsduname:Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
-rlimit: STACK 8192k, CORE 0k, NPROC 1418, NOFILE 10240, AS infinity
-load average:2.42 2.32 2.78
-
-CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx
-
-Memory: 4k page, physical 16777216k(884572k free)
-
-/proc/meminfo:
-
-
-vm_info: Java HotSpot(TM) 64-Bit Server VM (25.171-b11) for bsd-amd64 JRE (1.8.0_171-b11), built on Mar 28 2018 12:50:57 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
-
-time: Tue Aug 28 14:23:15 2018
-elapsed time: 707 seconds (0d 0h 11m 47s)
-

From e31942507c0bd965dd16361ad4bb867c5e2d77ed Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Tue, 28 Aug 2018 17:28:18 +0100
Subject: [PATCH 20/32] Delete hs_err_pid43526.log

---
 hs_err_pid43526.log | 705 --------------------------------------------
 1 file changed, 705 deletions(-)
 delete mode 100644 hs_err_pid43526.log

diff --git a/hs_err_pid43526.log b/hs_err_pid43526.log
deleted file mode 100644
index db4a570..0000000
--- a/hs_err_pid43526.log
+++ /dev/null
@@ -1,705 +0,0 @@
-#
-# A fatal error has been detected by the Java Runtime Environment:
-#
-#  SIGSEGV (0xb) at pc=0x0000000111d4a734, pid=43526, tid=0x0000000000015c57
-#
-# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
-# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode bsd-amd64 compressed oops)
-# Problematic frame:
-# j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
-#
-# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
-#
-# If you would like to submit a bug report, please visit:
-#   http://bugreport.java.com/bugreport/crash.jsp
-#
-
----------------  T H R E A D  ---------------
-
-Current thread (0x00007fc2427cb800):  JavaThread "Timer-371" [_thread_in_Java, id=89175, stack(0x000070000fd45000,0x000070000fe45000)]
-
-siginfo: si_signo: 11 (SIGSEGV), si_code: 1 (SEGV_MAPERR), si_addr: 0x0000000000015c57
-
-Registers:
-RAX=0x0000000000015c57, RBX=0x00000001415d8338, RCX=0x00007fc242c1c038, RDX=0x000000000009d460
-RSP=0x000070000fe445d0, RBP=0x000070000fe44650, RSI=0x000000010cafa400, RDI=0x00007fc242c1c038
-R8 =0x0000000000000005, R9 =0x00007fc241441ba0, R10=0x0000000000000000, R11=0x0000000111d43d1b
-R12=0x0000000000000000, R13=0x00000001415d8338, R14=0x000070000fe44690, R15=0x00007fc2427cb800
-RIP=0x0000000111d4a734, EFLAGS=0x0000000000010202, ERR=0x0000000000000004
-  TRAPNO=0x000000000000000e
-
-Top of Stack: (sp=0x000070000fe445d0)
-0x000070000fe445d0:   0000000000000000 0000000111d4a667
-0x000070000fe445e0:   00007fc2427cb800 00007fc2427cb800
-0x000070000fe445f0:   0000000172f64d70 00007fc2427cb800
-0x000070000fe44600:   000070000fe44700 0000000111d56523
-0x000070000fe44610:   000070000fe44610 0000000000000000
-0x000070000fe44620:   000070000fe44690 00000001415d9be0
-0x000070000fe44630:   0000000000000000 00000001415d8338
-0x000070000fe44640:   0000000000000000 000070000fe44670
-0x000070000fe44650:   000070000fe446d8 0000000111d3a040
-0x000070000fe44660:   0000000000000000 0000000111d43d1b
-0x000070000fe44670:   00000000000002b7 0000000000000188
-0x000070000fe44680:   00000007131b6658 00000004f4a6bb30
-0x000070000fe44690:   00000004f38cd3d0 000070000fe44698
-0x000070000fe446a0:   00000001415d83eb 000070000fe44720
-0x000070000fe446b0:   00000001415d9be0 0000000000000000
-0x000070000fe446c0:   00000001415d8498 000070000fe44670
-0x000070000fe446d0:   000070000fe44700 000070000fe44770
-0x000070000fe446e0:   0000000111d3a040 0000000000000000
-0x000070000fe446f0:   0000000000000000 0000000000000000
-0x000070000fe44700:   00000000000002b7 0000000000000188
-0x000070000fe44710:   00000007131b6658 00000004f4a6bb30
-0x000070000fe44720:   00000004f38cd3d0 0000000713190248
-0x000070000fe44730:   000070000fe44730 0000000172f64cbe
-0x000070000fe44740:   000070000fe447c8 00000001899317e8
-0x000070000fe44750:   0000000000000000 0000000172f64d70
-0x000070000fe44760:   000070000fe44700 000070000fe447b8
-0x000070000fe44770:   000070000fe44810 0000000111d3a2bd
-0x000070000fe44780:   00000004f38cd3d0 00000007131b6658
-0x000070000fe44790:   00000007131b2920 00000007131b1610
-0x000070000fe447a0:   00000004f3824268 00000007131b0278
-0x000070000fe447b0:   0000000713270f38 0000000704bb7e10
-0x000070000fe447c0:   00000004f4a6bb30 0000000713190248 
-
-Instructions: (pc=0x0000000111d4a734)
-0x0000000111d4a714:   11 01 00 00 00 4c 3b 5d 18 0f 85 20 00 00 00 48
-0x0000000111d4a724:   8b 04 24 48 83 c4 10 48 85 c0 0f 84 03 00 00 00
-0x0000000111d4a734:   48 8b 00 48 89 45 10 48 83 ec 10 48 89 04 24 41
-0x0000000111d4a744:   81 bf 9c 02 00 00 01 00 00 00 0f 85 bd 00 00 00 
-
-Register to memory mapping:
-
-RAX=0x0000000000015c57 is an unknown value
-RBX={method} {0x00000001415d8338} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
-RCX=0x00007fc242c1c038 is an unknown value
-RDX=0x000000000009d460 is an unknown value
-RSP=0x000070000fe445d0 is pointing into the stack for thread: 0x00007fc2427cb800
-RBP=0x000070000fe44650 is pointing into the stack for thread: 0x00007fc2427cb800
-RSI=0x000000010cafa400 is an unknown value
-RDI=0x00007fc242c1c038 is an unknown value
-R8 =0x0000000000000005 is an unknown value
-R9 =0x00007fc241441ba0 is an unknown value
-R10=0x0000000000000000 is an unknown value
-R11=0x0000000111d43d1b is at code_begin+27 in an Interpreter codelet
-result handlers for native calls  [0x0000000111d43d00, 0x0000000111d43d20]  32 bytes
-R12=0x0000000000000000 is an unknown value
-R13={method} {0x00000001415d8338} '_getHeavyWeightPopup' '(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;' in 'com/apple/laf/ScreenPopupFactory'
-R14=0x000070000fe44690 is pointing into the stack for thread: 0x00007fc2427cb800
-R15=0x00007fc2427cb800 is a thread
-
-
-Stack: [0x000070000fd45000,0x000070000fe45000],  sp=0x000070000fe445d0,  free space=1021k
-Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
-j  com.apple.laf.ScreenPopupFactory._getHeavyWeightPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+0
-j  com.apple.laf.ScreenPopupFactory.getPopup(Ljava/awt/Component;Ljava/awt/Component;II)Ljavax/swing/Popup;+27
-j  org.gephi.ui.components.richtooltip.RichTooltip.showTooltip(Ljavax/swing/JComponent;Ljava/awt/Point;)V+294
-j  org.gephi.desktop.timeline.TimelineTooltip$1.run()V+73
-J 8640 C1 java.util.TimerThread.mainLoop()V (232 bytes) @ 0x00000001131d6164 [0x00000001131d54e0+0xc84]
-J 9989 C1 java.util.TimerThread.run()V (74 bytes) @ 0x00000001127c6164 [0x00000001127c60e0+0x84]
-v  ~StubRoutines::call_stub
-V  [libjvm.dylib+0x2ef1f6]
-V  [libjvm.dylib+0x2ef99a]
-V  [libjvm.dylib+0x2efb46]
-V  [libjvm.dylib+0x34a46d]
-V  [libjvm.dylib+0x56eb0f]
-V  [libjvm.dylib+0x57020a]
-V  [libjvm.dylib+0x48d4a6]
-C  [libsystem_pthread.dylib+0x3661]  _pthread_body+0x154
-C  [libsystem_pthread.dylib+0x350d]  _pthread_body+0x0
-C  [libsystem_pthread.dylib+0x2bf9]  thread_start+0xd
-C  0x0000000000000000
-
-
----------------  P R O C E S S  ---------------
-
-Java Threads: ( => current thread )
-  0x00007fc2428bb000 JavaThread "sampler-awt" daemon [_thread_blocked, id=93371, stack(0x0000700011593000,0x0000700011693000)]
-=>0x00007fc2427cb800 JavaThread "Timer-371" [_thread_in_Java, id=89175, stack(0x000070000fd45000,0x000070000fe45000)]
-  0x00007fc2426ed800 JavaThread "UpdateAnimator" daemon [_thread_blocked, id=78659, stack(0x0000700011490000,0x0000700011590000)]
-  0x00007fc241c06800 JavaThread "DisplayAnimator" daemon [_thread_blocked, id=129379, stack(0x0000700010e7e000,0x0000700010f7e000)]
-  0x00007fc23f207800 JavaThread "Inactive RequestProcessor thread [Was:Timeable Event Queue Watch Dog/org.netbeans.core.TimableEventQueue]" daemon [_thread_blocked, id=125227, stack(0x0000700010560000,0x0000700010660000)]
-  0x00007fc2409f1800 JavaThread "SwingWorker-pool-3-thread-10" daemon [_thread_blocked, id=36871, stack(0x000070001138d000,0x000070001148d000)]
-  0x00007fc23a285000 JavaThread "SwingWorker-pool-3-thread-9" daemon [_thread_blocked, id=66315, stack(0x000070001128a000,0x000070001138a000)]
-  0x00007fc240e0a000 JavaThread "SwingWorker-pool-3-thread-8" daemon [_thread_blocked, id=59163, stack(0x0000700011187000,0x0000700011287000)]
-  0x00007fc2390a2000 JavaThread "SwingWorker-pool-3-thread-7" daemon [_thread_blocked, id=89383, stack(0x0000700011084000,0x0000700011184000)]
-  0x00007fc23f80e000 JavaThread "SwingWorker-pool-3-thread-6" daemon [_thread_blocked, id=69407, stack(0x0000700010f81000,0x0000700011081000)]
-  0x00007fc242995800 JavaThread "SwingWorker-pool-3-thread-5" daemon [_thread_blocked, id=89703, stack(0x0000700010d7b000,0x0000700010e7b000)]
-  0x00007fc2429e2000 JavaThread "SwingWorker-pool-3-thread-4" daemon [_thread_blocked, id=91179, stack(0x0000700010b75000,0x0000700010c75000)]
-  0x00007fc240e16000 JavaThread "SwingWorker-pool-3-thread-3" daemon [_thread_blocked, id=88603, stack(0x000070001045d000,0x000070001055d000)]
-  0x00007fc242bba800 JavaThread "SwingWorker-pool-3-thread-2" daemon [_thread_blocked, id=91887, stack(0x000070001035a000,0x000070001045a000)]
-  0x00007fc23f8ab000 JavaThread "SwingWorker-pool-3-thread-1" daemon [_thread_blocked, id=47991, stack(0x000070000ffce000,0x00007000100ce000)]
-  0x00007fc2397f6800 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=129579, stack(0x0000700010c78000,0x0000700010d78000)]
-  0x00007fc24247b800 JavaThread "pool-2-thread-3" [_thread_blocked, id=26887, stack(0x0000700010a72000,0x0000700010b72000)]
-  0x00007fc239320800 JavaThread "pool-2-thread-2" [_thread_blocked, id=130635, stack(0x000070001096f000,0x0000700010a6f000)]
-  0x00007fc24243a000 JavaThread "pool-2-thread-1" [_thread_blocked, id=55639, stack(0x000070001086c000,0x000070001096c000)]
-  0x00007fc242492000 JavaThread "layout" [_thread_in_Java, id=70647, stack(0x0000700010663000,0x0000700010763000)]
-  0x00007fc242296000 JavaThread "Filter Auto-Refresh - Workspace 1" daemon [_thread_blocked, id=94019, stack(0x000070000fe48000,0x000070000ff48000)]
-  0x00007fc23f2fd800 JavaThread "Filter Thread - Workspace 1" daemon [_thread_blocked, id=69959, stack(0x000070000dcdc000,0x000070000dddc000)]
-  0x00007fc242391800 JavaThread "Thread-13" [_thread_blocked, id=95243, stack(0x0000700010769000,0x0000700010869000)]
-  0x00007fc242883000 JavaThread "AppearanceColumnObserver" daemon [_thread_blocked, id=126739, stack(0x00007000100d1000,0x00007000101d1000)]
-  0x00007fc2422ba800 JavaThread "Context Refresh Thread" daemon [_thread_blocked, id=62495, stack(0x000070000fa3c000,0x000070000fb3c000)]
-  0x00007fc241acb800 JavaThread "Timer-0" daemon [_thread_blocked, id=90375, stack(0x00007000101d4000,0x00007000102d4000)]
-  0x00007fc23ad79800 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=76039, stack(0x000070000f224000,0x000070000f324000)]
-  0x00007fc23a1b6000 JavaThread "DestroyJavaVM" [_thread_blocked, id=10243, stack(0x000070000de65000,0x000070000df65000)]
-  0x00007fc23f81e800 JavaThread "TimerQueue" daemon [_thread_blocked, id=61443, stack(0x000070000fc42000,0x000070000fd42000)]
-  0x00007fc239cc0800 JavaThread "Thread-5" daemon [_thread_blocked, id=60947, stack(0x000070000fb3f000,0x000070000fc3f000)]
-  0x00007fc23a7f7800 JavaThread "File Watcher" daemon [_thread_blocked, id=58119, stack(0x000070000f939000,0x000070000fa39000)]
-  0x00007fc23a7f6800 JavaThread "Thread-1" daemon [_thread_in_native, id=65571, stack(0x000070000f836000,0x000070000f936000)]
-  0x00007fc23a2e9000 JavaThread "AWT-EventQueue-0" [_thread_blocked, id=55047, stack(0x000070000f630000,0x000070000f730000)]
-  0x00007fc239470000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=74771, stack(0x000070000f52d000,0x000070000f62d000)]
-  0x00007fc23ad06800 JavaThread "Java2D Queue Flusher" daemon [_thread_blocked, id=75271, stack(0x000070000f42a000,0x000070000f52a000)]
-  0x00007fc23acfb800 JavaThread "RequestProcessor queue manager" daemon [_thread_blocked, id=75783, stack(0x000070000f327000,0x000070000f427000)]
-  0x00007fc23937f800 JavaThread "AWT-Shutdown" [_thread_blocked, id=38699, stack(0x000070000ef18000,0x000070000f018000)]
-  0x00007fc23abb6000 JavaThread "AWT-AppKit" daemon [_thread_blocked, id=775, stack(0x00007ffee2926000,0x00007ffee3126000)]
-  0x00007fc239264000 JavaThread "CLI Requests Server" daemon [_thread_in_native, id=17155, stack(0x000070000ed92000,0x000070000ee92000)]
-  0x00007fc239171800 JavaThread "Active Reference Queue Daemon" daemon [_thread_blocked, id=15363, stack(0x000070000ec8f000,0x000070000ed8f000)]
-  0x00007fc239804000 JavaThread "Service Thread" daemon [_thread_blocked, id=17667, stack(0x000070000ea89000,0x000070000eb89000)]
-  0x00007fc23901c800 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=14595, stack(0x000070000e986000,0x000070000ea86000)]
-  0x00007fc23a85b000 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=14339, stack(0x000070000e883000,0x000070000e983000)]
-  0x00007fc239803000 JavaThread "C2 CompilerThread0" daemon [_thread_blocked, id=13827, stack(0x000070000e780000,0x000070000e880000)]
-  0x00007fc239049800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=18439, stack(0x000070000e67d000,0x000070000e77d000)]
-  0x00007fc23901b000 JavaThread "Finalizer" daemon [_thread_blocked, id=11779, stack(0x000070000e57a000,0x000070000e67a000)]
-  0x00007fc23a825800 JavaThread "Reference Handler" daemon [_thread_blocked, id=20739, stack(0x000070000e477000,0x000070000e577000)]
-
-Other Threads:
-  0x00007fc239802800 VMThread [stack: 0x000070000e374000,0x000070000e474000] [id=20995]
-  0x00007fc23a831800 WatcherThread [stack: 0x000070000eb8c000,0x000070000ec8c000] [id=15107]
-
-VM state:synchronizing (normal execution)
-
-VM Mutex/Monitor currently owned by a thread:  ([mutex/lock_event])
-[0x00007fc238f03ef0] Safepoint_lock - owner thread: 0x00007fc239802800
-[0x00007fc238f03f70] Threads_lock - owner thread: 0x00007fc239802800
-
-Heap:
- PSYoungGen      total 3900416K, used 1104675K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3887616K, 28% used [0x00000006d1180000,0x0000000713c4d308,0x00000007be600000)
-  from space 12800K, 95% used [0x00000007bf380000,0x00000007bff7ba00,0x00000007c0000000)
-  to   space 13312K, 0% used [0x00000007be600000,0x00000007be600000,0x00000007bf300000)
- ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
- Metaspace       used 58216K, capacity 63110K, committed 63384K, reserved 1103872K
-  class space    used 7038K, capacity 8514K, committed 8616K, reserved 1048576K
-
-Card table byte_map: [0x000000010e76e000,0x000000010fdd5000] byte_map_base: 0x000000010bfd4000
-
-Marking Bits: (ParMarkBitMap*) 0x000000010dcf76e0
- Begin Bits: [0x0000000120d32000, 0x000000012c062000)
- End Bits:   [0x000000012c062000, 0x0000000137392000)
-
-Polling page: 0x000000010cb57000
-
-CodeCache: size=245760Kb used=27912Kb max_used=28443Kb free=217847Kb
- bounds [0x0000000111d32000, 0x0000000113932000, 0x0000000120d32000]
- total_blobs=9480 nmethods=8321 adapters=1069
- compilation: enabled
-
-Compilation events (10 events):
-Event: 1194.342 Thread 0x00007fc239803000 nmethod 10548 0x0000000113695710 code [0x0000000113695860, 0x00000001136958d8]
-Event: 1194.343 Thread 0x00007fc23a85b000 10550       4       sun.font.SunFontManager::getInstance (9 bytes)
-Event: 1194.345 Thread 0x00007fc23901c800 10551       1       sun.font.GlyphLayout::access$000 (5 bytes)
-Event: 1194.345 Thread 0x00007fc23901c800 nmethod 10551 0x0000000113576910 code [0x0000000113576a60, 0x0000000113576b50]
-Event: 1194.346 Thread 0x00007fc23a85b000 nmethod 10550 0x00000001128980d0 code [0x0000000112898240, 0x00000001128984b8]
-Event: 1194.346 Thread 0x00007fc23a85b000 10553       4       sun.font.StandardGlyphVector::setFRCTX (26 bytes)
-Event: 1194.347 Thread 0x00007fc23901c800 10552       3       sun.font.StandardGlyphVector::getGlyphOutlineBounds (41 bytes)
-Event: 1194.348 Thread 0x00007fc239803000 10558       4       java.awt.geom.RectangularShape::getMinX (5 bytes)
-Event: 1194.348 Thread 0x00007fc23a85b000 nmethod 10553 0x0000000112e5b110 code [0x0000000112e5b260, 0x0000000112e5b438]
-Event: 1194.348 Thread 0x00007fc23a85b000 10559       4       java.awt.geom.RectangularShape::getMinY (5 bytes)
-
-GC Heap History (10 events):
-Event: 1169.280 GC heap before
-{Heap before GC invocations=387 (full 5):
- PSYoungGen      total 3903488K, used 3902650K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3892736K, 100% used [0x00000006d1180000,0x00000007beb00000,0x00000007beb00000)
-  from space 10752K, 92% used [0x00000007beb00000,0x00000007bf4ae810,0x00000007bf580000)
-  to   space 10752K, 0% used [0x00000007bf580000,0x00000007bf580000,0x00000007c0000000)
- ParOldGen       total 162304K, used 46355K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 28% used [0x00000004f3400000,0x00000004f6144d50,0x00000004fd280000)
- Metaspace       used 57831K, capacity 62756K, committed 63000K, reserved 1103872K
-  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
-Event: 1169.293 GC heap after
-Heap after GC invocations=387 (full 5):
