Add getNodeByStoreId and getEdgeByStoreId methods to Graph

src/main/java/org/gephi/graph/api/Configuration.java

@@ -27,7 +27,7 @@
  * create a <em>GraphModel</em> with custom configuration.
  * <p>
  * Create instances by using the builder:
- * 
+ *
  * <pre>
  * Configuration config = Configuration.builder().build();
  * </pre>
@@ -260,7 +260,7 @@ public boolean isEnableObservers() {
          * for each type.
          * <p>
          * Default is <code>true</code>.
-         * 
+         *
          * @param enableAutoEdgeTypeRegistration enable auto edge type registration
          * @return this builder
          */
@@ -281,7 +281,7 @@ public boolean isEnableAutoEdgeTypeRegistration() {
          * properties aren't needed, disabling them can save memory.
          * <p>
          * Default is <code>true</code>.
-         * 
+         *
          * @param enableNodeProperties enable node properties
          * @return this builder
          */
@@ -302,7 +302,7 @@ public boolean isEnableNodeProperties() {
          * properties aren't needed, disabling them can save memory.
          * <p>
          * Default is <code>true</code>.
-         * 
+         *
          * @param enableEdgeProperties enable edge properties
          * @return this builder
          */
@@ -325,7 +325,7 @@ public boolean isEnableEdgeProperties() {
          * The spatial index can be retrieved from {@link GraphModel#getSpatialIndex()}.
          * <p>
          * Default is <code>false</code>.
-         * 
+         *
          * @param enableSpatialIndex enable edge properties
          * @return this builder
          */
@@ -349,7 +349,7 @@ public boolean isEnableSpatialIndex() {
          * return results.
          * <p>
          * Default is <code>true</code>.
-         * 
+         *
          * @param enableIndexNodes enable node attribute indexing
          * @return this builder
          */
@@ -373,7 +373,7 @@ public boolean isEnableIndexNodes() {
          * return results.
          * <p>
          * Default is <code>true</code>.
-         * 
+         *
          * @param enableIndexEdges enable edge attribute indexing
          * @return this builder
          */
@@ -416,7 +416,7 @@ public boolean isEnableIndexTime() {
          * If disabled, only a single edge of a given type can exist between two nodes.
          * <p>
          * Default is <code>false</code>.
-         * 
+         *
          * @param enableParallelEdgesSameType enable parallel edges of the same type
          * @return this builder
          */
@@ -586,7 +586,7 @@ public Boolean getEdgeWeightColumn() {
     /**
      * Sets whether to create an edge weight column.
      * <p>
-     * 
+     *
      * @deprecated Use {@link #builder()} instead.
      *
      * @param edgeWeightColumn edge weight column

src/main/java/org/gephi/graph/api/Graph.java

@@ -131,6 +131,14 @@ public interface Graph {
      */
     public Node getNode(Object id);
 
+    /**
+     * Gets a node given its store id.
+     *
+     * @param storeId the store id
+     * @return the node, or null if not found
+     */
+    public Node getNodeByStoreId(int storeId);
+
     /**
      * Returns true if a node with <em>id</em> as identifier exists.
      *
@@ -147,6 +155,14 @@ public interface Graph {
      */
     public Edge getEdge(Object id);
 
+    /**
+     * Gets an edge given its store id.
+     *
+     * @param storeId the store id
+     * @return the edge, or null if not found
+     */
+    public Edge getEdgeByStoreId(int storeId);
+
     /**
      * Returns true if an edge with <em>id</em> as identifier exists.
      *

src/main/java/org/gephi/graph/api/GraphModel.java

@@ -38,7 +38,7 @@
  * </ul>
  * <p>
  * New instances can be obtained via the embedded factory:
- * 
+ *
  * <pre>
  * GraphModel model = GraphModel.Factory.newInstance();
  * </pre>
@@ -49,7 +49,7 @@
  * Configuration configuration = Configuration.builder().build();
  * GraphModel model = GraphModel.Factory.newInstance(configuration);
  * </pre>
- * 
+ *
  * This API revolves around a set of simple concepts. A <code>GraphModel</code>
  * encapsulate all elements and metadata associated with a graph structure. In
  * other words it's a single graph, but it also contains configuration, indices,

