Version 2.0.1 - Argh, paxtools and sbgn was not in the build script, so version 2.0 hat a serious bug!

Author: Clemens82

dist/build.xml

@@ -86,12 +86,16 @@
             <zipfileset excludes="META-INF/*.SF" src="${base}/lib/keggapi.jar"/>
             <!-- <zipfileset excludes="META-INF/*.SF" src="${base}/lib/stax-api-1.0.1.jar"/> -->
 
+      <zipfileset excludes="META-INF/*.SF" src="${base}/lib/paxtools-4.1.1_customJenaFix.jar"/>
+      <zipfileset excludes="META-INF/*.SF" src="${base}/lib/org.sbgn.jar"/>
+
+    	
     	      <filelist dir="${base}" files="libquaqua.jnilib,libquaqua64.jnilib"/>
 
 <!-- Uncomment for SysBio classes instead of compiled jar. -->
            <fileset dir="${SysBioPath}/bin">
-              <exclude name="de/zbit/resources/liftover/*"/>
-           	  <exclude name="de/zbit/mapper/*"/>
+              <exclude name="de/zbit/resources/liftover/**/*"/>
+           	  <exclude name="de/zbit/mapper/**/*"/>
             	<exclude name="**/package.html"/>
            	  <exclude name="overview.html"/>
            </fileset>
@@ -105,6 +109,7 @@
             <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/wsdl4j.jar"/>
             <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/axis.jar"/>
     	      <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/sysbio-osx-support.jar"/>
+            <zipfileset excludes="META-INF/*" src="${SysBioPath}/lib/quaqua.jar"/>
             <!-- <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/Java5/saaj.jar"/>-->
             <!-- <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/WSDbfetch.jar"/>-->
             <zipfileset excludes="META-INF/*" src="${SysBioPath}/lib/commons-cli-1.1.jar"/>
@@ -124,7 +129,7 @@
 
             <fileset dir="${SBML2LaTeXPath}/bin"/>
             <zipfileset excludes="META-INF/*.SF" src="${SBML2LaTeXPath}/lib/html2latex.jar"/>
-      
+    	      
     </jar>
   </target>
 

src/de/zbit/kegg/io/KEGG2yGraph.java

@@ -434,23 +434,34 @@ private static NodeList removeOutlier(NodeList nl, Graph2D graph, int threshold)
    */
   public static NodeRealizer setupGroupNode(NodeLabel nl, String changeCaption) {
     GroupNodeRealizer nr = new GroupNodeRealizer();
-    ((GroupNodeRealizer)nr).setGroupClosed(false);
-    nr.setTransparent(true);
+    setupGroupNode(nr);
 
-    if (changeCaption!=null) {
-      nl.setText(changeCaption);
+    if (nl!=null) {
+      if (changeCaption!=null) {
+        nl.setText(changeCaption);
+      }
+      
+      nl.setPosition(NodeLabel.TOP);
+      nl.setBackgroundColor(new Color((float)0.8,(float)0.8,(float)0.8,(float)0.5));
+      nl.setFontSize(10);
+      nl.setAutoSizePolicy(NodeLabel.AUTOSIZE_NODE_WIDTH);
+      
+      nr.setLabel(nl);
     }
 
+    return nr;
+  }
+  
+  public static void setupGroupNode(GroupNodeRealizer nr) {
+    ((GroupNodeRealizer)nr).setGroupClosed(false);
+    // Setting the transparency influences the edges, such that they
+    // will end in the middle of the group node, instead of the border!
+    //nr.setTransparent(true);
+    nr.setFillColor(null);
+    nr.setFillColor2(null);
+    
     nr.setMinimalInsets(new YInsets(5, 2, 2, 2)); // top, left, bottom, right
     nr.setAutoBoundsEnabled(true);
-    nl.setPosition(NodeLabel.TOP);
-    nl.setBackgroundColor(new Color((float)0.8,(float)0.8,(float)0.8,(float)0.5));
-    nl.setFontSize(10);
-    nl.setAutoSizePolicy(NodeLabel.AUTOSIZE_NODE_WIDTH);
-    
-    nr.setLabel(nl);
-    
-    return nr;
   }
 
   /**
@@ -610,11 +621,18 @@ protected Graph2D translateWithoutPreprocessing(Pathway p) {
           nl.setUserData(nodeLink);
         }
 
-        n = graph.createNode(nr);
+        // Crete the node => Either a group or normal node.
         if (addThisNodeToGroupNodeList) {
-          hm.convertToGroupNode(n);
+          n = hm.createGroupNode(graph);
+          //setupGroupNode((GroupNodeRealizer) graph.getRealizer(n));
+          graph.setRealizer(n, nr);
+          
+          //hm.convertToGroupNode(n);
           parentGroupNodes.add(n);
+        } else {
+          n = graph.createNode(nr);
         }
+        
         if (g.isDefaultPosition()) {
           toLayout.add(n);
         }
@@ -649,7 +667,7 @@ protected Graph2D translateWithoutPreprocessing(Pathway p) {
             nl.setUserData(nodeLink);
           }
 
-          // Create a node, but don't set the reference
+          // Create a node for each graphics attribute, but don't set the reference
           graph.createNode(nr);
         }
       }
@@ -970,6 +988,7 @@ else if (e.getType().equals(EntryType.gene))
 
           //gnr.setBorderInsets(new YInsets(1, 1, 1, 1));
 
+          // Create grouped node for all same edges
           Node n = graph.createNode(gnr);
           hm.convertToGroupNode(n);
           hm.setParentNode(nl, n);
@@ -1123,6 +1142,7 @@ private NodeRealizer setupGraphics(NodeRealizer nr, NodeLabel nl, Graphics g) {
     if (nr==null) {
       if (g.getType().equals(GraphicsType.rectangle)) {
         nr = new ShapeNodeRealizer(ShapeNodeRealizer.RECT);
+        //nr = new ShapeNodeRealizerRespectingLabels(ShapeNodeRealizer.RECT);
       } else if (g.getType().equals(GraphicsType.circle)) {
         nr = new ShapeNodeRealizer(ShapeNodeRealizer.ELLIPSE);
         nl.setFontSize(10); // looks better on small ellipses