- PSYoungGen      total 3902464K, used 10743K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3891712K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007bea00000)
-  from space 10752K, 99% used [0x00000007bf580000,0x00000007bfffddd0,0x00000007c0000000)
-  to   space 11264K, 0% used [0x00000007bea00000,0x00000007bea00000,0x00000007bf500000)
- ParOldGen       total 162304K, used 47833K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 29% used [0x00000004f3400000,0x00000004f62b6470,0x00000004fd280000)
- Metaspace       used 57831K, capacity 62756K, committed 63000K, reserved 1103872K
-  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
-}
-Event: 1174.467 GC heap before
-{Heap before GC invocations=388 (full 5):
- PSYoungGen      total 3902464K, used 3902455K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3891712K, 100% used [0x00000006d1180000,0x00000007bea00000,0x00000007bea00000)
-  from space 10752K, 99% used [0x00000007bf580000,0x00000007bfffddd0,0x00000007c0000000)
-  to   space 11264K, 0% used [0x00000007bea00000,0x00000007bea00000,0x00000007bf500000)
- ParOldGen       total 162304K, used 47833K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 29% used [0x00000004f3400000,0x00000004f62b6470,0x00000004fd280000)
- Metaspace       used 57854K, capacity 62756K, committed 63000K, reserved 1103872K
-  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
-Event: 1174.477 GC heap after
-Heap after GC invocations=388 (full 5):
- PSYoungGen      total 3902976K, used 11249K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3891712K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007bea00000)
-  from space 11264K, 99% used [0x00000007bea00000,0x00000007bf4fc770,0x00000007bf500000)
-  to   space 11264K, 0% used [0x00000007bf500000,0x00000007bf500000,0x00000007c0000000)
- ParOldGen       total 162304K, used 49069K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f63eb6f8,0x00000004fd280000)
- Metaspace       used 57854K, capacity 62756K, committed 63000K, reserved 1103872K
-  class space    used 6999K, capacity 8480K, committed 8488K, reserved 1048576K
-}
-Event: 1181.149 GC heap before
-{Heap before GC invocations=389 (full 5):
- PSYoungGen      total 3902976K, used 3902961K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3891712K, 100% used [0x00000006d1180000,0x00000007bea00000,0x00000007bea00000)
-  from space 11264K, 99% used [0x00000007bea00000,0x00000007bf4fc770,0x00000007bf500000)
-  to   space 11264K, 0% used [0x00000007bf500000,0x00000007bf500000,0x00000007c0000000)
- ParOldGen       total 162304K, used 49069K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f63eb6f8,0x00000004fd280000)
- Metaspace       used 57866K, capacity 62758K, committed 63000K, reserved 1103872K
-  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
-Event: 1181.166 GC heap after
-Heap after GC invocations=389 (full 5):
- PSYoungGen      total 3899904K, used 11246K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3888640K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007be700000)
-  from space 11264K, 99% used [0x00000007bf500000,0x00000007bfffba60,0x00000007c0000000)
-  to   space 12800K, 0% used [0x00000007be700000,0x00000007be700000,0x00000007bf380000)
- ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
- Metaspace       used 57866K, capacity 62758K, committed 63000K, reserved 1103872K
-  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
-}
-Event: 1186.598 GC heap before
-{Heap before GC invocations=390 (full 5):
- PSYoungGen      total 3899904K, used 3899886K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3888640K, 100% used [0x00000006d1180000,0x00000007be700000,0x00000007be700000)
-  from space 11264K, 99% used [0x00000007bf500000,0x00000007bfffba60,0x00000007c0000000)
-  to   space 12800K, 0% used [0x00000007be700000,0x00000007be700000,0x00000007bf380000)
- ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
- Metaspace       used 57868K, capacity 62758K, committed 63000K, reserved 1103872K
-  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
-Event: 1186.609 GC heap after
-Heap after GC invocations=390 (full 5):
- PSYoungGen      total 3901440K, used 11786K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3888640K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007be700000)
-  from space 12800K, 92% used [0x00000007be700000,0x00000007bf2829e8,0x00000007bf380000)
-  to   space 12800K, 0% used [0x00000007bf380000,0x00000007bf380000,0x00000007c0000000)
- ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
- Metaspace       used 57868K, capacity 62758K, committed 63000K, reserved 1103872K
-  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
-}
-Event: 1192.735 GC heap before
-{Heap before GC invocations=391 (full 5):
- PSYoungGen      total 3901440K, used 3900426K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3888640K, 100% used [0x00000006d1180000,0x00000007be700000,0x00000007be700000)
-  from space 12800K, 92% used [0x00000007be700000,0x00000007bf2829e8,0x00000007bf380000)
-  to   space 12800K, 0% used [0x00000007bf380000,0x00000007bf380000,0x00000007c0000000)
- ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
- Metaspace       used 57869K, capacity 62758K, committed 63000K, reserved 1103872K
-  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
-Event: 1192.742 GC heap after
-Heap after GC invocations=391 (full 5):
- PSYoungGen      total 3900416K, used 12270K [0x00000006d1180000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 3887616K, 0% used [0x00000006d1180000,0x00000006d1180000,0x00000007be600000)
-  from space 12800K, 95% used [0x00000007bf380000,0x00000007bff7ba00,0x00000007c0000000)
-  to   space 13312K, 0% used [0x00000007be600000,0x00000007be600000,0x00000007bf300000)
- ParOldGen       total 162304K, used 50177K [0x00000004f3400000, 0x00000004fd280000, 0x00000006d1180000)
-  object space 162304K, 30% used [0x00000004f3400000,0x00000004f6500458,0x00000004fd280000)
- Metaspace       used 57869K, capacity 62758K, committed 63000K, reserved 1103872K
-  class space    used 7001K, capacity 8482K, committed 8488K, reserved 1048576K
-}
-
-Deoptimization events (10 events):
-Event: 1178.582 Thread 0x00007fc241c06800 Uncommon trap: reason=class_check action=maybe_recompile pc=0x0000000112f573c0 method=java.awt.EventQueue.coalesceEvent(Ljava/awt/AWTEvent;I)Z @ 77
-Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
-Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
-Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
-Event: 1194.307 Thread 0x00007fc2427cb800 Uncommon trap: reason=bimorphic action=maybe_recompile pc=0x0000000111e5bb38 method=java.io.DataInputStream.readChar()C @ 4
-Event: 1194.330 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x00000001122b2474 method=java.awt.geom.AffineTransform.updateState()V @ 24
-Event: 1194.340 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d6e5c8 method=java.awt.geom.Path2D$Float.getBounds2D()Ljava/awt/geom/Rectangle2D; @ 8
-Event: 1194.340 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d26e24 method=java.awt.geom.Rectangle2D$Float.isEmpty()Z @ 6
-Event: 1194.344 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d711f0 method=java.awt.geom.Path2D$Float.getBounds2D()Ljava/awt/geom/Rectangle2D; @ 8
-Event: 1194.348 Thread 0x00007fc2427cb800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x0000000112d7bbdc method=java.awt.geom.Path2D$Float.getBounds2D()Ljava/awt/geom/Rectangle2D; @ 8
-
-Classes redefined (0 events):
-No events
-
-Internal exceptions (10 events):
-Event: 261.644 Thread 0x00007fc23a2e9000 Implicit null exception at 0x00000001132d0dd4 to 0x00000001132d1bf5
-Event: 261.943 Thread 0x00007fc23a2e9000 Implicit null exception at 0x000000011341f050 to 0x000000011341fe11
-Event: 261.943 Thread 0x00007fc23a2e9000 Implicit null exception at 0x00000001128a2414 to 0x00000001128a245e
-Event: 263.222 Thread 0x00007fc23a2e9000 Implicit null exception at 0x000000011266b76c to 0x000000011266d1a5
-Event: 1163.695 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000113654cfb to 0x000000011365962d
-Event: 1164.825 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000112e5b170 to 0x0000000112e5b2b1
-Event: 1165.479 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000112d3a255 to 0x0000000112d3a2c5
-Event: 1165.525 Thread 0x00007fc23a2e9000 Implicit null exception at 0x0000000112e12031 to 0x0000000112e120e9
-Event: 1194.348 Thread 0x00007fc2427cb800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException': -1> (0x0000000713279c58) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/interpreter/interpreterRuntime.cpp, line 366]
-Event: 1194.349 Thread 0x00007fc2427cb800 Exception <a 'java/lang/ArrayIndexOutOfBoundsException'> (0x0000000713279c58) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/prims/jni.cpp, line 709]
-
-Events (10 events):
-Event: 1194.346 Executing VM operation: RevokeBias done
-Event: 1194.346 Executing VM operation: RevokeBias
-Event: 1194.346 Executing VM operation: RevokeBias done
-Event: 1194.347 Executing VM operation: RevokeBias
-Event: 1194.347 Executing VM operation: RevokeBias done
-Event: 1194.348 Thread 0x00007fc2427cb800 Uncommon trap: trap_request=0xffffff65 fr.pc=0x0000000112d7bbdc
-Event: 1194.348 Executing VM operation: RevokeBias
-Event: 1194.348 Executing VM operation: RevokeBias done
-Event: 1194.348 Thread 0x00007fc2427cb800 DEOPT PACKING pc=0x0000000112d7bbdc sp=0x000070000fe43250
-Event: 1194.348 Thread 0x00007fc2427cb800 DEOPT UNPACKING pc=0x0000000111d7773a sp=0x000070000fe43090 mode 2
-
-
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-0x000000000f6fa000 	/System/Library/PrivateFrameworks/ProtectedCloudStorage.framework/Versions/A/ProtectedCloudStorage
-0x000000000f6fa000 	/usr/lib/libcurl.4.dylib
-0x000000000f6fa000 	/usr/lib/libcrypto.35.dylib
-0x000000000f6fa000 	/usr/lib/libssl.35.dylib
-0x000000000f6fa000 	/System/Library/Frameworks/LDAP.framework/Versions/A/LDAP
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent
-0x000000000f6fa000 	/usr/lib/libsasl2.2.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/CoreDaemon.framework/Versions/B/CoreDaemon
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/AppleSRP.framework/Versions/A/AppleSRP
-0x000000000f6fa000 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLEngine.bundle/GLEngine
-0x000000000f6fa000 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLProgrammability.dylib
-0x000000013f46f000 	/System/Library/Extensions/AppleIntelSKLGraphicsGLDriver.bundle/Contents/MacOS/AppleIntelSKLGraphicsGLDriver
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libGPUSupportMercury.dylib
-0x000000000f6fa000 	/System/Library/Frameworks/OpenGL.framework/Versions/A/Resources/GLRendererFloat.bundle/GLRendererFloat
-0x000000000f6fa000 	/System/Library/Frameworks/OpenCL.framework/Versions/A/Libraries/libcldcpuengine.dylib
-0x0000000141484000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libsplashscreen.dylib
-0x00000001416dc000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libfontmanager.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/ViewBridge.framework/Versions/A/ViewBridge
-0x0000000141743000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libosxui.dylib
-0x0000000140c85000 	/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/modules/lib/libjnidispatch-422.jnilib
-0x000000013c155000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7252960146856289272/jln2136519246097936140/natives/macosx-universal/libgluegen-rt.jnilib
-0x000000013c15a000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7252960146856289272/jln2136519246097936140/natives/macosx-universal/libnativewindow_awt.jnilib
-0x000000013c15d000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libjawt.dylib
-0x0000000140b17000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7252960146856289272/jln2136519246097936140/natives/macosx-universal/libnativewindow_macosx.jnilib
-0x0000000149ec4000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7252960146856289272/jln2136519246097936140/natives/macosx-universal/libjogl_desktop.jnilib
-0x000000015f50d000 	/private/var/folders/m5/fl6wrs3d7l7_6jbd0xrl5h580000gn/T/jogamp_0000/file_cache/jln7252960146856289272/jln2136519246097936140/natives/macosx-universal/libjogl_mobile.jnilib
-0x0000000140b03000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libmanagement.dylib
-0x000000013d4da000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libdcpr.dylib
-0x0000000160224000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libsunec.dylib
-0x000000013d556000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/libosx.dylib
-0x0000000143427000 	/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/liblcms.dylib
-0x000000000f6fa000 	/System/Library/PrivateFrameworks/login.framework/Versions/A/login
-
-VM Arguments:
-jvm_args: -Djdk.home=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home -Dnetbeans.dirs=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/gephi::/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/plugins_clusters/plugins -Dnetbeans.home=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform -Xms64m -Xmx11468m -Xverify:none -Dsun.java2d.noddraw=true -Dsun.awt.noerasebackground=true -Dnetbeans.indexing.noFileRefresh=true -Dplugin.manager.check.interval=EVERY_DAY -Dnetbeans.logger.console=true -ea -DaddExports:java.desktop/com.apple.eawt=ALL-UNNAMED -DaddExports:java.desktop/sun.awt=ALL-UNNAMED -DaddExports:java.base/jdk.internal.jrtfs=ALL-UNNAMED -DaddExports:java.desktop/apple.laf=ALL-UNNAMED -DaddExports:java.desktop/java.awt.peer=ALL-UNNAMED -DaddExports:java.desktop/com.sun.beans.editors=ALL-UNNAMED -DaddExports:java.desktop/sun.awt.im=ALL-UNNAMED -DaddExports:java.management/sun.management=ALL-UNNAMED -XX:+HeapDumpOnOutOfMemoryError -XX:HeapDumpPath=/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/log/heapdump.hprof 
-java_command: org.netbeans.Main --cachedir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir/var/cache --userdir /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/userdir --branding gephi --branding gephi
-java_class_path (initial): /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/boot.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-modules.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-lookup.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-ui.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ar_SA.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_bg.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ca.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_cs.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_de.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_es.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_fr.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_gl_ES.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_in_ID.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_it.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ja.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/li
-Launcher Type: SUN_STANDARD
-
-Environment Variables:
-JAVA_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home
-PATH=./bin:/usr/local/opt/rbenv/shims:/usr/local/opt/rbenv/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
-LD_LIBRARY_PATH=/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/amd64:/Library/Java/JavaVirtualMachines/jdk1.8.0_171.jdk/Contents/Home/jre/lib/i386:
-SHELL=/bin/zsh
-
-Signal Handlers:
-SIGSEGV: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_ONSTACK|SA_RESTART|SA_SIGINFO
-SIGBUS: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGFPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGPIPE: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGXFSZ: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGILL: [libjvm.dylib+0x48aa90], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGUSR1: SIG_DFL, sa_mask[0]=00000000000000000000000000000000, sa_flags=SA_RESTART
-SIGUSR2: [libjvm.dylib+0x48a5ae], sa_mask[0]=00100000000000000000000000000000, sa_flags=SA_RESTART|SA_SIGINFO
-SIGHUP: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGINT: SIG_IGN, sa_mask[0]=00000000000000000000000000000000, sa_flags=none
-SIGTERM: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-SIGQUIT: [libjvm.dylib+0x488b79], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
-
-
----------------  S Y S T E M  ---------------
-
-OS:Bsduname:Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
-rlimit: STACK 8192k, CORE 0k, NPROC 1418, NOFILE 10240, AS infinity
-load average:5.89 6.97 5.79
-
-CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx
-
-Memory: 4k page, physical 16777216k(15852k free)
-
-/proc/meminfo:
-
-
-vm_info: Java HotSpot(TM) 64-Bit Server VM (25.171-b11) for bsd-amd64 JRE (1.8.0_171-b11), built on Mar 28 2018 12:50:57 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
-
-time: Tue Aug 28 16:30:35 2018
-elapsed time: 1194 seconds (0d 0h 19m 54s)
-

