Fix #233 & Fix #232 library updates

matthiaskoenig · Jun 19, 2017 · 3ef400e · 3ef400e
1 parent b62707f
commit 3ef400e
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Showing 3 changed files with 15 additions and 8 deletions.
diff --git a/pom.xml b/pom.xml
@@ -13,7 +13,7 @@
             javafx.animation,javafx.application,javafx.collections,javafx.embed.swing,javafx.geometry,javafx.scene,javafx.scene.layout,javafx.scene.transform,javax.swing,javax.swing.border,javafx.fxml,org.osgi.framework
         </org.osgi.framework.system.packages.extra>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <cytoscape.api.version>3.4.0</cytoscape.api.version>
+        <cytoscape.api.version>3.5.0-RC2</cytoscape.api.version>
 
         <!-- Exclude the long running model tests. For all tests run
             mvn clean install -Dmodels.test.excludes=""
@@ -340,7 +340,7 @@
         <dependency>
             <groupId>net.sf.ehcache</groupId>
             <artifactId>ehcache</artifactId>
-            <version>2.10.3</version>
+            <version>2.10.4</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -444,7 +444,6 @@
             <version>2.8.6</version>
         </dependency>
 
-
         <!-- CombineArchive -->
         <dependency>
             <groupId>de.unirostock.sems</groupId>
@@ -546,7 +545,7 @@
         <dependency>
             <groupId>uk.ac.ebi.uniprot</groupId>
             <artifactId>japi</artifactId>
-            <version>1.0.12</version>
+            <version>1.0.13</version>
             <exclusions>
                 <exclusion>
                     <groupId>ch.qos.logback</groupId>

diff --git a/src/main/resources/styles/cy3sbml-dark.xml b/src/main/resources/styles/cy3sbml-dark.xml
@@ -122,6 +122,7 @@
                     <discreteMappingEntry attributeValue="qual_transition" value="15.0"/>
                     <discreteMappingEntry attributeValue="algebraicRule" value="20.0"/>
                     <discreteMappingEntry attributeValue="fbc_geneProduct" value="40.0"/>
+                    <discreteMappingEntry attributeValue="comp_replacedBy" value="20.0"/>
                     <discreteMappingEntry attributeValue="unit" value="20.0"/>
                     <discreteMappingEntry attributeValue="species" value="40.0"/>
                     <discreteMappingEntry attributeValue="unitDefinition" value="30.0"/>
@@ -132,6 +133,7 @@
                     <discreteMappingEntry attributeValue="eventAssignment" value="20.0"/>
                     <discreteMappingEntry attributeValue="compartment" value="90.0"/>
                     <discreteMappingEntry attributeValue="event" value="40.0"/>
+                    <discreteMappingEntry attributeValue="comp_replacedElement" value="20.0"/>
                     <discreteMappingEntry attributeValue="group" value="60.0"/>
                 </discreteMapping>
             </visualProperty>
@@ -143,11 +145,13 @@
             <visualProperty default="C,C,c,0.00,0.00" name="NODE_LABEL_POSITION">
                 <discreteMapping attributeName="sbml type" attributeType="string">
                     <discreteMappingEntry attributeValue="assignmentRule" value="N,S,c,0.00,0.00"/>
+                    <discreteMappingEntry attributeValue="comp_replacedBy" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="reaction" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="localParameter" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="rateRule" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="parameter" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="kineticLaw" value="N,S,c,0.00,0.00"/>
+                    <discreteMappingEntry attributeValue="comp_replacedElement" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="qual_transition" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="algebraicRule" value="N,S,c,0.00,0.00"/>
                 </discreteMapping>
@@ -157,15 +161,15 @@
                     <discreteMappingEntry attributeValue="reaction" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="qual_transition" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="fbc_geneProduct" value="TRIANGLE"/>
-                    <discreteMappingEntry attributeValue="comp_replacedBy" value="SQUARE"/>
+                    <discreteMappingEntry attributeValue="comp_replacedBy" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="unit" value="PARALLELOGRAM"/>
                     <discreteMappingEntry attributeValue="unitDefinition" value="PARALLELOGRAM"/>
                     <discreteMappingEntry attributeValue="localParameter" value="DIAMOND"/>
                     <discreteMappingEntry attributeValue="parameter" value="DIAMOND"/>
                     <discreteMappingEntry attributeValue="eventAssignment" value="HEXAGON"/>
                     <discreteMappingEntry attributeValue="compartment" value="HEXAGON"/>
                     <discreteMappingEntry attributeValue="event" value="HEXAGON"/>
-                    <discreteMappingEntry attributeValue="comp_replacedElement" value="SQUARE"/>
+                    <discreteMappingEntry attributeValue="comp_replacedElement" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="group" value="HEXAGON"/>
                 </discreteMapping>
             </visualProperty>