src/main/java/org/gephi/graph/api/SpatialIndex.java

@@ -17,7 +17,7 @@
 
 /**
  * Object to query the nodes and edges of the graph in a spatial context.
- * 
+ *
  * @author Eduardo Ramos
  */
 public interface SpatialIndex {

src/main/java/org/gephi/graph/api/package.html

@@ -1,8 +1,8 @@
-<html> 
-    <head></head> 
+<html>
+    <head></head>
     <body>
-         Complete API description, where 
+        Complete API description, where
         <code>GraphModel</code>
-         is the entry point.  
+        is the entry point.
     </body>
-</html>
+</html>

src/main/java/org/gephi/graph/api/types/package.html

@@ -1,6 +1,6 @@
-<html> 
-    <head></head> 
+<html>
+    <head></head>
     <body>
-         Custom types the API supports, in addition of primitive and arrays.  
+        Custom types the API supports, in addition of primitive and arrays.
     </body>
-</html>
+</html>

src/main/java/org/gephi/graph/impl/EdgeStore.java

@@ -448,6 +448,14 @@ public EdgeImpl get(int id) {
         return blocks[id / GraphStoreConfiguration.EDGESTORE_BLOCK_SIZE].get(id);
     }
 
+    // Only used for Graph.getEdgeByStoreId
+    public EdgeImpl getForGetByStoreId(int id) {
+        if (id < 0 || !isValidIndex(id)) {
+            return null;
+        }
+        return blocks[id / GraphStoreConfiguration.EDGESTORE_BLOCK_SIZE].get(id);
+    }
+
     public EdgeImpl get(final Object id) {
         checkNonNullObject(id);
 

src/main/java/org/gephi/graph/impl/GraphStore.java

@@ -197,6 +197,16 @@ public NodeImpl getNode(final Object id) {
         }
     }
 
+    @Override
+    public NodeImpl getNodeByStoreId(final int id) {
+        autoReadLock();
+        try {
+            return nodeStore.getForGetByStoreId(id);
+        } finally {
+            autoReadUnlock();
+        }
+    }
+
     @Override
     public boolean hasNode(final Object id) {
         return getNode(id) != null;
@@ -212,6 +222,16 @@ public EdgeImpl getEdge(final Object id) {
         }
     }
 
+    @Override
+    public EdgeImpl getEdgeByStoreId(final int id) {
+        autoReadLock();
+        try {
+            return edgeStore.getForGetByStoreId(id);
+        } finally {
+            autoReadUnlock();
+        }
+    }
+
     @Override
     public boolean hasEdge(final Object id) {
         return getEdge(id) != null;

src/main/java/org/gephi/graph/impl/GraphViewDecorator.java

@@ -318,6 +318,20 @@ public Node getNode(Object id) {
         }
     }
 
+    @Override
+    public Node getNodeByStoreId(int id) {
+        graphStore.autoReadLock();
+        try {
+            NodeImpl node = graphStore.getNodeByStoreId(id);
+            if (node != null && view.containsNode(node)) {
+                return node;
+            }
+            return null;
+        } finally {
+            graphStore.autoReadUnlock();
+        }
+    }
+
     @Override
     public boolean hasNode(final Object id) {
         return getNode(id) != null;
@@ -337,6 +351,20 @@ public Edge getEdge(Object id) {
         }
     }
 
+    @Override
+    public Edge getEdgeByStoreId(int id) {
+        graphStore.autoReadLock();
+        try {
+            EdgeImpl edge = graphStore.getEdgeByStoreId(id);
+            if (edge != null && view.containsEdge(edge)) {
+                return edge;
+            }
+            return null;
+        } finally {
+            graphStore.autoReadUnlock();
+        }
+    }
+
     @Override
     public boolean hasEdge(final Object id) {
         return getEdge(id) != null;

src/main/java/org/gephi/graph/impl/NodeStore.java

@@ -125,6 +125,14 @@ public NodeImpl get(final int id) {
         return blocks[id / GraphStoreConfiguration.NODESTORE_BLOCK_SIZE].get(id);
     }
 