From cc5b0b61d74308d16932caf14613fab5ddc0f2ff Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Tue, 28 Aug 2018 17:28:27 +0100
Subject: [PATCH 21/32] Delete hs_err_pid44976.log

---
 hs_err_pid44976.log | 707 --------------------------------------------
 1 file changed, 707 deletions(-)
 delete mode 100644 hs_err_pid44976.log

diff --git a/hs_err_pid44976.log b/hs_err_pid44976.log
deleted file mode 100644
index 3d6fe11..0000000
--- a/hs_err_pid44976.log
+++ /dev/null
@@ -1,707 +0,0 @@
-#
-# A fatal error has been detected by the Java Runtime Environment:
-#
-#  SIGILL (0x4) at pc=0x00007fff48537454, pid=44976, tid=0x0000000000000307
-#
-# JRE version: Java(TM) SE Runtime Environment (8.0_171-b11) (build 1.8.0_171-b11)
-# Java VM: Java HotSpot(TM) 64-Bit Server VM (25.171-b11 mixed mode bsd-amd64 compressed oops)
-# Problematic frame:
-# C  [AppKit+0x36c454]  -[NSApplication _crashOnException:]+0x6d
-#
-# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
-#
-# If you would like to submit a bug report, please visit:
-#   http://bugreport.java.com/bugreport/crash.jsp
-# The crash happened outside the Java Virtual Machine in native code.
-# See problematic frame for where to report the bug.
-#
-
----------------  T H R E A D  ---------------
-
-Current thread (0x00007f8b6587a000):  JavaThread "AWT-AppKit" daemon [_thread_in_native, id=775, stack(0x00007ffee1e1f000,0x00007ffee261f000)]
-
-siginfo: si_signo: 4 (SIGILL), si_code: 1 (ILL_ILLOPC), si_addr: 0x00007fff48537454
-
-Registers:
-RAX=0x00007f8b65737200, RBX=0x00007f8b697977f0, RCX=0x0000000000000000, RDX=0x0000000000000ead
-RSP=0x00007ffee2616e90, RBP=0x00007ffee2616ea0, RSI=0x00007f8b6c266ea1, RDI=0x0000000008000101
-R8 =0x0000000000000000, R9 =0x0000000000000000, R10=0x00007ffee2616998, R11=0xfffffffff94d11ff
-R12=0x00007f8b694bc200, R13=0x00007f8b65391068, R14=0x00007fff71e8ae80, R15=0x00007fff4ac8f6d0
-RIP=0x00007fff48537454, EFLAGS=0x0000000000010206, ERR=0x0000000000000000
-  TRAPNO=0x0000000000000006
-
-Top of Stack: (sp=0x00007ffee2616e90)
-0x00007ffee2616e90:   00007f8b6d99efc0 00007f8b6d8bfb70
-0x00007ffee2616ea0:   00007ffee2616fd0 00007fff48b03cb1
-0x00007ffee2616eb0:   0000000000000003 00007f8b644f29d0
-0x00007ffee2616ec0:   000000010d5fe080 000000010d5fe080
-0x00007ffee2616ed0:   00007ffee2616f60 00007fff72c7275a
-0x00007ffee2616ee0:   000000010d600a00 0000000100000002
-0x00007ffee2616ef0:   00007f8b6d9a2b80 00007f8b6d9fc080
-0x00007ffee2616f00:   00007ffee2616f60 0000000000000010
-0x00007ffee2616f10:   0000000000000001 00007f8b6d9a2b80
-0x00007ffee2616f20:   000000010d5fe080 00007f8b6d900000
-0x00007ffee2616f30:   000000010d601e00 0000000000000002
-0x00007ffee2616f40:   000000010d601e00 0000000000000003
-0x00007ffee2616f50:   000000010d5fe080 00007f8b6d900000
-0x00007ffee2616f60:   00007ffee2616fc0 00007fff72c73256
-0x00007ffee2616f70:   00007fffab488a80 00007f8b64600000
-0x00007ffee2616f80:   0000000000001400 0000000000000001
-0x00007ffee2616f90:   000000002b3100c5 00007f8b6d8bfb70
-0x00007ffee2616fa0:   7debe043e91500fd 00007f8b694bc200
-0x00007ffee2616fb0:   0000000000000002 00007f8b694bc208
-0x00007ffee2616fc0:   0000000000000000 00007fff4ac8f6d0
-0x00007ffee2616fd0:   00007ffee2616fe0 00007fff4ac8f417
-0x00007ffee2616fe0:   00007ffee26170b0 00007fff4ac8f33f
-0x00007ffee2616ff0:   00007f8b694bc200 00007f8b64600070
-0x00007ffee2617000:   00007fffa4e79f90 00007f8b64600200
-0x00007ffee2617010:   00007ffee26170b0 00007fff4ac8f19e
-0x00007ffee2617020:   0000000000000003 0000000500002d8a
-0x00007ffee2617030:   00007f8b64600200 00007f8b64600070
-0x00007ffee2617040:   00007ffee2617020 00007ffee2616ff0
-0x00007ffee2617050:   00007f8b64600210 00007f8b64600080
-0x00007ffee2617060:   00007f8b6d8bfb70 0000000000000002
-0x00007ffee2617070:   0000000000000001 00007ffee2616ff0
-0x00007ffee2617080:   7debe043e91500fd 00007f8b64600200 
-
-Instructions: (pc=0x00007fff48537454)
-0x00007fff48537434:   48 89 c7 ff 15 2b ad f4 5b 48 8b 35 4c b7 24 5c
-0x00007fff48537444:   48 89 c7 ff 15 1b ad f4 5b 48 89 05 cc 68 2c 5c
-0x00007fff48537454:   0f 0b 48 89 c7 e8 f0 3a 8a 00 31 ff 31 f6 31 c0
-0x00007fff48537464:   e8 28 89 e4 ff e8 04 3b 8a 00 48 89 c3 e8 f0 3a 
-
-Register to memory mapping:
-
-RAX=0x00007f8b65737200 is an unknown value
-RBX=0x00007f8b697977f0 is an unknown value
-RCX=0x0000000000000000 is an unknown value
-RDX=0x0000000000000ead is an unknown value
-RSP=0x00007ffee2616e90 is pointing into the stack for thread: 0x00007f8b6587a000
-RBP=0x00007ffee2616ea0 is pointing into the stack for thread: 0x00007f8b6587a000
-RSI=0x00007f8b6c266ea1 is an unknown value
-RDI=0x0000000008000101 is an unknown value
-R8 =0x0000000000000000 is an unknown value
-R9 =0x0000000000000000 is an unknown value
-R10=0x00007ffee2616998 is pointing into the stack for thread: 0x00007f8b6587a000
-R11=0xfffffffff94d11ff is an unknown value
-R12=0x00007f8b694bc200 is an unknown value
-R13=0x00007f8b65391068 is an unknown value
-R14=0x00007fff71e8ae80: objc_msgSend+0 in /usr/lib/libobjc.A.dylib at 0x00007fff71e84000
-R15=0x00007fff4ac8f6d0: _runLoopObserverWithBlockContext+0 in /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation at 0x00007fff4abec000
-
-
-Stack: [0x00007ffee1e1f000,0x00007ffee261f000],  sp=0x00007ffee2616e90,  free space=8159k
-Native frames: (J=compiled Java code, j=interpreted, Vv=VM code, C=native code)
-C  [AppKit+0x36c454]  -[NSApplication _crashOnException:]+0x6d
-C  [AppKit+0x938cb1]  __65+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayRefresh]_block_invoke+0x35a
-C  [CoreFoundation+0xa3417]  __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__+0x17
-C  [CoreFoundation+0xa333f]  __CFRunLoopDoObservers+0x20f
-C  [CoreFoundation+0x858b8]  __CFRunLoopRun+0x4d8
-C  [CoreFoundation+0x85153]  CFRunLoopRunSpecific+0x1e3
-C  [HIToolbox+0x2fd96]  RunCurrentEventLoopInMode+0x11e
-C  [HIToolbox+0x2fb06]  ReceiveNextEventCommon+0x265
-C  [HIToolbox+0x2f884]  _BlockUntilNextEventMatchingListInModeWithFilter+0x40
-C  [AppKit+0x41a73]  _DPSNextEvent+0x825
-C  [AppKit+0x7d7e34]  -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:]+0xbe4
-C  [libosxapp.dylib+0x2328]  -[NSApplicationAWT nextEventMatchingMask:untilDate:inMode:dequeue:]+0x7c
-C  [AppKit+0x36885]  -[NSApplication run]+0x2fc
-C  [libosxapp.dylib+0x1f72]  +[NSApplicationAWT runAWTLoopWithApp:]+0x9c
-C  [libawt_lwawt.dylib+0x4711f]  -[AWTStarter starter:]+0x389
-C  [Foundation+0x682b5]  __NSThreadPerformPerform+0x14e
-C  [CoreFoundation+0xa3a11]  __CFRUNLOOP_IS_CALLING_OUT_TO_A_SOURCE0_PERFORM_FUNCTION__+0x11
-C  [CoreFoundation+0x15d42c]  __CFRunLoopDoSource0+0x6c
-C  [CoreFoundation+0x86470]  __CFRunLoopDoSources0+0xd0
-C  [CoreFoundation+0x858ed]  __CFRunLoopRun+0x50d
-C  [CoreFoundation+0x85153]  CFRunLoopRunSpecific+0x1e3
-C  [java+0x6472]  CreateExecutionEnvironment+0x367
-C  [java+0x207c]  JLI_Launch+0x7a0
-C  [java+0x84cf]  main+0x65
-C  [java+0x18d4]  start+0x34
-C  0x0000000000000024
-
-
----------------  P R O C E S S  ---------------
-
-Java Threads: ( => current thread )
-  0x00007f8b6cd1b800 JavaThread "SwingWorker-pool-2-thread-10" daemon [_thread_blocked, id=123403, stack(0x000070000818b000,0x000070000828b000)]
-  0x00007f8b6550b800 JavaThread "SwingWorker-pool-2-thread-9" daemon [_thread_blocked, id=95235, stack(0x0000700008088000,0x0000700008188000)]
-  0x00007f8b6b1a4000 JavaThread "SwingWorker-pool-2-thread-8" daemon [_thread_blocked, id=123927, stack(0x0000700007f85000,0x0000700008085000)]
-  0x00007f8b64f7f800 JavaThread "SwingWorker-pool-2-thread-7" daemon [_thread_blocked, id=124419, stack(0x0000700007e82000,0x0000700007f82000)]
-  0x00007f8b6550b000 JavaThread "SwingWorker-pool-2-thread-6" daemon [_thread_blocked, id=124939, stack(0x0000700007d7f000,0x0000700007e7f000)]
-  0x00007f8b6d22f000 JavaThread "SwingWorker-pool-2-thread-5" daemon [_thread_blocked, id=125463, stack(0x0000700007c7c000,0x0000700007d7c000)]
-  0x00007f8b6b1a6800 JavaThread "SwingWorker-pool-2-thread-4" daemon [_thread_blocked, id=125959, stack(0x0000700007b79000,0x0000700007c79000)]
-  0x00007f8b6d077000 JavaThread "SwingWorker-pool-2-thread-3" daemon [_thread_blocked, id=91927, stack(0x0000700007a76000,0x0000700007b76000)]
-  0x00007f8b6b1a6000 JavaThread "SwingWorker-pool-2-thread-2" daemon [_thread_blocked, id=128507, stack(0x0000700007973000,0x0000700007a73000)]
-  0x00007f8b6d076000 JavaThread "SwingWorker-pool-2-thread-1" daemon [_thread_blocked, id=126251, stack(0x0000700006fd2000,0x00007000070d2000)]
-  0x00007f8b6afc3000 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=127303, stack(0x00007000072db000,0x00007000073db000)]
-  0x00007f8b6d0d5800 JavaThread "Thread-13" [_thread_blocked, id=92939, stack(0x0000700007870000,0x0000700007970000)]
-  0x00007f8b650cc000 JavaThread "AppearanceColumnObserver" daemon [_thread_blocked, id=126735, stack(0x000070000776d000,0x000070000786d000)]
-  0x00007f8b6a1bf000 JavaThread "Context Refresh Thread" daemon [_thread_blocked, id=91175, stack(0x000070000766a000,0x000070000776a000)]
-  0x00007f8b6bb6c800 JavaThread "Project IO" [_thread_blocked, id=91395, stack(0x00007000073de000,0x00007000074de000)]
-  0x00007f8b650dd800 JavaThread "Keep-Alive-Timer" daemon [_thread_blocked, id=128851, stack(0x00007000071d8000,0x00007000072d8000)]
-  0x00007f8b64918800 JavaThread "Timer-0" daemon [_thread_blocked, id=88867, stack(0x00007000070d5000,0x00007000071d5000)]
-  0x00007f8b65d99800 JavaThread "DataLaboratoryGraphObservers" [_thread_blocked, id=77575, stack(0x0000700006228000,0x0000700006328000)]
-  0x00007f8b64946800 JavaThread "DestroyJavaVM" [_thread_blocked, id=9475, stack(0x0000700004e69000,0x0000700004f69000)]
-  0x00007f8b6561b000 JavaThread "Flushing caches" [_thread_blocked, id=130575, stack(0x0000700006e4c000,0x0000700006f4c000)]
-  0x00007f8b6a241800 JavaThread "Inactive RequestProcessor thread [Was:OpenIDE-request-processor-1/org.netbeans.core.startup.preferences.NbPreferences$1]" daemon [_thread_blocked, id=64515, stack(0x0000700006d49000,0x0000700006e49000)]
-  0x00007f8b6b01e800 JavaThread "TimerQueue" daemon [_thread_blocked, id=64259, stack(0x0000700006c46000,0x0000700006d46000)]
-  0x00007f8b64f19800 JavaThread "Thread-5" daemon [_thread_blocked, id=65035, stack(0x0000700006b43000,0x0000700006c43000)]
-  0x00007f8b65993000 JavaThread "Image Fetcher 0" daemon [_thread_blocked, id=63507, stack(0x0000700006a40000,0x0000700006b40000)]
-  0x00007f8b65aa4000 JavaThread "File Watcher" daemon [_thread_blocked, id=67595, stack(0x000070000693d000,0x0000700006a3d000)]
-  0x00007f8b65d50800 JavaThread "Thread-1" daemon [_thread_in_native, id=69151, stack(0x000070000683a000,0x000070000693a000)]
-  0x00007f8b66237000 JavaThread "Inactive RequestProcessor thread [Was:Folder recognizer/org.openide.loaders.FolderList$ListTask]" daemon [_thread_blocked, id=71531, stack(0x0000700006737000,0x0000700006837000)]
-  0x00007f8b6611a000 JavaThread "AWT-EventQueue-0" [_thread_in_native, id=74503, stack(0x0000700006634000,0x0000700006734000)]
-  0x00007f8b65445000 JavaThread "Java2D Disposer" daemon [_thread_blocked, id=53011, stack(0x0000700006531000,0x0000700006631000)]
-  0x00007f8b64ee0800 JavaThread "Java2D Queue Flusher" daemon [_thread_blocked, id=52487, stack(0x000070000642e000,0x000070000652e000)]
-  0x00007f8b66145800 JavaThread "RequestProcessor queue manager" daemon [_thread_blocked, id=77319, stack(0x000070000632b000,0x000070000642b000)]
-  0x00007f8b65903800 JavaThread "Inactive RequestProcessor thread [Was:Asynch children creator /org.openide.nodes.AsynchChildren]" daemon [_thread_blocked, id=82439, stack(0x0000700006125000,0x0000700006225000)]
-  0x00007f8b64e02800 JavaThread "AWT-Shutdown" [_thread_blocked, id=25387, stack(0x0000700005e99000,0x0000700005f99000)]
-=>0x00007f8b6587a000 JavaThread "AWT-AppKit" daemon [_thread_in_native, id=775, stack(0x00007ffee1e1f000,0x00007ffee261f000)]
-  0x00007f8b65361800 JavaThread "CLI Requests Server" daemon [_thread_in_native, id=16643, stack(0x0000700005d96000,0x0000700005e96000)]
-  0x00007f8b6535e800 JavaThread "Active Reference Queue Daemon" daemon [_thread_blocked, id=16899, stack(0x0000700005c93000,0x0000700005d93000)]
-  0x00007f8b65037000 JavaThread "Service Thread" daemon [_thread_blocked, id=14595, stack(0x0000700005a8d000,0x0000700005b8d000)]
-  0x00007f8b65036800 JavaThread "C1 CompilerThread2" daemon [_thread_blocked, id=14083, stack(0x000070000598a000,0x0000700005a8a000)]
-  0x00007f8b65016800 JavaThread "C2 CompilerThread1" daemon [_thread_blocked, id=13571, stack(0x0000700005887000,0x0000700005987000)]
-  0x00007f8b64848800 JavaThread "C2 CompilerThread0" daemon [_thread_in_native, id=13059, stack(0x0000700005784000,0x0000700005884000)]
-  0x00007f8b64847800 JavaThread "Signal Dispatcher" daemon [_thread_blocked, id=17927, stack(0x0000700005681000,0x0000700005781000)]
-  0x00007f8b64841000 JavaThread "Finalizer" daemon [_thread_blocked, id=20739, stack(0x000070000557e000,0x000070000567e000)]
-  0x00007f8b6580e800 JavaThread "Reference Handler" daemon [_thread_blocked, id=11779, stack(0x000070000547b000,0x000070000557b000)]
-
-Other Threads:
-  0x00007f8b6483c000 VMThread [stack: 0x0000700005378000,0x0000700005478000] [id=21251]
-  0x00007f8b65000000 WatcherThread [stack: 0x0000700005b90000,0x0000700005c90000] [id=17411]
-
-VM state:not at safepoint (normal execution)
-
-VM Mutex/Monitor currently owned by a thread: None
-
-Heap:
- PSYoungGen      total 132096K, used 25330K [0x00000007b5580000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 112640K, 6% used [0x00000007b5580000,0x00000007b5c588f8,0x00000007bc380000)
-  from space 19456K, 94% used [0x00000007bc380000,0x00000007bd563f30,0x00000007bd680000)
-  to   space 22016K, 0% used [0x00000007bea80000,0x00000007bea80000,0x00000007c0000000)
- ParOldGen       total 110080K, used 59392K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
-  object space 110080K, 53% used [0x00000007a0000000,0x00000007a3a00398,0x00000007a6b80000)
- Metaspace       used 54664K, capacity 59482K, committed 59816K, reserved 1101824K
-  class space    used 6797K, capacity 8247K, committed 8360K, reserved 1048576K
-
-Card table byte_map: [0x000000010d6b1000,0x000000010d7b2000] byte_map_base: 0x00000001099b1000
-
-Marking Bits: (ParMarkBitMap*) 0x000000010e8f76e0
- Begin Bits: [0x000000010f419000, 0x000000010fc19000)
- End Bits:   [0x000000010fc19000, 0x0000000110419000)
-
-Polling page: 0x000000010d65e000
-
-CodeCache: size=245760Kb used=18815Kb max_used=19035Kb free=226945Kb
- bounds [0x000000011a969000, 0x000000011bc29000, 0x0000000129969000]
- total_blobs=7232 nmethods=6116 adapters=1022
- compilation: enabled
-
-Compilation events (10 events):
-Event: 13.777 Thread 0x00007f8b65036800 7258       1       org.netbeans.core.windows.ModeStructureSnapshot$ModeSnapshot::getBounds (5 bytes)
-Event: 13.777 Thread 0x00007f8b65036800 nmethod 7258 0x000000011b42e6d0 code [0x000000011b42e820, 0x000000011b42e930]
-Event: 13.777 Thread 0x00007f8b65036800 7259       1       org.netbeans.core.windows.view.ModeStructureAccessorImpl$SlidingAccessorImpl::getSlideInSizes (5 bytes)
-Event: 13.777 Thread 0x00007f8b65036800 nmethod 7259 0x000000011b42e410 code [0x000000011b42e560, 0x000000011b42e670]
-Event: 13.778 Thread 0x00007f8b64848800 nmethod 7256 0x000000011b099890 code [0x000000011b0999e0, 0x000000011b099a88]
-Event: 13.780 Thread 0x00007f8b65036800 7260       1       org.netbeans.swing.tabcontrol.TabbedContainer::getType (5 bytes)
-Event: 13.780 Thread 0x00007f8b65036800 nmethod 7260 0x000000011ae69410 code [0x000000011ae69560, 0x000000011ae69670]
-Event: 13.782 Thread 0x00007f8b65036800 7261       3       com.apple.laf.AquaButtonUI$AquaButtonListener::updateDefaultButton (60 bytes)
-Event: 13.783 Thread 0x00007f8b65036800 nmethod 7261 0x000000011b3089d0 code [0x000000011b308bc0, 0x000000011b3096a8]
-Event: 13.785 Thread 0x00007f8b64848800 7262       4       java.awt.Component::getHWPeerAboveMe (90 bytes)
-
-GC Heap History (10 events):
-Event: 7.914 GC heap before
-{Heap before GC invocations=12 (full 2):
- PSYoungGen      total 76800K, used 75482K [0x00000007b5580000, 0x00000007bbe80000, 0x00000007c0000000)
-  eden space 70144K, 100% used [0x00000007b5580000,0x00000007b9a00000,0x00000007b9a00000)
-  from space 6656K, 80% used [0x00000007b9a00000,0x00000007b9f36a30,0x00000007ba080000)
-  to   space 6656K, 0% used [0x00000007bb800000,0x00000007bb800000,0x00000007bbe80000)
- ParOldGen       total 51712K, used 12901K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
-  object space 51712K, 24% used [0x00000007a0000000,0x00000007a0c99768,0x00000007a3280000)
- Metaspace       used 48041K, capacity 51778K, committed 52008K, reserved 1093632K
-  class space    used 5858K, capacity 6918K, committed 6952K, reserved 1048576K
-Event: 7.935 GC heap after
-Heap after GC invocations=12 (full 2):
- PSYoungGen      total 95232K, used 6652K [0x00000007b5580000, 0x00000007bc780000, 0x00000007c0000000)
-  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
-  from space 6656K, 99% used [0x00000007bb800000,0x00000007bbe7f328,0x00000007bbe80000)
-  to   space 12288K, 0% used [0x00000007bac00000,0x00000007bac00000,0x00000007bb800000)
- ParOldGen       total 51712K, used 25758K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
-  object space 51712K, 49% used [0x00000007a0000000,0x00000007a1927a30,0x00000007a3280000)
- Metaspace       used 48041K, capacity 51778K, committed 52008K, reserved 1093632K
-  class space    used 5858K, capacity 6918K, committed 6952K, reserved 1048576K
-}
-Event: 8.392 GC heap before
-{Heap before GC invocations=13 (full 2):
- PSYoungGen      total 95232K, used 95228K [0x00000007b5580000, 0x00000007bc780000, 0x00000007c0000000)
-  eden space 88576K, 100% used [0x00000007b5580000,0x00000007bac00000,0x00000007bac00000)
-  from space 6656K, 99% used [0x00000007bb800000,0x00000007bbe7f328,0x00000007bbe80000)
-  to   space 12288K, 0% used [0x00000007bac00000,0x00000007bac00000,0x00000007bb800000)
- ParOldGen       total 51712K, used 25758K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
-  object space 51712K, 49% used [0x00000007a0000000,0x00000007a1927a30,0x00000007a3280000)
- Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
-  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
-Event: 8.420 GC heap after
-Heap after GC invocations=13 (full 2):
- PSYoungGen      total 100864K, used 12266K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
-  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
-  from space 12288K, 99% used [0x00000007bac00000,0x00000007bb7fa810,0x00000007bb800000)
-  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
- ParOldGen       total 51712K, used 42401K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
-  object space 51712K, 81% used [0x00000007a0000000,0x00000007a29686f0,0x00000007a3280000)
- Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
-  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
-}
-Event: 8.421 GC heap before
-{Heap before GC invocations=14 (full 3):
- PSYoungGen      total 100864K, used 12266K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
-  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
-  from space 12288K, 99% used [0x00000007bac00000,0x00000007bb7fa810,0x00000007bb800000)
-  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
- ParOldGen       total 51712K, used 42401K [0x00000007a0000000, 0x00000007a3280000, 0x00000007b5580000)
-  object space 51712K, 81% used [0x00000007a0000000,0x00000007a29686f0,0x00000007a3280000)
- Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
-  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
-Event: 8.673 GC heap after
-Heap after GC invocations=14 (full 3):
- PSYoungGen      total 100864K, used 989K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
-  eden space 88576K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bac00000)
-  from space 12288K, 8% used [0x00000007bac00000,0x00000007bacf7618,0x00000007bb800000)
-  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
- ParOldGen       total 110080K, used 51241K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
-  object space 110080K, 46% used [0x00000007a0000000,0x00000007a320a5b8,0x00000007a6b80000)
- Metaspace       used 49264K, capacity 53166K, committed 53288K, reserved 1095680K
-  class space    used 6037K, capacity 7110K, committed 7208K, reserved 1048576K
-}
-Event: 9.523 GC heap before
-{Heap before GC invocations=15 (full 3):
- PSYoungGen      total 100864K, used 89565K [0x00000007b5580000, 0x00000007bf000000, 0x00000007c0000000)
-  eden space 88576K, 100% used [0x00000007b5580000,0x00000007bac00000,0x00000007bac00000)
-  from space 12288K, 8% used [0x00000007bac00000,0x00000007bacf7618,0x00000007bb800000)
-  to   space 19968K, 0% used [0x00000007bdc80000,0x00000007bdc80000,0x00000007bf000000)
- ParOldGen       total 110080K, used 51241K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
-  object space 110080K, 46% used [0x00000007a0000000,0x00000007a320a5b8,0x00000007a6b80000)
- Metaspace       used 50999K, capacity 55474K, committed 55848K, reserved 1097728K
-  class space    used 6291K, capacity 7599K, committed 7720K, reserved 1048576K
-Event: 9.538 GC heap after
-Heap after GC invocations=15 (full 3):
- PSYoungGen      total 125952K, used 5892K [0x00000007b5580000, 0x00000007be980000, 0x00000007c0000000)
-  eden space 112640K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bc380000)
-  from space 13312K, 44% used [0x00000007bdc80000,0x00000007be241160,0x00000007be980000)
-  to   space 19456K, 0% used [0x00000007bc380000,0x00000007bc380000,0x00000007bd680000)
- ParOldGen       total 110080K, used 51265K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
-  object space 110080K, 46% used [0x00000007a0000000,0x00000007a32105b8,0x00000007a6b80000)
- Metaspace       used 50999K, capacity 55474K, committed 55848K, reserved 1097728K
-  class space    used 6291K, capacity 7599K, committed 7720K, reserved 1048576K
-}
-Event: 13.662 GC heap before
-{Heap before GC invocations=16 (full 3):
- PSYoungGen      total 125952K, used 118532K [0x00000007b5580000, 0x00000007be980000, 0x00000007c0000000)
-  eden space 112640K, 100% used [0x00000007b5580000,0x00000007bc380000,0x00000007bc380000)
-  from space 13312K, 44% used [0x00000007bdc80000,0x00000007be241160,0x00000007be980000)
-  to   space 19456K, 0% used [0x00000007bc380000,0x00000007bc380000,0x00000007bd680000)
- ParOldGen       total 110080K, used 51265K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
-  object space 110080K, 46% used [0x00000007a0000000,0x00000007a32105b8,0x00000007a6b80000)
- Metaspace       used 54598K, capacity 59322K, committed 59432K, reserved 1099776K
-  class space    used 6795K, capacity 8215K, committed 8232K, reserved 1048576K
-Event: 13.687 GC heap after
-Heap after GC invocations=16 (full 3):
- PSYoungGen      total 132096K, used 18319K [0x00000007b5580000, 0x00000007c0000000, 0x00000007c0000000)
-  eden space 112640K, 0% used [0x00000007b5580000,0x00000007b5580000,0x00000007bc380000)
-  from space 19456K, 94% used [0x00000007bc380000,0x00000007bd563f30,0x00000007bd680000)
-  to   space 22016K, 0% used [0x00000007bea80000,0x00000007bea80000,0x00000007c0000000)
- ParOldGen       total 110080K, used 59392K [0x00000007a0000000, 0x00000007a6b80000, 0x00000007b5580000)
-  object space 110080K, 53% used [0x00000007a0000000,0x00000007a3a00398,0x00000007a6b80000)
- Metaspace       used 54598K, capacity 59322K, committed 59432K, reserved 1099776K
-  class space    used 6795K, capacity 8215K, committed 8232K, reserved 1048576K
-}
-
-Deoptimization events (10 events):
-Event: 11.972 Thread 0x00007f8b6611a000 Uncommon trap: reason=class_check action=maybe_recompile pc=0x000000011b690030 method=java.io.DataInputStream.readUnsignedByte()I @ 4
-Event: 12.085 Thread 0x00007f8b6611a000 Uncommon trap: reason=predicate action=maybe_recompile pc=0x000000011b33e0d4 method=java.lang.String.regionMatches(ZILjava/lang/String;II)Z @ 63
-Event: 12.085 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b66598c method=sun.java2d.pipe.RegionSpanIterator.nextSpan([I)Z @ 13
-Event: 13.451 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b858edc method=com.apple.laf.AquaUtils$IconImageFilter.grayTransform(II)I @ 5
-Event: 13.451 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b2bd818 method=com.apple.laf.AquaUtils$IconImageFilter.grayTransform(II)I @ 5
-Event: 13.458 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b45b10c method=java.awt.Toolkit$SelectiveAWTEventListener.eventDispatched(Ljava/awt/AWTEvent;)V @ 195
-Event: 13.721 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b1b7af8 method=java.lang.ThreadLocal$ThreadLocalMap.set(Ljava/lang/ThreadLocal;Ljava/lang/Object;)V @ 119
-Event: 13.760 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b8dae00 method=org.openide.util.lookup.InheritanceTree.registerInterface(Lorg/openide/util/lookup/AbstractLookup$Pair;Ljava/util/Collection;)Z @ 62
-Event: 13.761 Thread 0x00007f8b6611a000 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011b792998 method=javax.swing.RepaintManager.addDirtyRegion0(Ljava/awt/Container;IIII)V @ 19
-Event: 13.766 Thread 0x00007f8b6a241800 Uncommon trap: reason=unstable_if action=reinterpret pc=0x000000011bbf5c64 method=org.openide.util.WeakListenerImpl.get(Ljava/util/EventObject;)Ljava/util/EventListener; @ 9
-
-Classes redefined (0 events):
-No events
-
-Internal exceptions (10 events):
-Event: 9.540 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x00000007b5581cc8) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 9.542 Thread 0x00007f8b6611a000 Implicit null exception at 0x000000011acf4b0c to 0x000000011acf4b89
-Event: 9.549 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/DoubleEditor> (0x00000007b560a398) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 11.001 Thread 0x00007f8b66644800 Implicit null exception at 0x000000011b82fe94 to 0x000000011b83215d
-Event: 11.178 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b84b9478) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 11.190 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b84fb130) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 11.199 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/awt/FontEditor> (0x00000007b851e038) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 11.208 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b8561c30) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 11.210 Thread 0x00007f8b6611a000 Exception <a 'java/lang/ClassNotFoundException': java/lang/FloatEditor> (0x00000007b857b770) thrown at [/Users/java_re/workspace/8-2-build-macosx-x86_64/jdk8u171/10807/hotspot/src/share/vm/classfile/systemDictionary.cpp, line 210]
-Event: 13.766 Thread 0x00007f8b6a241800 Implicit null exception at 0x000000011bbf5996 to 0x000000011bbf5c41
-
-Events (10 events):
-Event: 13.766 Executing VM operation: RevokeBias
-Event: 13.766 Executing VM operation: RevokeBias done
-Event: 13.770 Executing VM operation: RevokeBias
-Event: 13.770 Executing VM operation: RevokeBias done
-Event: 13.771 Executing VM operation: RevokeBias
-Event: 13.771 Executing VM operation: RevokeBias done
-Event: 13.771 Executing VM operation: RevokeBias
-Event: 13.771 Executing VM operation: RevokeBias done
-Event: 13.772 Executing VM operation: RevokeBias
-Event: 13.772 Executing VM operation: RevokeBias done
-
-
-Dynamic libraries:
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-java_class_path (initial): /Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/boot.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-modules.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-lookup.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util-ui.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/org-openide-util.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ar_SA.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_bg.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ca.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_cs.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_de.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_es.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_fr.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_gl_ES.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_in_ID.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_it.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/lib/locale/boot_ja.jar:/Users/julianne/ImperialComputingMScFinal/gephi-plugins-bootcamp/target/gephi-0.9.2/platform/li
-Launcher Type: SUN_STANDARD
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-PATH=./bin:/usr/local/opt/rbenv/shims:/usr/local/opt/rbenv/bin:/Library/Frameworks/Python.framework/Versions/3.6/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin
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-SHELL=/bin/zsh
-
-Signal Handlers:
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-SIGBUS: [libjvm.dylib+0x5b512d], sa_mask[0]=11111111011111110111111111111111, sa_flags=SA_RESTART|SA_SIGINFO
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-
-
----------------  S Y S T E M  ---------------
-
-OS:Bsduname:Darwin 17.7.0 Darwin Kernel Version 17.7.0: Thu Jun 21 22:53:14 PDT 2018; root:xnu-4570.71.2~1/RELEASE_X86_64 x86_64
-rlimit: STACK 8192k, CORE 0k, NPROC 1418, NOFILE 10240, AS infinity
-load average:6.54 5.20 4.83
-
-CPU:total 4 (initial active 4) (2 cores per cpu, 2 threads per core) family 6 model 78 stepping 3, cmov, cx8, fxsr, mmx, sse, sse2, sse3, ssse3, sse4.1, sse4.2, popcnt, avx, avx2, aes, clmul, erms, 3dnowpref, lzcnt, ht, tsc, tscinvbit, bmi1, bmi2, adx
-
-Memory: 4k page, physical 16777216k(2131984k free)
-
-/proc/meminfo:
-
-
-vm_info: Java HotSpot(TM) 64-Bit Server VM (25.171-b11) for bsd-amd64 JRE (1.8.0_171-b11), built on Mar 28 2018 12:50:57 by "java_re" with gcc 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
-
-time: Tue Aug 21 20:41:13 2018
-elapsed time: 13 seconds (0d 0h 0m 13s)
-