diff --git a/src/main/resources/styles/cy3sbml.xml b/src/main/resources/styles/cy3sbml.xml
@@ -122,6 +122,7 @@
                     <discreteMappingEntry attributeValue="qual_transition" value="15.0"/>
                     <discreteMappingEntry attributeValue="algebraicRule" value="20.0"/>
                     <discreteMappingEntry attributeValue="fbc_geneProduct" value="40.0"/>
+                    <discreteMappingEntry attributeValue="comp_replacedBy" value="20.0"/>
                     <discreteMappingEntry attributeValue="unit" value="20.0"/>
                     <discreteMappingEntry attributeValue="species" value="40.0"/>
                     <discreteMappingEntry attributeValue="unitDefinition" value="30.0"/>
@@ -132,6 +133,7 @@
                     <discreteMappingEntry attributeValue="eventAssignment" value="20.0"/>
                     <discreteMappingEntry attributeValue="compartment" value="90.0"/>
                     <discreteMappingEntry attributeValue="event" value="40.0"/>
+                    <discreteMappingEntry attributeValue="comp_replacedElement" value="20.0"/>
                     <discreteMappingEntry attributeValue="group" value="60.0"/>
                 </discreteMapping>
             </visualProperty>
@@ -143,11 +145,13 @@
             <visualProperty default="C,C,c,0.00,0.00" name="NODE_LABEL_POSITION">
                 <discreteMapping attributeName="sbml type" attributeType="string">
                     <discreteMappingEntry attributeValue="assignmentRule" value="N,S,c,0.00,0.00"/>
+                    <discreteMappingEntry attributeValue="comp_replacedBy" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="reaction" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="localParameter" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="rateRule" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="parameter" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="kineticLaw" value="N,S,c,0.00,0.00"/>
+                    <discreteMappingEntry attributeValue="comp_replacedElement" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="qual_transition" value="N,S,c,0.00,0.00"/>
                     <discreteMappingEntry attributeValue="algebraicRule" value="N,S,c,0.00,0.00"/>
                 </discreteMapping>
@@ -157,15 +161,15 @@
                     <discreteMappingEntry attributeValue="reaction" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="qual_transition" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="fbc_geneProduct" value="TRIANGLE"/>
-                    <discreteMappingEntry attributeValue="comp_replacedBy" value="SQUARE"/>
+                    <discreteMappingEntry attributeValue="comp_replacedBy" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="unit" value="PARALLELOGRAM"/>
                     <discreteMappingEntry attributeValue="unitDefinition" value="PARALLELOGRAM"/>
                     <discreteMappingEntry attributeValue="localParameter" value="DIAMOND"/>
                     <discreteMappingEntry attributeValue="parameter" value="DIAMOND"/>
                     <discreteMappingEntry attributeValue="eventAssignment" value="HEXAGON"/>
                     <discreteMappingEntry attributeValue="compartment" value="HEXAGON"/>
                     <discreteMappingEntry attributeValue="event" value="HEXAGON"/>
-                    <discreteMappingEntry attributeValue="comp_replacedElement" value="SQUARE"/>
+                    <discreteMappingEntry attributeValue="comp_replacedElement" value="RECTANGLE"/>
                     <discreteMappingEntry attributeValue="group" value="HEXAGON"/>
                 </discreteMapping>
             </visualProperty>