+    // Only used for Graph.getNodeByStoreId
+    public NodeImpl getForGetByStoreId(int id) {
+        if (id < 0 || !isValidIndex(id)) {
+            return null;
+        }
+        return blocks[id / GraphStoreConfiguration.NODESTORE_BLOCK_SIZE].get(id);
+    }
+
     public NodeImpl get(final Object id) {
         int index = dictionary.getInt(id);
         if (index != NodeStore.NULL_ID) {

src/main/java/org/gephi/graph/impl/NodesQuadTree.java

@@ -17,7 +17,7 @@
  * Adapted from https://bitbucket.org/C3/quadtree/wiki/Home
  *
  * TODO: unit tests!!
- * 
+ *
  * @author Eduardo Ramos
  */
 public class NodesQuadTree {

src/main/java/org/gephi/graph/impl/UndirectedDecorator.java

@@ -110,6 +110,11 @@ public Node getNode(Object id) {
         return store.getNode(id);
     }
 
+    @Override
+    public Node getNodeByStoreId(int id) {
+        return store.getNodeByStoreId(id);
+    }
+
     @Override
     public boolean hasNode(final Object id) {
         return store.hasNode(id);
@@ -120,6 +125,11 @@ public Edge getEdge(Object id) {
         return store.getEdge(id);
     }
 
+    @Override
+    public Edge getEdgeByStoreId(int storeId) {
+        return store.getEdgeByStoreId(storeId);
+    }
+
     @Override
     public boolean hasEdge(final Object id) {
         return store.hasEdge(id);

src/main/java/org/gephi/graph/spi/package.html

@@ -1,6 +1,6 @@
-<html> 
-    <head></head> 
+<html>
+    <head></head>
     <body>
-         SPI interfaces clients can implement to extend the API.  
+        SPI interfaces clients can implement to extend the API.
     </body>
-</html>
+</html>

src/test/java/org/gephi/graph/impl/BasicGraphStore.java

@@ -209,6 +209,10 @@ public Node getNode(Object id) {
         return nodeStore.get(id);
     }
 
+    public Node getNodeByStoreId(int storeId) {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
     @Override
     public boolean hasNode(Object id) {
         return nodeStore.get(id) != null;
@@ -219,6 +223,11 @@ public Edge getEdge(Object id) {
         return edgeStore.get(id);
     }
 
+    @Override
+    public Edge getEdgeByStoreId(int storeId) {
+        throw new UnsupportedOperationException("Not supported yet.");
+    }
+
     @Override
     public boolean hasEdge(Object id) {
         return edgeStore.get(id) != null;

src/test/java/org/gephi/graph/impl/GraphStoreTest.java

@@ -620,6 +620,24 @@ public void testGetNode() {
         Assert.assertFalse(graphStore.hasNode("bar"));
     }
 
+    @Test
+    public void testGetNodeByStoreId() {
+        GraphStore graphStore = GraphGenerator.generateTinyGraphStore();
+        for (Node node : graphStore.getNodes().toArray()) {
+            Assert.assertNotNull(graphStore.getNodeByStoreId(node.getStoreId()));
+        }
+    }
+
+    @Test
+    public void testGetNodeByStoreIdIsNull() {
+        GraphStore graphStore = GraphGenerator.generateTinyGraphStore();
+        for (Node node : graphStore.getNodes().toArray()) {
+            int storeId = node.getStoreId();
+            graphStore.removeNode(node);
+            Assert.assertNull(graphStore.getNodeByStoreId(storeId));
+        }
+    }
+
     @Test
     public void testGetEdge() {
         GraphStore graphStore = GraphGenerator.generateTinyGraphStore();
@@ -629,6 +647,23 @@ public void testGetEdge() {
         Assert.assertFalse(graphStore.hasEdge("bar"));
     }
 
+    @Test
+    public void testGetEdgeByStoreId() {
+        GraphStore graphStore = GraphGenerator.generateTinyGraphStore();
+        for (Edge edge : graphStore.getEdges().toArray()) {
+            Assert.assertNotNull(graphStore.getEdgeByStoreId(edge.getStoreId()));
+        }
+    }
+
+    @Test
+    public void testGetEdgeByStoreIdIsNull() {
+        GraphStore graphStore = GraphGenerator.generateTinyGraphStore();
+        Edge toRemove = graphStore.getEdge("0");
+        int storeId = toRemove.getStoreId();
+        graphStore.removeEdge(toRemove);
+        Assert.assertNull(graphStore.getEdgeByStoreId(storeId));
+    }
+
     @Test
     public void testGetMutualEdge() {
         GraphStore graphStore = new GraphStore();