From 264551ed8525870a321e91737f91239254a430f5 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Wed, 29 Aug 2018 20:33:53 +0100
Subject: [PATCH 22/32] code cleaned up a little bit and differences heat map
 finished

---
 .../layout/NodeWeight/ForceAtlas2.java        | 433 +++++++++++-------
 .../layout/NodeWeight/Bundle.properties       |   2 +
 2 files changed, 260 insertions(+), 175 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 70bfe1d..cf9ca45 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -76,6 +76,7 @@ Development and Distribution License("CDDL") (collectively, the
 import java.util.concurrent.Future;
 import java.util.Comparator;
 import java.util.Map;
+import java.util.Arrays;
 
 
 
@@ -115,6 +116,7 @@ public class ForceAtlas2 implements Layout {
     private double barnesHutTheta;
     private boolean linLogMode;
     private boolean strongGravityMode;
+    private boolean heatMapChangeMode;
     private boolean heatMapMode;
     private int threadCount;
     private int currentThreadCount;
@@ -203,20 +205,20 @@ public void initAlgo() {
         }
     }
 
-    // public static int[] calcHistogram(double[] data, double min, double max, int numBins) {
-    //   final int[] result = new int[numBins];
-    //   final double binSize = (max - min)/numBins;
+    public static int[] calcHistogram(double[] data, double min, double max, int numBins) {
+      final int[] result = new int[numBins];
+      final double binSize = (max - min)/numBins;
 
-    //   for (double d : data) {
-    //     int bin = (int) ((d - min) / binSize);
-    //     if (bin < 0) { /* this data is smaller than min */ }
-    //     else if (bin >= numBins) { /* this data point is bigger than max */ }
-    //     else {
-    //       result[bin] += 1;
-    //     }
-    //   }
-    //   return result;
-    // }
+      for (double d : data) {
+        int bin = (int) ((d - min) / binSize);
+        if (bin < 0) { /* this data is smaller than min */ }
+        else if (bin >= numBins) { /* this data point is bigger than max */ }
+        else {
+          result[bin] += 1;
+        }
+      }
+      return result;
+    }
 
 
 
@@ -254,7 +256,16 @@ private boolean hasNodeWeight(Node node) {
       }
     }
 
-
+    private double getNodeWeightChange(Node node, boolean isDynamicNodeWeight, Interval interval, Double weight) {
+      if (interval.getLow() != Interval.INFINITY_INTERVAL.getLow()) {
+        TimestampMap map = (TimestampMap) node.getAttribute(this.nodeWeightColumnName);
+        Interval prev_interval = new Interval (Interval.INFINITY_INTERVAL.getLow(), interval.getLow());
+        Double last_value = (Double) map.get(prev_interval, Estimator.LAST);
+        Double change = weight - last_value;
+        return change;
+      }
+      return 0.0;
+    }
 
     private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
 
@@ -277,127 +288,7 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
-
-    // private void setterMinWeight(Node[] nodes) {
-    //   Double min;
-
-    //   // seed min value from data
-    //   TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(this.nodeWeightColumnName);
-    //   double[] seed_weights = seed_map.toDoubleArray();
-    //   min = seed_weights[0];
-
-    //   for (Node n: nodes) {
-    //     TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
-    //     double[] weights = map.toDoubleArray();
-
-    //     for (Double wt: weights) {
-    //       if (wt < min) {
-    //         min = wt;
-    //       }
-
-    //     }
-    //   }
-    //   // System.out.println("");
-    //   // System.out.println("----------------------------");
-    //   // System.out.println("MIN: " +  min );
-    //   // System.out.println("----------------------------");
-    //   // System.out.println("");
-    //   this.minWeight = min;
-    // }
-
-    // private void setterMaxWeight(Node[] nodes) {
-    //     Double max;
-    //     String column_name = this.nodeWeightColumnName;
-    //     // seed min value from data
-    //     TimestampDoubleMap seed_map = (TimestampDoubleMap) nodes[0].getAttribute(column_name);
-    //     double[] seed_weights = seed_map.toDoubleArray();
-    //     max = seed_weights[0];
-
-    //     for (Node n: nodes) {
-    //       TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(column_name);
-    //       double[] weights = map.toDoubleArray();
-
-    //       for (Double wt: weights) {
-    //         if (wt > max) {
-    //           max = wt;
-    //         }
-
-    //       }
-    //     }
-    //     // System.out.println("");
-    //     // System.out.println("----------------------------");
-    //     // System.out.println("MAX: " +  max );
-    //     // System.out.println("----------------------------");
-    //     // System.out.println("");
-    //     this.maxWeight = max;
-    // }
-
-    private void adjustHue(Node[] nodes, Node node, Double weight){
-        // Double min = getMinWeight(nodes);
-        // Double max = getMaxWeight(nodes);
-
-        // Double min = this.minWeight;
-        // System.out.println("");
-        // System.out.println("----------------------------");
-        // System.out.println("MIN: " +  min );
-        // System.out.println("----------------------------");
-        // System.out.println("");
-        // Double max = this.maxWeight;
-        // System.out.println("");
-        // System.out.println("----------------------------");
-        // System.out.println("MAX: " +  max );
-        // System.out.println("----------------------------");
-        // System.out.println("");
-
-        // scale weights to lie between 0 and 0.66
-        // if (weight > -3 || weight < 3) {
-        //   double hue_double = (double)(((weight - (-3))/(3 - (-3)))*(0.66-0.0) + 0.0);
-        //   //node.getNodeData().setColor(float r, float g, float b)
-        //   float hue_float = (float) hue_double;
-        //   float s = 1.0f;
-        //   float b = 1.0f;
-        //   Color new_color = Color.getHSBColor(hue_float, s, b);
-        //   node.setColor(new_color);
-        // }
-
-      // float s = 1.0f;
-      // float b = 1.0f;
-      // float r = 0f;
-      // if (weight >= -3.0 && weight < -2.5) {
-      //   hue_float = (0)*(0.055f);
-      // } if (weight >= -2.5 && weight < -2.0) {
-      //   hue_float = (1)*(0.055f);
-      // } if (weight >= -2.0 && weight < -1.5) {
-      //   hue_float = (2)*(0.055f);
-      // } if (weight >= -1.5 && weight < -1.0) {
-      //   hue_float = (3)*(0.055f);
-      // } if (weight >= -1.0 && weight < -0.5) {
-      //   hue_float = (4)*(0.055f);
-      // } if (weight >= -0.5 && weight < 0) {
-      //   hue_float = (5)*(0.055f);
-      // } if (weight >= 0.0 && weight < 0.5) {
-      //   hue_float = (6)*(0.055f);
-      // } if (weight >= 0.5 && weight < 1.0) {
-      //   hue_float = (7)*(0.055f);
-      // } if (weight >= 1.0 && weight < 1.5) {
-      //   hue_float = (8)*(0.055f);
-      // } if (weight >= 1.5 && weight < 2.0) {
-      //   hue_float = (9)*(0.055f);
-      // } if (weight >= 2.0 && weight < 2.5) {
-      //   hue_float = (10)*(0.055f);
-      // } if (weight >= 2.5 && weight <= 3) {
-      //   hue_float = (11)*(0.055f);
-      // }
-    //         Color new_color = Color.getHSBColor(hue_float, s, b);
-    //   node.setColor(new_color);
-
-
-    //   if (weight < -3.0) {
-    //     node.setColor(Color.gray);
-    //   } if (weight > 3.0) {
-    //     node.setColor(Color.black);
-    //   }
-    // }
+    private void adjustHue(Node node, Double weight){
 
       float r = 0.0f;
       float g = 0.0f;
@@ -405,69 +296,69 @@ private void adjustHue(Node[] nodes, Node node, Double weight){
 
 
       if (weight >= -3.0 && weight < -2.5) {
-        // rgb(0,51,153)
+      // rgb(0,51,153)
         r = 0f;
         g = 51/255f;
         b = 153/255f;
       } if (weight >= -2.5 && weight < -2.0) {
-// rgb(43,85,170)
+      // rgb(43,85,170)
         r = 43/255f;
         g = 85/255f;
         b = 170/255f;
       } if (weight >= -2.0 && weight < -1.5) {
-// rgb(85,119,187)
+      // rgb(85,119,187)
         r = 85/255f;
         g = 119/255f;
         b = 187/255f;
 
       } if (weight >= -1.5 && weight < -1.0) {
-// rgb(128,153,204)
+      // rgb(128,153,204)
         r = 153/255f;
         g = 173/255f;
         b = 214/255f;
       } if (weight >= -1.0 && weight < -0.5) {
-// rgb(170,187,221)
+      // rgb(170,187,221)
         r = 204/255f;
         g = 214/255f;
         b = 235/255f;
       } if (weight >= -0.5 && weight < 0) {
-// rgb(213,221,238)
+      // rgb(213,221,238)
         r = 213/255f;
         g = 221/255f;
         b = 238/255f;
       }
       if (weight == 0) {
-// rgb(255,255,255)
+      // rgb(255,255,255)
         r = 255/255f;
         g = 255/255f;
         b = 255/255f;
       } if (weight > 0.0 && weight < 0.5) {
-// rgb(238,213,213)
+      // rgb(238,213,213)
         r = 238/255f;
         g = 213/255f;
         b = 213/255f;
       } if (weight >= 0.5 && weight < 1.0) {
-// rgb(221,170,170)
+      // rgb(221,170,170)
         r = 221/255f;
         g = 170/255f;
         b = 170/255f;
       } if (weight >= 1.0 && weight < 1.5) {
-// rgb(204,128,128)
+      // rgb(204,128,128)
         r = 204/255f;
         g = 128/255f;
         b = 128/255f;
       } if (weight >= 1.5 && weight < 2.0) {
-// rgb(187,85,85)
+      // rgb(187,85,85)
         r = 187/255f;
         g = 85/255f;
         b = 85/255f;
       } if (weight >= 2.0 && weight < 2.5) {
-// rgb(170,43,43)
+      // rgb(170,43,43)
         r = 170/255f;
         g = 43/255f;
         b = 43/255f;
       } if (weight >= 2.5 && weight <= 3) {
-// rgb(153,0,0)
+      // rgb(153,0,0)
         r = 153/255f;
         g = 0f;
         b = 0f;
@@ -482,6 +373,102 @@ private void adjustHue(Node[] nodes, Node node, Double weight){
         node.setColor(Color.black);
       }
     }
+
+
+
+
+    private void adjustHueChange(Node node, Double diff){
+
+      float r = 0f;
+      float g = 0f;
+      float b = 0f;
+
+
+      if (diff >= -3.0 && diff < -2.5) {
+      // rgb(255,51,0)
+        r = 255/255f;
+        g = 51/255f;
+        b = 0f;
+      } if (diff >= -2.5 && diff < -2.0) {
+      // rgb(255,85,43)
+        r = 255/255f;
+        g = 85/255f;
+        b = 43/255f;
+      } if (diff >= -2.0 && diff < -1.5) {
+      // rgb(255,119,85)
+        r = 255/255f;
+        g = 119/255f;
+        b = 85/255f;
+
+      } if (diff >= -1.5 && diff < -1.0) {
+      // rgb(255,153,128)
+        r = 255/255f;
+        g = 153/255f;
+        b = 128/255f;
+      } if (diff >= -1.0 && diff < -0.5) {
+      // rgb(255,187,170)
+        r = 255/255f;
+        g = 187/255f;
+        b = 170/255f;
+      } if (diff >= -0.5 && diff < 0) {
+      // rgb(255,221,213)
+        r = 255/255f;
+        g = 221/255f;
+        b = 213/255f;
+      }
+
+
+
+      if (diff == 0.0) {
+      // rgb(255,255,255)
+
+      }
+
+
+      if (diff > 0.0 && diff < 0.5) {
+      // rgb(213,247,213)
+        r = 213/255f;
+        g = 247/255f;
+        b = 213/255f;
+      } if (diff >= 0.5 && diff < 1.0) {
+      // rgb(170,238,170)
+        r = 170/255f;
+        g = 238/255f;
+        b = 170/255f;
+      } if (diff >= 1.0 && diff < 1.5) {
+      // rgb(128,230,128)
+        r = 128/255f;
+        g = 230/255f;
+        b = 128/255f;
+      } if (diff >= 1.5 && diff < 2.0) {
+      // rgb(85,221,85)
+        r = 85/255f;
+        g = 221/255f;
+        b = 85/255f;
+      } if (diff >= 2.0 && diff < 2.5) {
+      // rgb(43,213,43)
+        r = 43/255f;
+        g = 213/255f;
+        b = 43/255f;
+      } if (diff >= 2.5 && diff < 3) {
+      // rgb(0,204,0)
+        r = 0f;
+        g = 204/255f;
+        b = 0f;
+      }
+
+      if (diff != 0.0) {
+        Color new_color = new Color(r, g, b);
+        node.setColor(new_color);
+      }
+
+
+      if (diff < -3.0) {
+        node.setColor(Color.gray);
+      } if (diff > 3.0) {
+        node.setColor(Color.black);
+      }
+    }
 //Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
 
 
@@ -514,38 +501,88 @@ public void goAlgo() {
             // setterMinWeight(nodes);
             // setterMaxWeight(nodes);
             // List<Double> all_weights = new ArrayList<Double>();
+            List<Double> all_changes = new ArrayList<Double>();
 
-            // for (Node n: nodes) {
-            //   TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
-            //   double[] weights = map.toDoubleArray();
+            for (Node n: nodes) {
+              TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
 
-            //   for (Double wt: weights) {
-            //     if (wt != null) {
-            //     all_weights.add(wt);
-            //     }
+              double[] weights = map.toDoubleArray();
+              // Interval[] intervals = getIntervals(map);
+              double[] timestamps = map.getTimestamps();
 
-            //   }
-            // }
-            // // Double[] all_weights_array = new Double[all_weights.size()];
-            // // all_weights_array = all_weights.toArray(all_weights_array);
 
+              Interval int_1 = new Interval(timestamps[0], timestamps[1]);
+              Interval int_2 = new Interval(timestamps[1], timestamps[2]);
+              Interval int_3 = new Interval(timestamps[2], timestamps[3]);
+              Interval int_4 = new Interval(timestamps[3], timestamps[4]);
 
-            // double[] tempArray = new double[all_weights.size()];
-            // int i = 0;
-            // for(Double d : all_weights) {
-            //   tempArray[i] = (double) d;
-            //   i++;
-            // }
+              // Interval[] intervals = {int_1, int_2, int_3, int_4, int_5};
+              // 1 2
+              // 2 3
+              // 4 5
+
+
+
+              // for (int k = 0; k < num_intervals - 1 ; k++ ) {
+              //   Interval ntvl = new Interval(timestamps[k + 1], timestamps[k + 2]);
+              //   intervals[k] = ntvl;
+              // }
+
+              Double wt_4 = getNodeWeight(n, isDynamicNodeWeight, int_4);
+              Double wt_3 = getNodeWeight(n, isDynamicNodeWeight, int_3);
+              Double wt_2 = getNodeWeight(n, isDynamicNodeWeight, int_2);
+              Double wt_1 = getNodeWeight(n, isDynamicNodeWeight, int_1);
+
+              all_changes.add(wt_2 - wt_1);
+              all_changes.add(wt_3 - wt_2);
+              all_changes.add(wt_4 - wt_3);
+
+
+
+              // for (Double wt: weights) {
+              //   if (wt != null) {
+              //     valugetNodeWeight(n, isDynamicNodeWeight, intervals[1])
+              //     all_changes.add(getNodeWeightChange(n, isDynamicWeight, intervals[1], wt));
+              //     all_changes.add(getNodeWeightChange(n, isDynamicWeight, intervals[2], wt));
+              //     all_changes.add(getNodeWeightChange(n, isDynamicWeight, intervals[3], wt));
+              //     // for (Interval intrvl: intervals)
+              //         // for (int x = 1; x < intervals.length; x++) {
+              //         //   Double change = getNodeWeightChange(n, isDynamicNodeWeight, intervals[x], wt);
+              //         //   all_changes.add(change);
+              //         // }
+
+              //   }
+
+              }
+
+            // Double[] all_weights_array = new Double[all_weights.size()];
+            // all_weights_array = all_weights.toArray(all_weights_array);
+
+
+
+
+            double[] tempArray = new double[all_changes.size()];
+            int i = 0;
+            for(Double d : all_changes) {
+              tempArray[i] = (double) d;
+              i++;
+            }
+            Arrays.sort(tempArray);
+            Double min = tempArray[0];
+            Double max = tempArray[tempArray.length - 1];
+            int[] histogram = calcHistogram(tempArray, min, max, 12);
+            Double bin_diff = (max - min) / 12;
+
+            for (int j=0; j<12 ; j++ ) {
+              System.out.println(String.valueOf(min + ((j)*(bin_diff))) + "-" + String.valueOf(min + ((j+1)*(bin_diff))) + ": " + String.valueOf(histogram[j]));
+            }
+
+            System.out.println("min: " + String.valueOf(min) + "max: " + String.valueOf(max));
+
+              // System.out.println(histogram[j]);
 
 
-            // int[] histogram = calcHistogram(tempArray, -3.0, 3.0, 12);
-            // Double bin_diff = 0.5;
-            // for (int j=0; j<12 ; j++ ) {
-            //   System.out.println(String.valueOf(-3 + ((j)*(bin_diff))) + "-" + String.valueOf(-3 + ((j+1)*(bin_diff))) + ": " + String.valueOf(histogram[j]));
-            //   // System.out.println(histogram[j]);
-            // }
 
-            // This is a histogram with 4 bins, 0-2.5, 2.5-5, 5-7.5, 7.5-10.
 
             // Initialise layout data
             for (Node n : nodes) {
@@ -633,13 +670,43 @@ public void goAlgo() {
                 // setterMinWeight();
                 // setterMaxWeight();
                 if (isHeatMapMode()) {
-                  adjustHue(nodes, node_a, wt_a);
-                  adjustHue(nodes, node_b, wt_b);
+                  adjustHue(node_a, wt_a);
+                  adjustHue(node_b, wt_b);
+                }
+                //if (isHeatMapChangeMode()){
+                if (isHeatMapChangeMode() && isDynamicNodeWeight) {
+///BOOKMARKME
+
+                  Double change_a = getNodeWeightChange(node_a, isDynamicNodeWeight, interval, wt_a);
+                  Double change_b = getNodeWeightChange(node_b, isDynamicNodeWeight, interval, wt_b);
+                  adjustHueChange(node_a, change_a);
+                  adjustHueChange(node_b, change_b);
+
+
                 }
                 NodeAttraction.apply(node_a, node_b, (getNodeWeightScaling()*(wt_a + wt_b)/2));
 
             }
-
+    // private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
+
+    //     if (isDynamicNodeWeight) {
+    //         // node_weight = (Double) n.getAttribute("gravity_x");
+    //         TimestampMap map = (TimestampMap) node.getAttribute(this.nodeWeightColumnName);
+    //         // Estimator estimator = (Estimator) AVERAGE;
+
+    //         Double value = (Double) map.get(interval, Estimator.AVERAGE);
+    //         if (value == null) {
+    //           Interval prev_interval = new Interval (Interval.INFINITY_INTERVAL.getLow(), interval.getLow());
+    //           value = (Double) map.get(prev_interval, Estimator.LAST);
+    //           if (value == null) {
+    //             value = 0.0;
+    //           }
+    //         }
+    //         return value;
+    //     } else {
+    //       return (Double) node.getAttribute(this.nodeWeightColumnName);
+    //     }
+    // }
 
 
 
@@ -823,6 +890,13 @@ public LayoutProperty[] getProperties() {
                     "ForceAtlas2.heatMapMode.name",
                     NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapMode.desc"),
                     "isHeatMapMode", "setHeatMapMode"));
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapChangeMode.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.heatMapChangeMode.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapChangeMode.desc"),
+                    "isHeatMapChangeMode", "setHeatMapChangeMode"));
             properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.gravity.name"),
@@ -920,6 +994,7 @@ public void resetPropertiesValues() {
         // setNodeWeightAttraction(false);
         setNodeWeightScaling(1.);
         setHeatMapMode(false);
+        setHeatMapChangeMode(false);
         setGravity(1.);
 
         // Behavior
@@ -1023,6 +1098,14 @@ public void setHeatMapMode(Boolean heatMapMode) {
         this.heatMapMode = heatMapMode;
     }
 
+    public Boolean isHeatMapChangeMode() {
+        return heatMapChangeMode;
+    }
+
+    public void setHeatMapChangeMode(Boolean heatMapChangeMode) {
+        this.heatMapChangeMode = heatMapChangeMode;
+    }
+
     public Double getGravity() {
         return gravity;
     }
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index ca6c0a0..16afe18 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -27,6 +27,8 @@ ForceAtlas2.threads=Threads
 ForceAtlas2.heatMapMode.name=Heat Map
 ForceAtlas2.heatMapMode.desc=Turn on heat map based on normalized node weights
 
+ForceAtlas2.heatMapChangeMode.name=Heat Map for Change
+ForceAtlas2.heatMapChangeMode.desc=Turn on heat map to show change between time slices in dynamic data
 
 ForceAtlas2.nodeWeightScaling.name=Node Weight Scaling
 ForceAtlas2.nodeWeightScaling.desc=Adjust scaling on node weight attraction. More creates larger distance between nodes.

From 6d442c1385b693cd20f699f16690674b809e2793 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Thu, 30 Aug 2018 17:33:25 +0100
Subject: [PATCH 23/32] added transparency in preview mode

---
 .../layout/NodeWeight/ForceAtlas2.java        | 110 ++++++++++++++----
 .../layout/NodeWeight/Bundle.properties       |   3 +
 2 files changed, 93 insertions(+), 20 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index cf9ca45..f92be2d 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -118,6 +118,7 @@ public class ForceAtlas2 implements Layout {
     private boolean strongGravityMode;
     private boolean heatMapChangeMode;
     private boolean heatMapMode;
+    private boolean opacityMode;
     private int threadCount;
     private int currentThreadCount;
     private Region rootRegion;
@@ -386,34 +387,34 @@ private void adjustHueChange(Node node, Double diff){
 
       if (diff >= -3.0 && diff < -2.5) {
       // rgb(255,51,0)
-        r = 255/255f;
-        g = 51/255f;
+        r = 204/255f;
+        g = 0f;
         b = 0f;
       } if (diff >= -2.5 && diff < -2.0) {
       // rgb(255,85,43)
-        r = 255/255f;
-        g = 85/255f;
+        r = 213/255f;
+        g = 43/255f;
         b = 43/255f;
       } if (diff >= -2.0 && diff < -1.5) {
       // rgb(255,119,85)
-        r = 255/255f;
-        g = 119/255f;
+        r = 221/255f;
+        g = 85/255f;
         b = 85/255f;
 
       } if (diff >= -1.5 && diff < -1.0) {
       // rgb(255,153,128)
-        r = 255/255f;
-        g = 153/255f;
+        r = 230/255f;
+        g = 128/255f;
         b = 128/255f;
       } if (diff >= -1.0 && diff < -0.5) {
       // rgb(255,187,170)
-        r = 255/255f;
-        g = 187/255f;
+        r = 238/255f;
+        g = 170/255f;
         b = 170/255f;
       } if (diff >= -0.5 && diff < 0) {
       // rgb(255,221,213)
-        r = 255/255f;
-        g = 221/255f;
+        r = 247/255f;
+        g = 213/255f;
         b = 213/255f;
       }
 
@@ -428,32 +429,32 @@ private void adjustHueChange(Node node, Double diff){
       if (diff > 0.0 && diff < 0.5) {
       // rgb(213,247,213)
         r = 213/255f;
-        g = 247/255f;
+        g = 238/255f;
         b = 213/255f;
       } if (diff >= 0.5 && diff < 1.0) {
       // rgb(170,238,170)
         r = 170/255f;
-        g = 238/255f;
+        g = 221/255f;
         b = 170/255f;
       } if (diff >= 1.0 && diff < 1.5) {
       // rgb(128,230,128)
         r = 128/255f;
-        g = 230/255f;
+        g = 204/255f;
         b = 128/255f;
       } if (diff >= 1.5 && diff < 2.0) {
       // rgb(85,221,85)
         r = 85/255f;
-        g = 221/255f;
+        g = 187/255f;
         b = 85/255f;
       } if (diff >= 2.0 && diff < 2.5) {
       // rgb(43,213,43)
         r = 43/255f;
-        g = 213/255f;
+        g = 170/255f;
         b = 43/255f;
       } if (diff >= 2.5 && diff < 3) {
       // rgb(0,204,0)
         r = 0f;
-        g = 204/255f;
+        g = 153/255f;
         b = 0f;
       }
 
@@ -471,7 +472,51 @@ private void adjustHueChange(Node node, Double diff){
     }
 //Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
 
+    public void adjustOpacity(Node node, Double weight){
+      if (weight >= -3.0 && weight < -2.5) {
+        node.setAlpha(0.0833f*1f);
+
+      } if (weight >= -2.5 && weight < -2.0) {
+        node.setAlpha(0.0833f*2f);
+
+      } if (weight >= -2.0 && weight < -1.5) {
+        node.setAlpha(0.0833f*3f);
+
+      } if (weight >= -1.5 && weight < -1.0) {
+        node.setAlpha(0.0833f*4f);
+
+      } if (weight >= -1.0 && weight < -0.5) {
+        node.setAlpha(0.0833f*5f);
+
+      } if (weight >= -0.5 && weight < 0) {
+        node.setAlpha(0.0833f*6f);
 
+      } if (weight >= 0.0 && weight < 0.5) {
+        node.setAlpha(0.0833f*7f);
+
+      } if (weight >= 0.5 && weight < 1.0) {
+        node.setAlpha(0.0833f*8f);
+
+      } if (weight >= 1.0 && weight < 1.5) {
+        node.setAlpha(0.0833f*9f);
+
+      } if (weight >= 1.5 && weight < 2.0) {
+        node.setAlpha(0.0833f*10f);
+
+      } if (weight >= 2.0 && weight < 2.5) {
+        node.setAlpha(0.0833f*11f);
+
+      } if (weight >= 2.5 && weight <= 3) {
+       node.setAlpha(0.0833f*12f);
+      }
+
+      if (weight < -3) {
+        node.setColor(Color.white);
+      }
+      if (weight > 3) {
+        node.setColor(Color.black);
+      }
+    }
 
 
 
@@ -673,10 +718,10 @@ public void goAlgo() {
                   adjustHue(node_a, wt_a);
                   adjustHue(node_b, wt_b);
                 }
+
+
                 //if (isHeatMapChangeMode()){
                 if (isHeatMapChangeMode() && isDynamicNodeWeight) {
-///BOOKMARKME
-
                   Double change_a = getNodeWeightChange(node_a, isDynamicNodeWeight, interval, wt_a);
                   Double change_b = getNodeWeightChange(node_b, isDynamicNodeWeight, interval, wt_b);
                   adjustHueChange(node_a, change_a);
@@ -684,6 +729,15 @@ public void goAlgo() {
 
 
                 }
+                // Opacity applied last so both can be used
+                if (isOpacityMode()){
+                  adjustOpacity(node_a, wt_a);
+                  adjustOpacity(node_b, wt_b);
+                }
+
+
+
+
                 NodeAttraction.apply(node_a, node_b, (getNodeWeightScaling()*(wt_a + wt_b)/2));
 
             }
@@ -883,6 +937,13 @@ public LayoutProperty[] getProperties() {
                     "ForceAtlas2.strongGravityMode.name",
                     NbBundle.getMessage(getClass(), "ForceAtlas2.strongGravityMode.desc"),
                     "isStrongGravityMode", "setStrongGravityMode"));
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.opacityMode.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.opacityMode.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.opacityMode.desc"),
+                    "isOpacityMode", "setOpacityMode"));
             properties.add(LayoutProperty.createProperty(
                     this, Boolean.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapMode.name"),
@@ -995,6 +1056,7 @@ public void resetPropertiesValues() {
         setNodeWeightScaling(1.);
         setHeatMapMode(false);
         setHeatMapChangeMode(false);
+        setOpacityMode(false);
         setGravity(1.);
 
         // Behavior
@@ -1090,6 +1152,14 @@ public void setStrongGravityMode(Boolean strongGravityMode) {
         this.strongGravityMode = strongGravityMode;
     }
 
+    public Boolean isOpacityMode() {
+        return opacityMode;
+    }
+
+    public void setOpacityMode(Boolean opacityMode) {
+        this.opacityMode = opacityMode;
+    }
+
     public Boolean isHeatMapMode() {
         return heatMapMode;
     }
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index 16afe18..6bd6d83 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -23,6 +23,9 @@ ForceAtlas2.threads=Threads
 # ForceAtlas2.maxWeight.desc=maximum of node weights
 # ForceAtlas2.minWeight.name=Minimum Weight
 # ForceAtlas2.minWeight.desc=minimum of node weights
+ForceAtlas2.opacityMode.name=Opacity mode
+ForceAtlas2.opacityMode.desc=Opacity changes according to weight (in preview / export), turn on per-node opacity in preview tab to activate
+
 
 ForceAtlas2.heatMapMode.name=Heat Map
 ForceAtlas2.heatMapMode.desc=Turn on heat map based on normalized node weights

From 1abefc3ec84028b9c89330c02276c4ca8d6cb047 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Sun, 9 Sep 2018 23:29:22 +0100
Subject: [PATCH 24/32] changed minimum gravity to avoid runaway nodes

---
 .../layout/NodeWeight/ForceAtlas2.java        | 211 +++++++++++++-----
 .../layout/NodeWeight/Bundle.properties       |   4 +-
 pom.xml                                       |   8 +-
 3 files changed, 166 insertions(+), 57 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index f92be2d..bbd630f 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -156,6 +156,7 @@ public void initAlgo() {
         speed = 1.;
         speedEfficiency = 1.;
 
+
         Table table = graphModel.getNodeTable();
 
 
@@ -199,6 +200,9 @@ public void initAlgo() {
                 nLayout.dy = 0;
             }
 
+
+
+
             pool = Executors.newFixedThreadPool(threadCount);
             currentThreadCount = threadCount;
         } finally {
@@ -289,6 +293,68 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
+    // private Color colorBlender(Color a, Color b, Double proportion){
+    //   float propA = (float) proportion;
+    //   float propB = 1.0 - propA;
+
+    //   float rgbA[] = new float[3];
+    //   float rgbB[] = new float[3];
+
+    //   a.getColorComponents(rgbA);
+    //   b.getColorComponents(rgbB);
+
+    //   Color blend_color = new Color (rgbA[0] * propA + rgbB[0] * propB,
+    //   regbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
+
+    //   return blend_color;
+    // }
+
+//     private Color adjustHueRedBlue() {
+// if (weight >= -3.0 && weight < -2.5) {
+//         node.setAlpha(0.0833f*1f);
+
+//       } if (weight >= -2.5 && weight < -2.0) {
+//         node.setAlpha(0.0833f*2f);
+
+//       } if (weight >= -2.0 && weight < -1.5) {
+//         node.setAlpha(0.0833f*3f);
+
+//       } if (weight >= -1.5 && weight < -1.0) {
+//         node.setAlpha(0.0833f*4f);
+
+//       } if (weight >= -1.0 && weight < -0.5) {
+//         node.setAlpha(0.0833f*5f);
+
+//       } if (weight >= -0.5 && weight < 0) {
+//         node.setAlpha(0.0833f*6f);
+
+//       } if (weight >= 0.0 && weight < 0.5) {
+//         node.setAlpha(0.0833f*7f);
+
+//       } if (weight >= 0.5 && weight < 1.0) {
+//         node.setAlpha(0.0833f*8f);
+
+//       } if (weight >= 1.0 && weight < 1.5) {
+//         node.setAlpha(0.0833f*9f);
+
+//       } if (weight >= 1.5 && weight < 2.0) {
+//         node.setAlpha(0.0833f*10f);
+
+//       } if (weight >= 2.0 && weight < 2.5) {
+//         node.setAlpha(0.0833f*11f);
+
+//       } if (weight >= 2.5 && weight <= 3) {
+//        node.setAlpha(0.0833f*12f);
+//       }
+
+//       if (weight < -3) {
+//         node.setColor(Color.white);
+//       }
+//       if (weight > 3) {
+//         node.setColor(Color.black);
+//       }
+//     }
+
     private void adjustHue(Node node, Double weight){
 
       float r = 0.0f;
@@ -369,9 +435,18 @@ private void adjustHue(Node node, Double weight){
 
 
       if (weight < -3.0) {
-        node.setColor(Color.gray);
+        r = 0f;
+        g = 51/255f;
+        b = 153/255f;
+        new_color = new Color(r, g, b);
+        node.setColor(new_color.brighter());
       } if (weight > 3.0) {
-        node.setColor(Color.black);
+        r = 153/255f;
+        g = 0f;
+        b = 0f;
+        new_color = new Color(r, g, b);
+        node.setColor(new_color.darker());
+
       }
     }
 
@@ -465,9 +540,17 @@ private void adjustHueChange(Node node, Double diff){
 
 
       if (diff < -3.0) {
-        node.setColor(Color.gray);
+        r = 204/255f;
+        g = 0f;
+        b = 0f;
+        Color new_color = new Color(r, g, b);
+        node.setColor(new_color.brighter());
       } if (diff > 3.0) {
-        node.setColor(Color.black);
+        r = 0f;
+        g = 153/255f;
+        b = 0f;
+        Color new_color = new Color(r, g, b);
+        node.setColor(new_color.darker());
       }
     }
 //Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
@@ -543,44 +626,62 @@ public void goAlgo() {
         try {
             Node[] nodes = graph.getNodes().toArray();
             Edge[] edges = graph.getEdges().toArray();
+
+
+            Double min_avg_wt = 0.0;
+
+            for (Edge e : edges) {
+
+
+
+              Node a = e.getSource();
+              Node b = e.getTarget();
+              if (hasNodeWeight(a) && hasNodeWeight(b)){
+                Double wta = getNodeWeight(a, isDynamicNodeWeight, interval);
+                Double wtb = getNodeWeight(b, isDynamicNodeWeight, interval);
+                Double avg_wt = (wta + wtb)/2;
+                if (avg_wt < min_avg_wt) {
+                  min_avg_wt = avg_wt;
+                }
+              }
+              Double potential_gravity = -(min_avg_wt) + 10;
+              if (min_avg_wt < 0.0 && getGravity() < potential_gravity) {
+                // setStrongGravityMode(true);
+                setGravity(potential_gravity);
+              }
+            }
+
+
+
+
             // setterMinWeight(nodes);
             // setterMaxWeight(nodes);
             // List<Double> all_weights = new ArrayList<Double>();
-            List<Double> all_changes = new ArrayList<Double>();
+            // List<Double> all_changes = new ArrayList<Double>();
 
-            for (Node n: nodes) {
-              TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
+            // for (Node n: nodes) {
+            //   TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
 
-              double[] weights = map.toDoubleArray();
-              // Interval[] intervals = getIntervals(map);
-              double[] timestamps = map.getTimestamps();
+            //   double[] weights = map.toDoubleArray();
+            //   // Interval[] intervals = getIntervals(map);
+            //   double[] timestamps = map.getTimestamps();
 
 
-              Interval int_1 = new Interval(timestamps[0], timestamps[1]);
-              Interval int_2 = new Interval(timestamps[1], timestamps[2]);
-              Interval int_3 = new Interval(timestamps[2], timestamps[3]);
-              Interval int_4 = new Interval(timestamps[3], timestamps[4]);
+            //   Interval int_1 = new Interval(timestamps[0], timestamps[1]);
+            //   Interval int_2 = new Interval(timestamps[1], timestamps[2]);
+            //   Interval int_3 = new Interval(timestamps[2], timestamps[3]);
+            //   Interval int_4 = new Interval(timestamps[3], timestamps[4]);
 
-              // Interval[] intervals = {int_1, int_2, int_3, int_4, int_5};
-              // 1 2
-              // 2 3
-              // 4 5
 
 
+            //   Double wt_4 = getNodeWeight(n, isDynamicNodeWeight, int_4);
+            //   Double wt_3 = getNodeWeight(n, isDynamicNodeWeight, int_3);
+            //   Double wt_2 = getNodeWeight(n, isDynamicNodeWeight, int_2);
+            //   Double wt_1 = getNodeWeight(n, isDynamicNodeWeight, int_1);
 
-              // for (int k = 0; k < num_intervals - 1 ; k++ ) {
-              //   Interval ntvl = new Interval(timestamps[k + 1], timestamps[k + 2]);
-              //   intervals[k] = ntvl;
-              // }
-
-              Double wt_4 = getNodeWeight(n, isDynamicNodeWeight, int_4);
-              Double wt_3 = getNodeWeight(n, isDynamicNodeWeight, int_3);
-              Double wt_2 = getNodeWeight(n, isDynamicNodeWeight, int_2);
-              Double wt_1 = getNodeWeight(n, isDynamicNodeWeight, int_1);
-
-              all_changes.add(wt_2 - wt_1);
-              all_changes.add(wt_3 - wt_2);
-              all_changes.add(wt_4 - wt_3);
+            //   all_changes.add(wt_2 - wt_1);
+            //   all_changes.add(wt_3 - wt_2);
+            //   all_changes.add(wt_4 - wt_3);
 
 
 
@@ -598,7 +699,7 @@ public void goAlgo() {
 
               //   }
 
-              }
+              // }
 
             // Double[] all_weights_array = new Double[all_weights.size()];
             // all_weights_array = all_weights.toArray(all_weights_array);
@@ -606,23 +707,23 @@ public void goAlgo() {
 
 
 
-            double[] tempArray = new double[all_changes.size()];
-            int i = 0;
-            for(Double d : all_changes) {
-              tempArray[i] = (double) d;
-              i++;
-            }
-            Arrays.sort(tempArray);
-            Double min = tempArray[0];
-            Double max = tempArray[tempArray.length - 1];
-            int[] histogram = calcHistogram(tempArray, min, max, 12);
-            Double bin_diff = (max - min) / 12;
-
-            for (int j=0; j<12 ; j++ ) {
-              System.out.println(String.valueOf(min + ((j)*(bin_diff))) + "-" + String.valueOf(min + ((j+1)*(bin_diff))) + ": " + String.valueOf(histogram[j]));
-            }
+            // double[] tempArray = new double[all_changes.size()];
+            // int i = 0;
+            // for(Double d : all_changes) {
+            //   tempArray[i] = (double) d;
+            //   i++;
+            // }
+            // Arrays.sort(tempArray);
+            // Double min = tempArray[0];
+            // Double max = tempArray[tempArray.length - 1];
+            // int[] histogram = calcHistogram(tempArray, min, max, 12);
+            // Double bin_diff = (max - min) / 12;
+
+            // for (int j=0; j<12 ; j++ ) {
+            //   System.out.println(String.valueOf(min + ((j)*(bin_diff))) + "-" + String.valueOf(min + ((j+1)*(bin_diff))) + ": " + String.valueOf(histogram[j]));
+            // }
 
-            System.out.println("min: " + String.valueOf(min) + "max: " + String.valueOf(max));
+            // System.out.println("min: " + String.valueOf(min) + "max: " + String.valueOf(max));
 
               // System.out.println(histogram[j]);
 
@@ -706,21 +807,24 @@ public void goAlgo() {
             for (Edge e : edges) {
               Node node_a = e.getSource();
               Node node_b = e.getTarget();
+              // setStrongGravityMode(true);
+              // setGravity(abs(min_avg_wt) + 10);
 
               if (hasNodeWeight(node_a) && hasNodeWeight(node_b)) {
                 Double wt_a = 0.0;
                 Double wt_b = 0.0;
                 wt_a = getNodeWeight(node_a, isDynamicNodeWeight, interval);
                 wt_b = getNodeWeight(node_b, isDynamicNodeWeight, interval);
-                // setterMinWeight();
-                // setterMaxWeight();
+
+
+
+
                 if (isHeatMapMode()) {
                   adjustHue(node_a, wt_a);
                   adjustHue(node_b, wt_b);
                 }
 
 
-                //if (isHeatMapChangeMode()){
                 if (isHeatMapChangeMode() && isDynamicNodeWeight) {
                   Double change_a = getNodeWeightChange(node_a, isDynamicNodeWeight, interval, wt_a);
                   Double change_b = getNodeWeightChange(node_b, isDynamicNodeWeight, interval, wt_b);
@@ -729,6 +833,7 @@ public void goAlgo() {
 
 
                 }
+
                 // Opacity applied last so both can be used
                 if (isOpacityMode()){
                   adjustOpacity(node_a, wt_a);
@@ -1059,6 +1164,8 @@ public void resetPropertiesValues() {
         setOpacityMode(false);
         setGravity(1.);
 
+
+
         // Behavior
         setOutboundAttractionDistribution(false);
         setLinLogMode(false);
@@ -1076,6 +1183,8 @@ public void resetPropertiesValues() {
         setThreadsCount(Math.max(1, Runtime.getRuntime().availableProcessors() - 1));
     }
 
+
+
     @Override
     public LayoutBuilder getBuilder() {
         return layoutBuilder;
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index 6bd6d83..64b035b 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -42,9 +42,9 @@ ForceAtlas2.scalingRatio.name=Scaling
 ForceAtlas2.scalingRatio.desc=How much repulsion you want. More makes a more sparse graph.
 
 ForceAtlas2.gravity.name=Gravity
-ForceAtlas2.gravity.desc=Attracts nodes to the center. Prevents islands from drifting away.
+ForceAtlas2.gravity.desc=Attracts nodes to the center. Prevents islands from drifting away. If negative weight averages in your network, minimum gravity set to avoid nodes floating out of graph space.
 ForceAtlas2.strongGravityMode.name=Stronger Gravity
-ForceAtlas2.strongGravityMode.desc=A stronger gravity law
+ForceAtlas2.strongGravityMode.desc=A stronger gravity law. Highly recommended to keep nodes in graph space.
 
 ForceAtlas2.distributedAttraction.name=Dissuade Hubs
 ForceAtlas2.distributedAttraction.desc=Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders.
diff --git a/pom.xml b/pom.xml
index 6d0c3d6..e0ac83d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,7 @@
     <!-- List of modules -->
     <modules>
         <!-- Add here the paths of all modules (e.g. <module>modules/MyModule</module>) -->
-        <!-- <module>modules/PluginsSubMenuExample</module>
+<!--         <module>modules/PluginsSubMenuExample</module>
         <module>modules/StatisticsPluginExample</module>
         <module>modules/ToolPluginExample</module>
         <module>modules/ImportPluginExample</module>
@@ -23,9 +23,9 @@
         <module>modules/FilterPluginExample</module>
         <module>modules/ExecuteAtStartupExample</module>
         <module>modules/ExportPluginExample</module>
-        <module>modules/PreviewPluginExample</module>
-        <module>modules/LayoutPluginExample</module>
-        <module>modules/LayoutPluginExample</module> -->
+        <module>modules/PreviewPluginExample</module> -->
+<!--         <module>modules/LayoutPluginExample</module> -->
+<!--         <module>modules/LayoutPluginExample</module> -->
         <module>modules/NodeWeight</module>
     </modules>
 

From 5b1cb72a5a1fcdbba8678c1fad5ae3885dc9317a Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 18 Sep 2018 13:00:18 +0100
Subject: [PATCH 25/32] changed red blue to simplistic colorblend (linear
 interpolating)

---
 .../layout/NodeWeight/ForceAtlas2.java        | 240 +++++++++---------
 1 file changed, 118 insertions(+), 122 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index bbd630f..1891d89 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -293,163 +293,159 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
-    // private Color colorBlender(Color a, Color b, Double proportion){
-    //   float propA = (float) proportion;
-    //   float propB = 1.0 - propA;
+    private Color colorBlender(Color a, Color b, Double proportion){
+      float propA = (float) proportion;
+      float propB = 1.0 - propA;
 
-    //   float rgbA[] = new float[3];
-    //   float rgbB[] = new float[3];
+      float rgbA[] = new float[3];
+      float rgbB[] = new float[3];
 
-    //   a.getColorComponents(rgbA);
-    //   b.getColorComponents(rgbB);
+      a.getColorComponents(rgbA);
+      b.getColorComponents(rgbB);
 
-    //   Color blend_color = new Color (rgbA[0] * propA + rgbB[0] * propB,
-    //   regbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
+      Color blend_color = new Color (rgbA[0] * propA + rgbB[0] * propB,
+      regbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
 
-    //   return blend_color;
-    // }
-
-//     private Color adjustHueRedBlue() {
-// if (weight >= -3.0 && weight < -2.5) {
-//         node.setAlpha(0.0833f*1f);
-
-//       } if (weight >= -2.5 && weight < -2.0) {
-//         node.setAlpha(0.0833f*2f);
-
-//       } if (weight >= -2.0 && weight < -1.5) {
-//         node.setAlpha(0.0833f*3f);
-
-//       } if (weight >= -1.5 && weight < -1.0) {
-//         node.setAlpha(0.0833f*4f);
-
-//       } if (weight >= -1.0 && weight < -0.5) {
-//         node.setAlpha(0.0833f*5f);
-
-//       } if (weight >= -0.5 && weight < 0) {
-//         node.setAlpha(0.0833f*6f);
-
-//       } if (weight >= 0.0 && weight < 0.5) {
-//         node.setAlpha(0.0833f*7f);
-
-//       } if (weight >= 0.5 && weight < 1.0) {
-//         node.setAlpha(0.0833f*8f);
-
-//       } if (weight >= 1.0 && weight < 1.5) {
-//         node.setAlpha(0.0833f*9f);
-
-//       } if (weight >= 1.5 && weight < 2.0) {
-//         node.setAlpha(0.0833f*10f);
-
-//       } if (weight >= 2.0 && weight < 2.5) {
-//         node.setAlpha(0.0833f*11f);
-
-//       } if (weight >= 2.5 && weight <= 3) {
-//        node.setAlpha(0.0833f*12f);
-//       }
-
-//       if (weight < -3) {
-//         node.setColor(Color.white);
-//       }
-//       if (weight > 3) {
-//         node.setColor(Color.black);
-//       }
-//     }
-
-    private void adjustHue(Node node, Double weight){
+      return blend_color;
+    }
+private void adjustHue(Node node, Double weight){
 
       float r = 0.0f;
       float g = 0.0f;
       float b = 0.0f;
 
+      Color blue = new Color(0f, 51/255f, 153/255f)
+      Color white = new Color.white
+      Color red = new Color(153/255f, 0f, 0f)
 
       if (weight >= -3.0 && weight < -2.5) {
-      // rgb(0,51,153)
-        r = 0f;
-        g = 51/255f;
-        b = 153/255f;
+        Color new_color = colorBlender(blue, white, 1);
       } if (weight >= -2.5 && weight < -2.0) {
-      // rgb(43,85,170)
-        r = 43/255f;
-        g = 85/255f;
-        b = 170/255f;
+        Color new_color = colorBlender(blue, white, (1-0.16667));
       } if (weight >= -2.0 && weight < -1.5) {
-      // rgb(85,119,187)
-        r = 85/255f;
-        g = 119/255f;
-        b = 187/255f;
-
+        Color new_color = colorBlender(blue, white, (1-(2*0.16667)));
       } if (weight >= -1.5 && weight < -1.0) {
-      // rgb(128,153,204)
-        r = 153/255f;
-        g = 173/255f;
-        b = 214/255f;
+        Color new_color = colorBlender(blue, white, (1-(3*0.16667)));
       } if (weight >= -1.0 && weight < -0.5) {
-      // rgb(170,187,221)
-        r = 204/255f;
-        g = 214/255f;
-        b = 235/255f;
+        Color new_color = colorBlender(blue, white, (1-(4*0.16667)));
       } if (weight >= -0.5 && weight < 0) {
-      // rgb(213,221,238)
-        r = 213/255f;
-        g = 221/255f;
-        b = 238/255f;
+        Color new_color = colorBlender(blue, white, (1-(5*0.16667)));
       }
       if (weight == 0) {
       // rgb(255,255,255)
-        r = 255/255f;
-        g = 255/255f;
-        b = 255/255f;
+        Color new_color = colorBlender(blue, white, 0);
       } if (weight > 0.0 && weight < 0.5) {
-      // rgb(238,213,213)
-        r = 238/255f;
-        g = 213/255f;
-        b = 213/255f;
+        Color new_color = colorBlender(white, red, (1-0.16667));
       } if (weight >= 0.5 && weight < 1.0) {
-      // rgb(221,170,170)
-        r = 221/255f;
-        g = 170/255f;
-        b = 170/255f;
+        Color new_color = colorBlender(white, red, (1-(2*0.16667)));
       } if (weight >= 1.0 && weight < 1.5) {
-      // rgb(204,128,128)
-        r = 204/255f;
-        g = 128/255f;
-        b = 128/255f;
+        Color new_color = colorBlender(white, red, (1-(3*0.16667)));
       } if (weight >= 1.5 && weight < 2.0) {
-      // rgb(187,85,85)
-        r = 187/255f;
-        g = 85/255f;
-        b = 85/255f;
+        Color new_color = colorBlender(white, red, (1-(4*0.16667)));
       } if (weight >= 2.0 && weight < 2.5) {
-      // rgb(170,43,43)
-        r = 170/255f;
-        g = 43/255f;
-        b = 43/255f;
+        Color new_color = colorBlender(white, red, (1-(5*0.16667)));
       } if (weight >= 2.5 && weight <= 3) {
-      // rgb(153,0,0)
-        r = 153/255f;
-        g = 0f;
-        b = 0f;
+        Color new_color = colorBlender(white, red, 0);
       }
-      Color new_color = new Color(r, g, b);
+
       node.setColor(new_color);
 
 
       if (weight < -3.0) {
-        r = 0f;
-        g = 51/255f;
-        b = 153/255f;
-        new_color = new Color(r, g, b);
-        node.setColor(new_color.brighter());
+        node.setColor(Color.black);
       } if (weight > 3.0) {
-        r = 153/255f;
-        g = 0f;
-        b = 0f;
-        new_color = new Color(r, g, b);
-        node.setColor(new_color.darker());
+        node.setColor(Color.gray);
 
       }
     }
 
+    // private void adjustHue(Node node, Double weight){
+
+    //   float r = 0.0f;
+    //   float g = 0.0f;
+    //   float b = 0.0f;
+
+
+    //   if (weight >= -3.0 && weight < -2.5) {
+    //   // rgb(0,51,153)
+    //     r = 0f;
+    //     g = 51/255f;
+    //     b = 153/255f;
+    //   } if (weight >= -2.5 && weight < -2.0) {
+    //   // rgb(43,85,170)
+    //     r = 43/255f;
+    //     g = 85/255f;
+    //     b = 170/255f;
+    //   } if (weight >= -2.0 && weight < -1.5) {
+    //   // rgb(85,119,187)
+    //     r = 85/255f;
+    //     g = 119/255f;
+    //     b = 187/255f;
+
+    //   } if (weight >= -1.5 && weight < -1.0) {
+    //   // rgb(128,153,204)
+    //     r = 153/255f;
+    //     g = 173/255f;
+    //     b = 214/255f;
+    //   } if (weight >= -1.0 && weight < -0.5) {
+    //   // rgb(170,187,221)
+    //     r = 204/255f;
+    //     g = 214/255f;
+    //     b = 235/255f;
+    //   } if (weight >= -0.5 && weight < 0) {
+    //   // rgb(213,221,238)
+    //     r = 213/255f;
+    //     g = 221/255f;
+    //     b = 238/255f;
+    //   }
+    //   if (weight == 0) {
+    //   // rgb(255,255,255)
+    //     r = 255/255f;
+    //     g = 255/255f;
+    //     b = 255/255f;
+    //   } if (weight > 0.0 && weight < 0.5) {
+    //   // rgb(238,213,213)
+    //     r = 238/255f;
+    //     g = 213/255f;
+    //     b = 213/255f;
+    //   } if (weight >= 0.5 && weight < 1.0) {
+    //   // rgb(221,170,170)
+    //     r = 221/255f;
+    //     g = 170/255f;
+    //     b = 170/255f;
+    //   } if (weight >= 1.0 && weight < 1.5) {
+    //   // rgb(204,128,128)
+    //     r = 204/255f;
+    //     g = 128/255f;
+    //     b = 128/255f;
+    //   } if (weight >= 1.5 && weight < 2.0) {
+    //   // rgb(187,85,85)
+    //     r = 187/255f;
+    //     g = 85/255f;
+    //     b = 85/255f;
+    //   } if (weight >= 2.0 && weight < 2.5) {
+    //   // rgb(170,43,43)
+    //     r = 170/255f;
+    //     g = 43/255f;
+    //     b = 43/255f;
+    //   } if (weight >= 2.5 && weight <= 3) {
+    //   // rgb(153,0,0)
+    //     r = 153/255f;
+    //     g = 0f;
+    //     b = 0f;
+    //   }
+    //   Color new_color = new Color(r, g, b);
+    //   node.setColor(new_color);
+
+
+    //   if (weight < -3.0) {
+    //     node.setColor(Color.black);
+    //   } if (weight > 3.0) {
+    //     node.setColor(Color.gray);
+
+    //   }
+    // }
+
 
 
 

From 8dc35733eb6fade9d733986dcb760c90aa8e56b8 Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Tue, 18 Sep 2018 16:24:58 +0100
Subject: [PATCH 26/32] refactored blending code

---
 .../layout/NodeWeight/ForceAtlas2.java        | 279 ++++--------------
 1 file changed, 52 insertions(+), 227 deletions(-)

diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 1891d89..9959182 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -69,6 +69,7 @@ Development and Distribution License("CDDL") (collectively, the
 
 
 
+
 import java.util.ArrayList;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
@@ -293,9 +294,9 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
         }
     }
 
-    private Color colorBlender(Color a, Color b, Double proportion){
+    private Color colorBlender(Color a, Color b, double proportion){
       float propA = (float) proportion;
-      float propB = 1.0 - propA;
+      float propB = 1.0f - propA;
 
       float rgbA[] = new float[3];
       float rgbB[] = new float[3];
@@ -304,251 +305,75 @@ private Color colorBlender(Color a, Color b, Double proportion){
       b.getColorComponents(rgbB);
 
       Color blend_color = new Color (rgbA[0] * propA + rgbB[0] * propB,
-      regbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
+      rgbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
 
       return blend_color;
     }
-private void adjustHue(Node node, Double weight){
-
-      float r = 0.0f;
-      float g = 0.0f;
-      float b = 0.0f;
-
-      Color blue = new Color(0f, 51/255f, 153/255f)
-      Color white = new Color.white
-      Color red = new Color(153/255f, 0f, 0f)
 
-      if (weight >= -3.0 && weight < -2.5) {
-        Color new_color = colorBlender(blue, white, 1);
-      } if (weight >= -2.5 && weight < -2.0) {
-        Color new_color = colorBlender(blue, white, (1-0.16667));
-      } if (weight >= -2.0 && weight < -1.5) {
-        Color new_color = colorBlender(blue, white, (1-(2*0.16667)));
-      } if (weight >= -1.5 && weight < -1.0) {
-        Color new_color = colorBlender(blue, white, (1-(3*0.16667)));
-      } if (weight >= -1.0 && weight < -0.5) {
-        Color new_color = colorBlender(blue, white, (1-(4*0.16667)));
-      } if (weight >= -0.5 && weight < 0) {
-        Color new_color = colorBlender(blue, white, (1-(5*0.16667)));
-      }
-      if (weight == 0) {
-      // rgb(255,255,255)
-        Color new_color = colorBlender(blue, white, 0);
-      } if (weight > 0.0 && weight < 0.5) {
-        Color new_color = colorBlender(white, red, (1-0.16667));
-      } if (weight >= 0.5 && weight < 1.0) {
-        Color new_color = colorBlender(white, red, (1-(2*0.16667)));
-      } if (weight >= 1.0 && weight < 1.5) {
-        Color new_color = colorBlender(white, red, (1-(3*0.16667)));
-      } if (weight >= 1.5 && weight < 2.0) {
-        Color new_color = colorBlender(white, red, (1-(4*0.16667)));
-      } if (weight >= 2.0 && weight < 2.5) {
-        Color new_color = colorBlender(white, red, (1-(5*0.16667)));
-      } if (weight >= 2.5 && weight <= 3) {
-        Color new_color = colorBlender(white, red, 0);
+    private void adjustColor(Node node, Double value, Color lo, Color md, Color hi){
+
+      Color low = lo;
+      Color mid = md;
+      Color high = hi;
+
+      if (value >= -3.0 && value < -2.5) {
+        node.setColor(low);
+      } if (value >= -2.5 && value < -2.0) {
+        node.setColor(colorBlender(low, mid, (1-0.16667)));
+      } if (value >= -2.0 && value < -1.5) {
+        node.setColor(colorBlender(low, mid, (1-(2*0.16667))));
+      } if (value >= -1.5 && value < -1.0) {
+        node.setColor(colorBlender(low, mid, (1-(3*0.16667))));
+      } if (value >= -1.0 && value < -0.5) {
+        node.setColor(colorBlender(low, mid, (1-(4*0.16667))));
+      } if (value >= -0.5 && value < 0) {
+        node.setColor(colorBlender(low, mid, (1-(5*0.16667))));
       }
 
-      node.setColor(new_color);
+      if (value == 0.0) {
+        node.setColor(mid);
+      }
 
+      if (value > 0.0 && value < 0.5) {
+        node.setColor(colorBlender(mid, high, (1-0.16667)));
+      } if (value >= 0.5 && value < 1.0) {
+        node.setColor(colorBlender(mid, high, (1-(2*0.16667))));
+      } if (value >= 1.0 && value < 1.5) {
+        node.setColor(colorBlender(mid, high, (1-(3*0.16667))));
+      } if (value >= 1.5 && value < 2.0) {
+        node.setColor(colorBlender(mid, high, (1-(4*0.16667))));
+      } if (value >= 2.0 && value < 2.5) {
+        node.setColor(colorBlender(mid, high, (1-(5*0.16667))));
+      } if (value >= 2.5 && value < 3) {
+        node.setColor(high);
+      }
 
-      if (weight < -3.0) {
-        node.setColor(Color.black);
-      } if (weight > 3.0) {
+      if (value < -3.0) {
         node.setColor(Color.gray);
-
+      } if (value > 3.0) {
+        node.setColor(Color.black);
       }
     }
 
-    // private void adjustHue(Node node, Double weight){
-
-    //   float r = 0.0f;
-    //   float g = 0.0f;
-    //   float b = 0.0f;
-
-
-    //   if (weight >= -3.0 && weight < -2.5) {
-    //   // rgb(0,51,153)
-    //     r = 0f;
-    //     g = 51/255f;
-    //     b = 153/255f;
-    //   } if (weight >= -2.5 && weight < -2.0) {
-    //   // rgb(43,85,170)
-    //     r = 43/255f;
-    //     g = 85/255f;
-    //     b = 170/255f;
-    //   } if (weight >= -2.0 && weight < -1.5) {
-    //   // rgb(85,119,187)
-    //     r = 85/255f;
-    //     g = 119/255f;
-    //     b = 187/255f;
-
-    //   } if (weight >= -1.5 && weight < -1.0) {
-    //   // rgb(128,153,204)
-    //     r = 153/255f;
-    //     g = 173/255f;
-    //     b = 214/255f;
-    //   } if (weight >= -1.0 && weight < -0.5) {
-    //   // rgb(170,187,221)
-    //     r = 204/255f;
-    //     g = 214/255f;
-    //     b = 235/255f;
-    //   } if (weight >= -0.5 && weight < 0) {
-    //   // rgb(213,221,238)
-    //     r = 213/255f;
-    //     g = 221/255f;
-    //     b = 238/255f;
-    //   }
-    //   if (weight == 0) {
-    //   // rgb(255,255,255)
-    //     r = 255/255f;
-    //     g = 255/255f;
-    //     b = 255/255f;
-    //   } if (weight > 0.0 && weight < 0.5) {
-    //   // rgb(238,213,213)
-    //     r = 238/255f;
-    //     g = 213/255f;
-    //     b = 213/255f;
-    //   } if (weight >= 0.5 && weight < 1.0) {
-    //   // rgb(221,170,170)
-    //     r = 221/255f;
-    //     g = 170/255f;
-    //     b = 170/255f;
-    //   } if (weight >= 1.0 && weight < 1.5) {
-    //   // rgb(204,128,128)
-    //     r = 204/255f;
-    //     g = 128/255f;
-    //     b = 128/255f;
-    //   } if (weight >= 1.5 && weight < 2.0) {
-    //   // rgb(187,85,85)
-    //     r = 187/255f;
-    //     g = 85/255f;
-    //     b = 85/255f;
-    //   } if (weight >= 2.0 && weight < 2.5) {
-    //   // rgb(170,43,43)
-    //     r = 170/255f;
-    //     g = 43/255f;
-    //     b = 43/255f;
-    //   } if (weight >= 2.5 && weight <= 3) {
-    //   // rgb(153,0,0)
-    //     r = 153/255f;
-    //     g = 0f;
-    //     b = 0f;
-    //   }
-    //   Color new_color = new Color(r, g, b);
-    //   node.setColor(new_color);
-
-
-    //   if (weight < -3.0) {
-    //     node.setColor(Color.black);
-    //   } if (weight > 3.0) {
-    //     node.setColor(Color.gray);
-
-    //   }
-    // }
-
-
+    private void adjustHue(Node node, Double weight){
+      Color blue = new Color(0f, 51/255f, 153/255f);
+      Color white = Color.white;
+      Color red = new Color(153/255f, 0f, 0f);
 
+      adjustColor(node, weight, blue, white, red);
+    }
 
     private void adjustHueChange(Node node, Double diff){
-
-      float r = 0f;
-      float g = 0f;
-      float b = 0f;
-
-
-      if (diff >= -3.0 && diff < -2.5) {
-      // rgb(255,51,0)
-        r = 204/255f;
-        g = 0f;
-        b = 0f;
-      } if (diff >= -2.5 && diff < -2.0) {
-      // rgb(255,85,43)
-        r = 213/255f;
-        g = 43/255f;
-        b = 43/255f;
-      } if (diff >= -2.0 && diff < -1.5) {
-      // rgb(255,119,85)
-        r = 221/255f;
-        g = 85/255f;
-        b = 85/255f;
-
-      } if (diff >= -1.5 && diff < -1.0) {
-      // rgb(255,153,128)
-        r = 230/255f;
-        g = 128/255f;
-        b = 128/255f;
-      } if (diff >= -1.0 && diff < -0.5) {
-      // rgb(255,187,170)
-        r = 238/255f;
-        g = 170/255f;
-        b = 170/255f;
-      } if (diff >= -0.5 && diff < 0) {
-      // rgb(255,221,213)
-        r = 247/255f;
-        g = 213/255f;
-        b = 213/255f;
-      }
-
-
-
-      if (diff == 0.0) {
-      // rgb(255,255,255)
-
-      }
-
-
-      if (diff > 0.0 && diff < 0.5) {
-      // rgb(213,247,213)
-        r = 213/255f;
-        g = 238/255f;
-        b = 213/255f;
-      } if (diff >= 0.5 && diff < 1.0) {
-      // rgb(170,238,170)
-        r = 170/255f;
-        g = 221/255f;
-        b = 170/255f;
-      } if (diff >= 1.0 && diff < 1.5) {
-      // rgb(128,230,128)
-        r = 128/255f;
-        g = 204/255f;
-        b = 128/255f;
-      } if (diff >= 1.5 && diff < 2.0) {
-      // rgb(85,221,85)
-        r = 85/255f;
-        g = 187/255f;
-        b = 85/255f;
-      } if (diff >= 2.0 && diff < 2.5) {
-      // rgb(43,213,43)
-        r = 43/255f;
-        g = 170/255f;
-        b = 43/255f;
-      } if (diff >= 2.5 && diff < 3) {
-      // rgb(0,204,0)
-        r = 0f;
-        g = 153/255f;
-        b = 0f;
-      }
+      Color red = new Color(204/255f, 0f, 0f);
+      Color white = Color.white;
+      Color green = new Color(0f, 204/255f, 0f);
 
       if (diff != 0.0) {
-        Color new_color = new Color(r, g, b);
-        node.setColor(new_color);
+        adjustColor(node, diff, red, white, green);
       }
+    }
 
 
-      if (diff < -3.0) {
-        r = 204/255f;
-        g = 0f;
-        b = 0f;
-        Color new_color = new Color(r, g, b);
-        node.setColor(new_color.brighter());
-      } if (diff > 3.0) {
-        r = 0f;
-        g = 153/255f;
-        b = 0f;
-        Color new_color = new Color(r, g, b);
-        node.setColor(new_color.darker());
-      }
-    }
 //Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
 
     public void adjustOpacity(Node node, Double weight){

From 84ea36845c9366389b73bd6341690a7c7f70354b Mon Sep 17 00:00:00 2001
From: Julianne Joswiak <juliannej@mac.com>
Date: Thu, 20 Sep 2018 18:08:37 +0100
Subject: [PATCH 27/32] final draft except if want to clean up package
 hierarchy

---
 modules/NodeWeight/README.md                  |  31 +-
 modules/NodeWeight/pom.xml                    |   7 +
 .../layout/plugins/layout/NodeWeight/#TODO    |  31 --
 .../layout/NodeWeight/ForceAtlas2.java        | 484 +++++-------------
 .../layout/NodeWeight/HeatmapFeatures.java    | 202 ++++++++
 .../layout/NodeWeight/Bundle.properties       |  25 +-
 6 files changed, 386 insertions(+), 394 deletions(-)
 delete mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
 create mode 100644 modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/HeatmapFeatures.java

diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
index 95d48ca..0a7e0f6 100644
--- a/modules/NodeWeight/README.md
+++ b/modules/NodeWeight/README.md
@@ -1,4 +1,31 @@
-## Node Weight
+User Guide for Node Weight Plugin
+
+1. Launch Gephi
+2. Install Node Weight plugin from Plugin menu in Gephi
+3. Import data or a .gexf file
+  * Dynamic data should be in string form like  [Timestamp: data], [timestamp: data].
+    e.g. : “[2018-07-21T00:00:00.000Z, 0.21100000000000002]; [2018-07-21T00:30:00.000Z, 0.429]; [2018-07-21T03:00:00.000Z, 0.525]; [2018-07-21T06:00:00.000Z, 0.465]; [2018-07-21T12:00:00.000Z, 0.545]”
+  * Edges should have an ID in ‘Source’ and an ID in ‘Target’ that corresponds to the correct node IDs
+  * To use the Node Weight plugin functionality, you should have data in the nodes table in a column entitled ‘weight’ or ‘weight_dynamic’ (either will accept dynamic and non dynamic data)
+4. In Data Observatory, designate dynamic data columns as appropriate with your data.
+5. Go to Overview
+6. In the Layout tab select ‘Node Weight’ from the drop-down list
+7. Important fields for the Node Layout are:
+  * Node Weight Influence: Adjust scaling on node weight attraction. More creates larger distance between nodes.
+  * Opacity mode: Requires data scaled to its standard deviation. Opacity changes according to weight (in preview / export), turn on per-node opacity in preview tab to activate.
+  * Heat Map: Checkbox to turn on heat map based on normalized node weights. Requires data scaled to its standard deviation.
+  * Change Heat Map: Checkbox to turn on heat map to show change of normalized node weights between time slices in dynamic data. Red-green.
+  * Alternative Change Heat Map: Checkbox to turn on heat map to show change of normalized node weights between time slices in dynamic data Requires data scaled to its standard deviation. Blue-yellow.
+  * Gravity: Attracts nodes to the center. Prevents islands from drifting away. If negative weight averages in your network, minimum gravity set to avoid nodes floating out of graph space.
+  * Stronger Gravity: A stronger gravity law. Highly recommended to keep nodes in graph space if there are negative weights.
+  * Scaling: Because of the stronger gravity anchoring nodes with negative weights, you will probably want to turn this up.
+
+8. Experiment with features. Select one of the heat maps. Select opacity. Change the Node Weight influence.
+  Dynamic-specific
+    A. Turn on the Timeline feature: Select Timeline from the Window drop-down menu. Go to the bottom of the Gephi interface and click ‘Enable Timeline’
+    B. Adjust the intervals by sliding the edges of the translucent blue bar.
+    C. Drag your interval to the 1 marker and press the play button or manually drag the interval around. The interval for which you have data must be completed: e.g. if you want data for hour 3, cover the whole of 3 with an hour-long interval or with a smaller time-slice go to the next hour area not covered by your data. Mouse over the interval for a tooltip telling the duration and bounds of your interval. For the change heat maps, offset your interval an hour (or whatever other unit your timeline is using) later to see the change.
+
+
 
-This README supports Markdown, see [syntax](https://help.github.com/articles/markdown-basics/)
 
diff --git a/modules/NodeWeight/pom.xml b/modules/NodeWeight/pom.xml
index 0cacab7..cf64804 100644
--- a/modules/NodeWeight/pom.xml
+++ b/modules/NodeWeight/pom.xml
@@ -19,6 +19,13 @@
             <groupId>org.netbeans.api</groupId>
             <artifactId>org-openide-util-lookup</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.netbeans.api</groupId>
+            <artifactId>org-openide-dialogs</artifactId>
+            <type>jar</type>
+            <version>RELEASE81</version>
+
+        </dependency>
         <dependency>
             <groupId>org.gephi</groupId>
             <artifactId>graph-api</artifactId>
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
deleted file mode 100644
index 6922322..0000000
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/#TODO
+++ /dev/null
@@ -1,31 +0,0 @@
-#TODO
-
-To-do:
-1. add transparency for nodes based on weight
-2. make transparency for nodes optional
-3. make the node weight attraction more meaningful
-4. make good visualizations to be tested
-5. Make app more robust (OR CATCH EXCEPTIONS AND TELL USER WHAT TO DO)
-
-  ii. Figure out exception if data in incorrect (non-double) format…. Either be able to handle this or catch exception
-
-  iii. Catch exception if there exists a node weight outside of the provided range
-
-6. test some use-cases to see what errors appear
-
-
-Done:
- check and validate if the column already exists
-  1a. check whether the column is dynamic
- add a column that can accept dynamic or not dynamic value
-  called "weight"
-
-    i. Resolve use of weight vs weight_dynamic
-  Check if weight is dynamic; check if dynamic_weight is dynamic; use whichever one exists
-
-
-
-
-
-verifying weight column contains doubles in the initAlgo method
-
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
index 9959182..9ef7487 100644
--- a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/ForceAtlas2.java
@@ -39,9 +39,13 @@ Development and Distribution License("CDDL") (collectively, the
 
  Portions Copyrighted 2011 Gephi Consortium.
  */
+
+// all code attributable to Julianne Joswiak lies between tags: //jj2018 and //
+
 package org.gephi.layout.plugins.layout.NodeWeight;
+
 import java.awt.Color;
-// org.gephi.layout.plugins.layout.NodeWeight
+
 
 import org.gephi.graph.api.Edge;
 import org.gephi.graph.api.Element;
@@ -55,21 +59,19 @@ Development and Distribution License("CDDL") (collectively, the
 import org.gephi.graph.api.types.TimeMap;
 import org.gephi.graph.api.types.TimestampMap;
 import org.gephi.graph.api.types.TimestampDoubleMap;
+import org.gephi.graph.api.Interval;
 
-
-
-// import org.gephi.layout.plugin.NodeWeight.ForceFactory.AttractionForce;
-// import org.gephi.layout.plugin.NodeWeight.ForceFactory.RepulsionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.HeatmapFeatures;
 import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
 import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
 
+
 import org.gephi.layout.spi.Layout;
 import org.gephi.layout.spi.LayoutBuilder;
 import org.gephi.layout.spi.LayoutProperty;
 
 
 
-
 import java.util.ArrayList;
 import java.util.List;
 import java.util.concurrent.ExecutorService;
@@ -81,22 +83,17 @@ Development and Distribution License("CDDL") (collectively, the
 
 
 
-import org.gephi.graph.api.Interval;
-
-// import org.gephi.layout.plugin.AbstractLayout;
-import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
-
-
-
-
 import org.openide.util.Exceptions;
 import org.openide.util.NbBundle;
+import org.openide.NotifyDescriptor;
+import org.openide.DialogDisplayer;
 
+import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
 
 
 
 /**
- * ForceAtlas 2 Layout, manages each step of the computations.
+ * Node Weight Influence added to ForceAtlas 2 Layout, manages each step of the computations.
  *
  * @author Mathieu Jacomy
  */
@@ -118,6 +115,7 @@ public class ForceAtlas2 implements Layout {
     private boolean linLogMode;
     private boolean strongGravityMode;
     private boolean heatMapChangeMode;
+    private boolean heatMapChangeModeCB;
     private boolean heatMapMode;
     private boolean opacityMode;
     private int threadCount;
@@ -132,17 +130,16 @@ public class ForceAtlas2 implements Layout {
 
 
 
-
+    //by jj2018
     private void setNodeWeightColumnName(Table table) {
       if (table.hasColumn("weight")) {
         this.nodeWeightColumnName = "weight";
       }
-      // weight_dynamic
       if (table.hasColumn("weight_dynamic")) {
         this.nodeWeightColumnName = "weight_dynamic";
       }
     }
-
+    //
 
 
     public ForceAtlas2(ForceAtlas2Builder layoutBuilder) {
@@ -160,7 +157,7 @@ public void initAlgo() {
 
         Table table = graphModel.getNodeTable();
 
-
+        //by jj2018
         if (!(table.hasColumn("weight") || table.hasColumn("weight_dynamic"))) {
           table.addColumn("weight", Double.class);
         }
@@ -168,16 +165,13 @@ public void initAlgo() {
         setNodeWeightColumnName(table);
 
         if (!(table.getColumn(nodeWeightColumnName).getTypeClass()==Double.class || (table.getColumn(nodeWeightColumnName).getTypeClass()==TimestampDoubleMap.class))) {
-          // try {
-          //           future.get();
-          //       } catch (Exception e) {
-          //           throw new RuntimeException("Unable to layout " + this.getClass().getSimpleName() + ".", e);
-          //       }
 
+          NotifyDescriptor d = new NotifyDescriptor.Message("The Node Weight plugin requires types\n Double or TimestampDoubleMap", NotifyDescriptor.INFORMATION_MESSAGE);
+          DialogDisplayer.getDefault().notify(d);
 
-          //alert the user that need type double and abort algorithm
-        }
 
+        }
+        //
 
 
 
@@ -209,22 +203,9 @@ public void initAlgo() {
         } finally {
             graph.readUnlockAll();
         }
-    }
 
-    public static int[] calcHistogram(double[] data, double min, double max, int numBins) {
-      final int[] result = new int[numBins];
-      final double binSize = (max - min)/numBins;
+}
 
-      for (double d : data) {
-        int bin = (int) ((d - min) / binSize);
-        if (bin < 0) { /* this data is smaller than min */ }
-        else if (bin >= numBins) { /* this data point is bigger than max */ }
-        else {
-          result[bin] += 1;
-        }
-      }
-      return result;
-    }
 
 
 
@@ -235,9 +216,9 @@ private double getEdgeWeight(Edge edge, boolean isDynamicWeight, Interval interv
             return edge.getWeight();
         }
     }
-
+    // jj2018
+    // hasNodeWeightStop refers to 'has node weight.' (full stop)
     private boolean hasNodeWeightStop(Node node) {
-
       if (graphModel.getNodeTable().hasColumn("weight") && node.getAttribute("weight") != null) {
         return true;
       } else {
@@ -245,6 +226,7 @@ private boolean hasNodeWeightStop(Node node) {
       }
     }
 
+
     private boolean hasNodeWeightDynamic(Node node) {
       if (graphModel.getNodeTable().hasColumn("weight_dynamic") && node.getAttribute("weight_dynamic") != null) {
         return true;
@@ -253,7 +235,7 @@ private boolean hasNodeWeightDynamic(Node node) {
       }
     }
 
-    //// DYNAMIC
+
     private boolean hasNodeWeight(Node node) {
       if (hasNodeWeightStop(node) || hasNodeWeightDynamic(node)){
         return true;
@@ -293,134 +275,7 @@ private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval in
           return (Double) node.getAttribute(this.nodeWeightColumnName);
         }
     }
-
-    private Color colorBlender(Color a, Color b, double proportion){
-      float propA = (float) proportion;
-      float propB = 1.0f - propA;
-
-      float rgbA[] = new float[3];
-      float rgbB[] = new float[3];
-
-      a.getColorComponents(rgbA);
-      b.getColorComponents(rgbB);
-
-      Color blend_color = new Color (rgbA[0] * propA + rgbB[0] * propB,
-      rgbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
-
-      return blend_color;
-    }
-
-    private void adjustColor(Node node, Double value, Color lo, Color md, Color hi){
-
-      Color low = lo;
-      Color mid = md;
-      Color high = hi;
-
-      if (value >= -3.0 && value < -2.5) {
-        node.setColor(low);
-      } if (value >= -2.5 && value < -2.0) {
-        node.setColor(colorBlender(low, mid, (1-0.16667)));
-      } if (value >= -2.0 && value < -1.5) {
-        node.setColor(colorBlender(low, mid, (1-(2*0.16667))));
-      } if (value >= -1.5 && value < -1.0) {
-        node.setColor(colorBlender(low, mid, (1-(3*0.16667))));
-      } if (value >= -1.0 && value < -0.5) {
-        node.setColor(colorBlender(low, mid, (1-(4*0.16667))));
-      } if (value >= -0.5 && value < 0) {
-        node.setColor(colorBlender(low, mid, (1-(5*0.16667))));
-      }
-
-      if (value == 0.0) {
-        node.setColor(mid);
-      }
-
-      if (value > 0.0 && value < 0.5) {
-        node.setColor(colorBlender(mid, high, (1-0.16667)));
-      } if (value >= 0.5 && value < 1.0) {
-        node.setColor(colorBlender(mid, high, (1-(2*0.16667))));
-      } if (value >= 1.0 && value < 1.5) {
-        node.setColor(colorBlender(mid, high, (1-(3*0.16667))));
-      } if (value >= 1.5 && value < 2.0) {
-        node.setColor(colorBlender(mid, high, (1-(4*0.16667))));
-      } if (value >= 2.0 && value < 2.5) {
-        node.setColor(colorBlender(mid, high, (1-(5*0.16667))));
-      } if (value >= 2.5 && value < 3) {
-        node.setColor(high);
-      }
-
-      if (value < -3.0) {
-        node.setColor(Color.gray);
-      } if (value > 3.0) {
-        node.setColor(Color.black);
-      }
-    }
-
-    private void adjustHue(Node node, Double weight){
-      Color blue = new Color(0f, 51/255f, 153/255f);
-      Color white = Color.white;
-      Color red = new Color(153/255f, 0f, 0f);
-
-      adjustColor(node, weight, blue, white, red);
-    }
-
-    private void adjustHueChange(Node node, Double diff){
-      Color red = new Color(204/255f, 0f, 0f);
-      Color white = Color.white;
-      Color green = new Color(0f, 204/255f, 0f);
-
-      if (diff != 0.0) {
-        adjustColor(node, diff, red, white, green);
-      }
-    }
-
-
-//Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
-
-    public void adjustOpacity(Node node, Double weight){
-      if (weight >= -3.0 && weight < -2.5) {
-        node.setAlpha(0.0833f*1f);
-
-      } if (weight >= -2.5 && weight < -2.0) {
-        node.setAlpha(0.0833f*2f);
-
-      } if (weight >= -2.0 && weight < -1.5) {
-        node.setAlpha(0.0833f*3f);
-
-      } if (weight >= -1.5 && weight < -1.0) {
-        node.setAlpha(0.0833f*4f);
-
-      } if (weight >= -1.0 && weight < -0.5) {
-        node.setAlpha(0.0833f*5f);
-
-      } if (weight >= -0.5 && weight < 0) {
-        node.setAlpha(0.0833f*6f);
-
-      } if (weight >= 0.0 && weight < 0.5) {
-        node.setAlpha(0.0833f*7f);
-
-      } if (weight >= 0.5 && weight < 1.0) {
-        node.setAlpha(0.0833f*8f);
-
-      } if (weight >= 1.0 && weight < 1.5) {
-        node.setAlpha(0.0833f*9f);
-
-      } if (weight >= 1.5 && weight < 2.0) {
-        node.setAlpha(0.0833f*10f);
-
-      } if (weight >= 2.0 && weight < 2.5) {
-        node.setAlpha(0.0833f*11f);
-
-      } if (weight >= 2.5 && weight <= 3) {
-       node.setAlpha(0.0833f*12f);
-      }
-
-      if (weight < -3) {
-        node.setColor(Color.white);
-      }
-      if (weight > 3) {
-        node.setColor(Color.black);
-      }
-    }
+    //
 
 
 
@@ -436,11 +291,10 @@ public void goAlgo() {
 
         graph.readLock();
         boolean isDynamicWeight = graphModel.getEdgeTable().getColumn("weight").isDynamic();
-        // to-do: make compatible with weight_dynamic
-        // provide exception catch otherwise
-        boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn(this.nodeWeightColumnName).isDynamic();
-
 
+        //by jj2018
+        boolean isDynamicNodeWeight = graphModel.getNodeTable().getColumn(this.nodeWeightColumnName).isDynamic();
+        //
 
         Interval interval = graph.getView().getTimeInterval();
 
@@ -448,107 +302,62 @@ public void goAlgo() {
             Node[] nodes = graph.getNodes().toArray();
             Edge[] edges = graph.getEdges().toArray();
 
-
-            Double min_avg_wt = 0.0;
+            //by jj2018
+            //minimums of node averages and of edges
+            Double min_avg_wt_n = 0.0;
+            Double min_wt_e = 0.0;
+            //
 
             for (Edge e : edges) {
 
+            //by jj2018
+            // calculate minimum of edge weights
+            if (getEdgeWeightInfluence() != 0){
+                Double edge_wt = e.getWeight();
+                if (edge_wt < min_wt_e) {
+                  min_wt_e = edge_wt;
+                }
+              }
 
 
+              // calculate minimum of node weight averages
               Node a = e.getSource();
               Node b = e.getTarget();
               if (hasNodeWeight(a) && hasNodeWeight(b)){
                 Double wta = getNodeWeight(a, isDynamicNodeWeight, interval);
                 Double wtb = getNodeWeight(b, isDynamicNodeWeight, interval);
-                Double avg_wt = (wta + wtb)/2;
-                if (avg_wt < min_avg_wt) {
-                  min_avg_wt = avg_wt;
+                Double avg_wt_n = (wta + wtb)/2;
+                if (avg_wt_n < min_avg_wt_n) {
+                  min_avg_wt_n = avg_wt_n;
                 }
               }
-              Double potential_gravity = -(min_avg_wt) + 10;
-              if (min_avg_wt < 0.0 && getGravity() < potential_gravity) {
-                // setStrongGravityMode(true);
-                setGravity(potential_gravity);
-              }
-            }
 
+              // anchor nodes: counteract weight negativity;
+              // negative attraction acts as repulsion and nodes can be pushed out of bounds
 
+              // account for minimum node weight average value
+              Double potential_gravity_e = 2*(-(min_wt_e) + 10);
+              if (min_wt_e < 0.0 && getGravity() < potential_gravity_e) {
+                  setGravity(potential_gravity_e);
+              }
+              // account for minimum edge weight average value
+              Double potential_gravity_n = -(min_avg_wt_n) + 10;
+              if (min_avg_wt_n < 0.0 && getGravity() < potential_gravity_n) {
+                  setGravity(potential_gravity_n);
+              }
 
-
-            // setterMinWeight(nodes);
-            // setterMaxWeight(nodes);
-            // List<Double> all_weights = new ArrayList<Double>();
-            // List<Double> all_changes = new ArrayList<Double>();
-
-            // for (Node n: nodes) {
-            //   TimestampDoubleMap map = (TimestampDoubleMap) n.getAttribute(this.nodeWeightColumnName);
-
-            //   double[] weights = map.toDoubleArray();
-            //   // Interval[] intervals = getIntervals(map);
-            //   double[] timestamps = map.getTimestamps();
-
-
-            //   Interval int_1 = new Interval(timestamps[0], timestamps[1]);
-            //   Interval int_2 = new Interval(timestamps[1], timestamps[2]);
-            //   Interval int_3 = new Interval(timestamps[2], timestamps[3]);
-            //   Interval int_4 = new Interval(timestamps[3], timestamps[4]);
-
-
-
-            //   Double wt_4 = getNodeWeight(n, isDynamicNodeWeight, int_4);
-            //   Double wt_3 = getNodeWeight(n, isDynamicNodeWeight, int_3);
-            //   Double wt_2 = getNodeWeight(n, isDynamicNodeWeight, int_2);
-            //   Double wt_1 = getNodeWeight(n, isDynamicNodeWeight, int_1);
-
-            //   all_changes.add(wt_2 - wt_1);
-            //   all_changes.add(wt_3 - wt_2);
-            //   all_changes.add(wt_4 - wt_3);
-
-
-
-              // for (Double wt: weights) {
-              //   if (wt != null) {
-              //     valugetNodeWeight(n, isDynamicNodeWeight, intervals[1])
-              //     all_changes.add(getNodeWeightChange(n, isDynamicWeight, intervals[1], wt));
-              //     all_changes.add(getNodeWeightChange(n, isDynamicWeight, intervals[2], wt));
-              //     all_changes.add(getNodeWeightChange(n, isDynamicWeight, intervals[3], wt));
-              //     // for (Interval intrvl: intervals)
-              //         // for (int x = 1; x < intervals.length; x++) {
-              //         //   Double change = getNodeWeightChange(n, isDynamicNodeWeight, intervals[x], wt);
-              //         //   all_changes.add(change);
-              //         // }
-
-              //   }
-
-              // }
-
-            // Double[] all_weights_array = new Double[all_weights.size()];
-            // all_weights_array = all_weights.toArray(all_weights_array);
-
-
-
-
-            // double[] tempArray = new double[all_changes.size()];
-            // int i = 0;
-            // for(Double d : all_changes) {
-            //   tempArray[i] = (double) d;
-            //   i++;
-            // }
-            // Arrays.sort(tempArray);
-            // Double min = tempArray[0];
-            // Double max = tempArray[tempArray.length - 1];
-            // int[] histogram = calcHistogram(tempArray, min, max, 12);
-            // Double bin_diff = (max - min) / 12;
-
-            // for (int j=0; j<12 ; j++ ) {
-            //   System.out.println(String.valueOf(min + ((j)*(bin_diff))) + "-" + String.valueOf(min + ((j+1)*(bin_diff))) + ": " + String.valueOf(histogram[j]));
-            // }
-
-            // System.out.println("min: " + String.valueOf(min) + "max: " + String.valueOf(max));
-
-              // System.out.println(histogram[j]);
+              // combine the adjusted gravity for if both edges and nodes have
+              // significant negatives
+              if (min_wt_e < 0 && min_avg_wt_n < 0){
+                Double potential_gravity_combined = (potential_gravity_n + potential_gravity_e);
+                if (getGravity() < potential_gravity_combined) {
+                  setGravity(potential_gravity_combined);
+                }
+              }
 
 
+            }
+            //
 
 
             // Initialise layout data
@@ -619,17 +428,15 @@ public void goAlgo() {
                 }
             }
 
+            //by jj2018
             // Node Weight
             AttractionForce NodeAttraction = ForceFactory.builder.buildAttraction(isLinLogMode(), isOutboundAttractionDistribution(), isAdjustSizes(), 1 * ((isOutboundAttractionDistribution()) ? (outboundAttCompensation) : (1)));
 
-            // setterMinWeight(nodes);
-            // setterMaxWeight(nodes);
 
             for (Edge e : edges) {
               Node node_a = e.getSource();
               Node node_b = e.getTarget();
-              // setStrongGravityMode(true);
-              // setGravity(abs(min_avg_wt) + 10);
+
 
               if (hasNodeWeight(node_a) && hasNodeWeight(node_b)) {
                 Double wt_a = 0.0;
@@ -639,72 +446,64 @@ public void goAlgo() {
 
 
 
-
+                // red-blue heat map mode
                 if (isHeatMapMode()) {
-                  adjustHue(node_a, wt_a);
-                  adjustHue(node_b, wt_b);
-                }
 
+                  HeatmapFeatures.adjustColorWeight(node_a, wt_a);
+                  HeatmapFeatures.adjustColorWeight(node_b, wt_b);
+                }
 
+                // red-green change-oriented heat map mode
                 if (isHeatMapChangeMode() && isDynamicNodeWeight) {
+
+
+                  Double change_a = getNodeWeightChange(node_a, isDynamicNodeWeight, interval, wt_a);
+                  Double change_b = getNodeWeightChange(node_b, isDynamicNodeWeight, interval, wt_b);
+                  HeatmapFeatures.adjustColorChange(node_a, change_a);
+                  HeatmapFeatures.adjustColorChange(node_b, change_b);
+
+
+                }
+                // blue-yellow change-oriented heat map mode
+                if (isHeatMapChangeModeCB() && isDynamicNodeWeight) {
+
                   Double change_a = getNodeWeightChange(node_a, isDynamicNodeWeight, interval, wt_a);
                   Double change_b = getNodeWeightChange(node_b, isDynamicNodeWeight, interval, wt_b);
-                  adjustHueChange(node_a, change_a);
-                  adjustHueChange(node_b, change_b);
+                  HeatmapFeatures.adjustColorblindChange(node_a, change_a);
+                  HeatmapFeatures.adjustColorblindChange(node_b, change_b);
 
 
                 }
 
                 // Opacity applied last so both can be used
                 if (isOpacityMode()){
-                  adjustOpacity(node_a, wt_a);
-                  adjustOpacity(node_b, wt_b);
+                  HeatmapFeatures.adjustOpacity(node_a, wt_a);
+                  HeatmapFeatures.adjustOpacity(node_b, wt_b);
                 }
 
 
 
-
-                NodeAttraction.apply(node_a, node_b, (getNodeWeightScaling()*(wt_a + wt_b)/2));
+                // Node forces applied
+                NodeAttraction.apply(node_a, node_b, (getNodeWeightScaling()*(wt_a + wt_b)/2)); }
 
             }
-    // private double getNodeWeight(Node node, boolean isDynamicNodeWeight, Interval interval) {
-
-    //     if (isDynamicNodeWeight) {
-    //         // node_weight = (Double) n.getAttribute("gravity_x");
-    //         TimestampMap map = (TimestampMap) node.getAttribute(this.nodeWeightColumnName);
-    //         // Estimator estimator = (Estimator) AVERAGE;
-
-    //         Double value = (Double) map.get(interval, Estimator.AVERAGE);
-    //         if (value == null) {
-    //           Interval prev_interval = new Interval (Interval.INFINITY_INTERVAL.getLow(), interval.getLow());
-    //           value = (Double) map.get(prev_interval, Estimator.LAST);
-    //           if (value == null) {
-    //             value = 0.0;
-    //           }
-    //         }
-    //         return value;
-    //     } else {
-    //       return (Double) node.getAttribute(this.nodeWeightColumnName);
-    //     }
-    // }
-
-
-
-              // Attraction.apply(node_a, node_b, getNodeWeight())
+            //
+
+
+
+            if (getEdgeWeightInfluence() == 0) {
+                for (Edge e : edges) {
+                    Attraction.apply(e.getSource(), e.getTarget(), 1);
+                }
+            } else if (getEdgeWeightInfluence() == 1) {
+                for (Edge e : edges) {
+                    Attraction.apply(e.getSource(), e.getTarget(), getEdgeWeight(e, isDynamicWeight, interval));
+                }
+            } else {
+                for (Edge e : edges) {
+                    Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
+                }
             }
-            // if (getEdgeWeightInfluence() == 0) {
-            //     for (Edge e : edges) {
-            //         Attraction.apply(e.getSource(), e.getTarget(), 1);
-            //     }
-            // } else if (getEdgeWeightInfluence() == 1) {
-            //     for (Edge e : edges) {
-            //         Attraction.apply(e.getSource(), e.getTarget(), getEdgeWeight(e, isDynamicWeight, interval));
-            //     }
-            // } else {
-            //     for (Edge e : edges) {
-            //         Attraction.apply(e.getSource(), e.getTarget(), Math.pow(getEdgeWeight(e, isDynamicWeight, interval), getEdgeWeightInfluence()));
-            //     }
-            // }
 
             // Auto adjust speed
             double totalSwinging = 0d;  // How much irregular movement
@@ -817,7 +616,7 @@ public void endAlgo() {
         }
     }
 
-    // BOOKMARK FOR POSSIBLE NAME CHANGE
+
 
     @Override
     public LayoutProperty[] getProperties() {
@@ -828,20 +627,6 @@ public LayoutProperty[] getProperties() {
         final String FORCEATLAS2_THREADS = NbBundle.getMessage(getClass(), "ForceAtlas2.threads");
 
         try {
-            // properties.add(LayoutProperty.createProperty(
-            //         this, Double.class,
-            //         NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.name"),
-            //         FORCEATLAS2_TUNING,
-            //         "ForceAtlas2.maxWeight.name",
-            //         NbBundle.getMessage(getClass(), "ForceAtlas2.maxWeight.desc"),
-            //         "getMaxWeight", "setMaxWeight"));
-            // properties.add(LayoutProperty.createProperty(
-            //         this, Double.class,
-            //         NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.name"),
-            //         FORCEATLAS2_TUNING,
-            //         "ForceAtlas2.minWeight.name",
-            //         NbBundle.getMessage(getClass(), "ForceAtlas2.minWeight.desc"),
-            //         "getMinWeight", "setMinWeight"));
             properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.scalingRatio.name"),
@@ -884,6 +669,13 @@ public LayoutProperty[] getProperties() {
                     "ForceAtlas2.heatMapChangeMode.name",
                     NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapChangeMode.desc"),
                     "isHeatMapChangeMode", "setHeatMapChangeMode"));
+            properties.add(LayoutProperty.createProperty(
+                    this, Boolean.class,
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapChangeModeCB.name"),
+                    FORCEATLAS2_TUNING,
+                    "ForceAtlas2.heatMapChangeModeCB.name",
+                    NbBundle.getMessage(getClass(), "ForceAtlas2.heatMapChangeModeCB.desc"),
+                    "isHeatMapChangeModeCB", "setHeatMapChangeModeCB"));
             properties.add(LayoutProperty.createProperty(
                     this, Double.class,
                     NbBundle.getMessage(getClass(), "ForceAtlas2.gravity.name"),
@@ -977,12 +769,15 @@ public void resetPropertiesValues() {
         } else {
             setScalingRatio(10.0);
         }
-        setStrongGravityMode(false);
-        // setNodeWeightAttraction(false);
+        // strong gravity a default to counteract runaway nodes
+        //by jj2018
+        setStrongGravityMode(true);
         setNodeWeightScaling(1.);
         setHeatMapMode(false);
         setHeatMapChangeMode(false);
+        setHeatMapChangeModeCB(false);
         setOpacityMode(false);
+        //
         setGravity(1.);
 
 
@@ -1050,22 +845,6 @@ public void setLinLogMode(Boolean linLogMode) {
         this.linLogMode = linLogMode;
     }
 
-    public Double getMaxWeight() {
-      return maxWeight;
-    }
-
-    public void setMaxWeight(Double maxWeight) {
-      this.maxWeight = maxWeight;
-    }
-
-    public Double getMinWeight() {
-      return minWeight;
-    }
-
-    public void setMinWeight(Double minWeight) {
-        this.minWeight = minWeight;
-    }
-
     public Double getScalingRatio() {
         return scalingRatio;
     }
@@ -1073,7 +852,7 @@ public Double getScalingRatio() {
     public void setScalingRatio(Double scalingRatio) {
         this.scalingRatio = scalingRatio;
     }
-
+    //by jj2018
     public Boolean isStrongGravityMode() {
         return strongGravityMode;
     }
@@ -1106,12 +885,12 @@ public void setHeatMapChangeMode(Boolean heatMapChangeMode) {
         this.heatMapChangeMode = heatMapChangeMode;
     }
 
-    public Double getGravity() {
-        return gravity;
+    public Boolean isHeatMapChangeModeCB() {
+        return heatMapChangeModeCB;
     }
 
-    public void setGravity(Double gravity) {
-        this.gravity = gravity;
+    public void setHeatMapChangeModeCB(Boolean heatMapChangeModeCB) {
+        this.heatMapChangeModeCB = heatMapChangeModeCB;
     }
 
     public Double getNodeWeightScaling() {
@@ -1122,6 +901,15 @@ public void setNodeWeightScaling(Double factor) {
       this.nodeWeightScaling = factor;
     }
 
+    //
+
+    public Double getGravity() {
+        return gravity;
+    }
+
+    public void setGravity(Double gravity) {
+        this.gravity = gravity;
+    }
 
     public Integer getThreadsCount() {
         return threadCount;
diff --git a/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/HeatmapFeatures.java b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/HeatmapFeatures.java
new file mode 100644
index 0000000..f5f5be2
--- /dev/null
+++ b/modules/NodeWeight/src/main/java/org/gephi/layout/plugins/layout/NodeWeight/HeatmapFeatures.java
@@ -0,0 +1,202 @@
+
+// Appearance features for node weight plugin
+// Submitted in partial fulfillment for the Imperial Computing MSc
+// Authors : Julianne Joswiak <jj2816@imperial.ac.uk>
+
+package org.gephi.layout.plugins.layout.NodeWeight;
+
+import java.awt.Color;
+
+
+import org.gephi.graph.api.Edge;
+import org.gephi.graph.api.Element;
+import org.gephi.graph.api.Graph;
+import org.gephi.graph.api.GraphModel;
+import org.gephi.graph.api.Node;
+import org.gephi.graph.api.Table;
+import org.gephi.graph.api.Estimator;
+import org.gephi.graph.api.Interval;
+import org.gephi.graph.api.types.IntervalMap;
+import org.gephi.graph.api.types.TimeMap;
+import org.gephi.graph.api.types.TimestampMap;
+import org.gephi.graph.api.types.TimestampDoubleMap;
+import org.gephi.graph.api.Interval;
+
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.AttractionForce;
+import org.gephi.layout.plugins.layout.NodeWeight.ForceFactory.RepulsionForce;
+
+
+import org.gephi.layout.spi.Layout;
+import org.gephi.layout.spi.LayoutBuilder;
+import org.gephi.layout.spi.LayoutProperty;
+
+
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.Comparator;
+import java.util.Map;
+import java.util.Arrays;
+
+
+
+import org.openide.util.Exceptions;
+import org.openide.util.NbBundle;
+import org.openide.NotifyDescriptor;
+import org.openide.DialogDisplayer;
+
+import org.gephi.layout.plugins.layout.NodeWeight.AbstractLayout;
+
+
+
+
+
+public class HeatmapFeatures {
+
+  private static Color colorBlender(Color a, Color b, double proportion){
+        float propA = (float) proportion;
+        float propB = 1.0f - propA;
+
+        float rgbA[] = new float[3];
+        float rgbB[] = new float[3];
+
+        a.getColorComponents(rgbA);
+        b.getColorComponents(rgbB);
+
+        Color blend_color = new Color (rgbA[0] * propA + rgbB[0] * propB,
+        rgbA[1] * propA + rgbB[1] * propB, rgbA[2] * propA + rgbB[2] * propB);
+
+        return blend_color;
+      };
+
+    private static void adjustColor(Node node, Double value, Color lo, Color md, Color hi){
+
+      Color low = lo;
+      Color mid = md;
+      Color high = hi;
+
+      if (value >= -3.0 && value < -2.5) {
+        node.setColor(low);
+      } if (value >= -2.5 && value < -2.0) {
+        node.setColor(colorBlender(low, mid, (1-0.16667)));
+      } if (value >= -2.0 && value < -1.5) {
+        node.setColor(colorBlender(low, mid, (1-(2*0.16667))));
+      } if (value >= -1.5 && value < -1.0) {
+        node.setColor(colorBlender(low, mid, (1-(3*0.16667))));
+      } if (value >= -1.0 && value < -0.5) {
+        node.setColor(colorBlender(low, mid, (1-(4*0.16667))));
+      } if (value >= -0.5 && value < 0) {
+        node.setColor(colorBlender(low, mid, (1-(5*0.16667))));
+      }
+
+      if (value == 0.0) {
+        node.setColor(mid);
+      }
+
+      if (value > 0.0 && value < 0.5) {
+        node.setColor(colorBlender(mid, high, (1-0.16667)));
+      } if (value >= 0.5 && value < 1.0) {
+        node.setColor(colorBlender(mid, high, (1-(2*0.16667))));
+      } if (value >= 1.0 && value < 1.5) {
+        node.setColor(colorBlender(mid, high, (1-(3*0.16667))));
+      } if (value >= 1.5 && value < 2.0) {
+        node.setColor(colorBlender(mid, high, (1-(4*0.16667))));
+      } if (value >= 2.0 && value < 2.5) {
+        node.setColor(colorBlender(mid, high, (1-(5*0.16667))));
+      } if (value >= 2.5 && value < 3) {
+        node.setColor(high);
+      }
+
+      if (value < -3.0) {
+        node.setColor(Color.gray);
+      } if (value > 3.0) {
+        node.setColor(Color.black);
+      }
+    };
+
+      protected static void adjustColorWeight(Node node, Double weight){
+        Color blue = new Color(0f, 51/255f, 153/255f);
+        Color white = Color.white;
+        Color red = new Color(153/255f, 0f, 0f);
+
+        adjustColor(node, weight, blue, white, red);
+      };
+
+      protected static void adjustColorChange(Node node, Double diff){
+        Color red = new Color(204/255f, 0f, 0f);
+        Color white = Color.white;
+        Color green = new Color(0f, 204/255f, 0f);
+
+        if (diff != 0.0) {
+          adjustColor(node, diff, red, white, green);
+        }
+      };
+
+      protected static void adjustColorblindChange(Node node, Double diff){
+        Color yellow = new Color(255/255f, 255/255f, 0f);
+        Color white = Color.white;
+        Color blue = new Color(0f, 0f, 255/255f);
+
+        if (diff != 0.0) {
+          adjustColor(node, diff, yellow, white, blue);
+        }
+      };
+
+
+  //Converts the components of a color, as specified by the HSB model, to an equivalent set of values for the default RGB model.
+
+      protected static void adjustOpacity(Node node, Double weight){
+        if (weight >= -3.0 && weight < -2.5) {
+          node.setAlpha(0.0833f*1f);
+
+        } if (weight >= -2.5 && weight < -2.0) {
+          node.setAlpha(0.0833f*2f);
+
+        } if (weight >= -2.0 && weight < -1.5) {
+          node.setAlpha(0.0833f*3f);
+
+        } if (weight >= -1.5 && weight < -1.0) {
+          node.setAlpha(0.0833f*4f);
+
+        } if (weight >= -1.0 && weight < -0.5) {
+          node.setAlpha(0.0833f*5f);
+
+        } if (weight >= -0.5 && weight < 0) {
+          node.setAlpha(0.0833f*6f);
+
+        } if (weight >= 0.0 && weight < 0.5) {
+          node.setAlpha(0.0833f*7f);
+
+        } if (weight >= 0.5 && weight < 1.0) {
+          node.setAlpha(0.0833f*8f);
+
+        } if (weight >= 1.0 && weight < 1.5) {
+          node.setAlpha(0.0833f*9f);
+
+        } if (weight >= 1.5 && weight < 2.0) {
+          node.setAlpha(0.0833f*10f);
+
+        } if (weight >= 2.0 && weight < 2.5) {
+          node.setAlpha(0.0833f*11f);
+
+        } if (weight >= 2.5 && weight <= 3) {
+         node.setAlpha(0.0833f*12f);
+        }
+
+        if (weight < -3) {
+          node.setColor(Color.white);
+        }
+        if (weight > 3) {
+          node.setColor(Color.black);
+        }
+      };
+
+}
+
+
+
+
+
diff --git a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
index 64b035b..b7474b5 100644
--- a/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
+++ b/modules/NodeWeight/src/main/resources/org/gephi/layout/plugins/layout/NodeWeight/Bundle.properties
@@ -11,36 +11,35 @@
 
 
 NodeWeight.name=Node Weight
-NodeWeight.description=Quality layout: a linear-attraction linear-repulsion model with few approximations (BarnesHut). Speed automatically computed.
-
+NodeWeight.description=Force Atlas 2 with node weight influence and appearance features.
 
 ForceAtlas2.tuning=Tuning
 ForceAtlas2.behavior=Behavior Alternatives
 ForceAtlas2.performance=Performance
 ForceAtlas2.threads=Threads
 
-# ForceAtlas2.maxWeight.name=Maximum Weight
-# ForceAtlas2.maxWeight.desc=maximum of node weights
-# ForceAtlas2.minWeight.name=Minimum Weight
-# ForceAtlas2.minWeight.desc=minimum of node weights
+# jj2018
 ForceAtlas2.opacityMode.name=Opacity mode
-ForceAtlas2.opacityMode.desc=Opacity changes according to weight (in preview / export), turn on per-node opacity in preview tab to activate
-
+ForceAtlas2.opacityMode.desc=Requires data scaled to its standard deviation. Opacity changes according to weight (in preview / export), turn on per-node opacity in preview tab to activate.
 
 ForceAtlas2.heatMapMode.name=Heat Map
-ForceAtlas2.heatMapMode.desc=Turn on heat map based on normalized node weights
+ForceAtlas2.heatMapMode.desc=Turn on heat map based on normalized node weights. Requires data scaled to its standard deviation.
 
-ForceAtlas2.heatMapChangeMode.name=Heat Map for Change
-ForceAtlas2.heatMapChangeMode.desc=Turn on heat map to show change between time slices in dynamic data
+ForceAtlas2.heatMapChangeMode.name=Change Heat Map
+ForceAtlas2.heatMapChangeMode.desc=Turn on heat map to show change of normalized node weights between time slices in dynamic data.
 
-ForceAtlas2.nodeWeightScaling.name=Node Weight Scaling
-ForceAtlas2.nodeWeightScaling.desc=Adjust scaling on node weight attraction. More creates larger distance between nodes.
+ForceAtlas2.heatMapChangeModeCB.name=Alternative Change Heat Map (Colorblind accessible)
+ForceAtlas2.heatMapChangeModeCB.desc=Turn on heat map to show change of normalized node weights between time slices in dynamic data Requires data scaled to its standard deviation.
 
+ForceAtlas2.nodeWeightScaling.name=Node Weight Influence
+ForceAtlas2.nodeWeightScaling.desc=Adjust scaling on node weight attraction. More creates larger distance between nodes.
+#
 
 
 ForceAtlas2.scalingRatio.name=Scaling
 ForceAtlas2.scalingRatio.desc=How much repulsion you want. More makes a more sparse graph.
 
+# annotations by jj2018 on stronger gravity description
 ForceAtlas2.gravity.name=Gravity
 ForceAtlas2.gravity.desc=Attracts nodes to the center. Prevents islands from drifting away. If negative weight averages in your network, minimum gravity set to avoid nodes floating out of graph space.
 ForceAtlas2.strongGravityMode.name=Stronger Gravity

From 0b1f6476c53a30317922e7e860088643f5acecef Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Thu, 20 Sep 2018 18:10:14 +0100
Subject: [PATCH 28/32] Update README.md

---
 modules/NodeWeight/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
index 0a7e0f6..66788cc 100644
--- a/modules/NodeWeight/README.md
+++ b/modules/NodeWeight/README.md
@@ -1,4 +1,4 @@
-User Guide for Node Weight Plugin
+H1 User Guide for Node Weight Plugin
 
 1. Launch Gephi
 2. Install Node Weight plugin from Plugin menu in Gephi

From dd57f61ffb8e0c4a16e1193b954316b5846f0236 Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Thu, 20 Sep 2018 18:10:31 +0100
Subject: [PATCH 29/32] Update README.md

---
 modules/NodeWeight/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
index 66788cc..4fd148e 100644
--- a/modules/NodeWeight/README.md
+++ b/modules/NodeWeight/README.md
@@ -1,4 +1,4 @@
-H1 User Guide for Node Weight Plugin
+#H1 User Guide for Node Weight Plugin
 
 1. Launch Gephi
 2. Install Node Weight plugin from Plugin menu in Gephi

From 4d2725c11c799f4a32a90e6fc717b1dc142b8795 Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Thu, 20 Sep 2018 18:11:10 +0100
Subject: [PATCH 30/32] Update README.md

---
 modules/NodeWeight/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
index 4fd148e..55c556f 100644
--- a/modules/NodeWeight/README.md
+++ b/modules/NodeWeight/README.md
@@ -1,4 +1,4 @@
-#H1 User Guide for Node Weight Plugin
+# Header 1 User Guide for Node Weight Plugin
 
 1. Launch Gephi
 2. Install Node Weight plugin from Plugin menu in Gephi

From 760b17a24405166c857f585a763594371d24ec7e Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Thu, 20 Sep 2018 18:11:25 +0100
Subject: [PATCH 31/32] Update README.md

---
 modules/NodeWeight/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
index 55c556f..0843f34 100644
--- a/modules/NodeWeight/README.md
+++ b/modules/NodeWeight/README.md
@@ -1,4 +1,4 @@
-# Header 1 User Guide for Node Weight Plugin
+# User Guide for Node Weight Plugin
 
 1. Launch Gephi
 2. Install Node Weight plugin from Plugin menu in Gephi

From 558acf6690510bc191251ceb81e726e89f2958f3 Mon Sep 17 00:00:00 2001
From: Julianne <juliannej@mac.com>
Date: Thu, 20 Sep 2018 18:12:04 +0100
Subject: [PATCH 32/32] Update README.md

---
 modules/NodeWeight/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/NodeWeight/README.md b/modules/NodeWeight/README.md
index 0843f34..a1c45c3 100644
--- a/modules/NodeWeight/README.md
+++ b/modules/NodeWeight/README.md
@@ -1,6 +1,6 @@
 # User Guide for Node Weight Plugin
 
-1. Launch Gephi
+1. Launch Gephi (to get started with Gephi visit https://gephi.org or https://github.com/gephi/gephi)
 2. Install Node Weight plugin from Plugin menu in Gephi
 3. Import data or a .gexf file
   * Dynamic data should be in string form like  [Timestamp: data], [timestamp: data].