Generic Model Organism Database Project

Revision: 22279
          http://gmod.svn.sourceforge.net/gmod/?rev=22279&view=rev
Author:   mgibson
Date:     2009-11-19 20:31:56 +0000 (Thu, 19 Nov 2009)

Log Message:
-----------
fixed bug where to-from and from-to were ending up as 2 separate edges
for same type between 2 nodes
no directionality at the moment so same edge!

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/Node.java
    nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
    nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java
    nbrowse/trunk/src/org/nbrowse/io/DBReader.java

Modified: nbrowse/trunk/src/org/jnet/modelset/Node.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Node.java	2009-11-19 19:30:06 UTC (rev 22278)
+++ nbrowse/trunk/src/org/jnet/modelset/Node.java	2009-11-19 20:31:56 UTC (rev 22279)
@@ -592,7 +592,7 @@
      screenY = screen.y;
      screenZ = screen.z;
      screenDiameter = viewer.scaleToScreen(screenZ, Math.abs(madNode));
-     ErrorUtil.debug(this,"new node screen radius "+screenDiameter/2);
+     //ErrorUtil.debug(this,"new node screen radius "+screenDiameter/2);
    }
 
    // note: nodeName cannot be null

Modified: nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2009-11-19 19:30:06 UTC (rev 22278)
+++ nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2009-11-19 20:31:56 UTC (rev 22279)
@@ -312,11 +312,11 @@
               (int)(xA+viewer.calculateStretch(edge.getNode1().screenDiameter/2)*(0.8+Math.sin(0.0175*i))),
               (int)(yA+viewer.calculateStretch(edge.getNode1().screenDiameter/2)*(0.8+Math.cos(0.0175*i))),
               zA);
-            if (i==359)
-              ErrorUtil.debug(this,"**Rendered self edge node radius "+edge.getNode1().screenDiameter/2
-                  +" stretch "+viewer.calculateStretch(edge.getNode1().screenDiameter/2)
-                  +"\n\t\ttm.zoomPercent "+viewer.getZoomPercentFloat()
-                  +" zoom setting "+viewer.getZoomSetting()+"\n");
+//            if (i==359)
+//              ErrorUtil.debug(this,"**Rendered self edge node radius "+edge.getNode1().screenDiameter/2
+//                  +" stretch "+viewer.calculateStretch(edge.getNode1().screenDiameter/2)
+//                  +"\n\t\ttm.zoomPercent "+viewer.getZoomPercentFloat()
+//                  +" zoom setting "+viewer.getZoomSetting()+"\n");
           }
         }
     }

Modified: nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java	2009-11-19 19:30:06 UTC (rev 22278)
+++ nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java	2009-11-19 20:31:56 UTC (rev 22279)
@@ -397,9 +397,12 @@
   public NBEdge findEdge(NBNode from, NBNode to, String type) {
     for (int i = 0; i < from.edgeNum(); i++) {
       NBEdge e = from.edgeAt(i);
-      if (e.toNode == to && e.fromNode == from && (e.getType()).equals(type)) {
-        return e;
-      }
+      if (!e.getType().equals(type)) continue;
+      if (e.toNode == to && e.fromNode == from) return e;
+      // no directionality - assume at the moment - so from-to and to-from
+      // are equivalent and go in same edge!
+      // if !e.isDirectional()...
+      if (e.toNode == from && e.fromNode == to) return e;
     }
     return null;
   }

Modified: nbrowse/trunk/src/org/nbrowse/io/DBReader.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/DBReader.java	2009-11-19 19:30:06 UTC (rev 22278)
+++ nbrowse/trunk/src/org/nbrowse/io/DBReader.java	2009-11-19 20:31:56 UTC (rev 22279)
@@ -12,6 +12,10 @@
 import org.nbrowse.io.database.AmbiguousSearchJdbc;
 import org.nbrowse.utils.ErrorUtil;
 
+/** calls nyuWormRnai for jdbc -> xml and then pipes xml into XMLIO 
+ * which makes graphEltSet - refactor - take out xml (see JdbcGraph work in progress)
+ */
+
 public final class DBReader {
 
     private final XMLio xmlio = new XMLio();


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Revision: 22302
          http://gmod.svn.sourceforge.net/gmod/?rev=22302&view=rev
Author:   mgibson
Date:     2009-12-02 15:49:32 +0000 (Wed, 02 Dec 2009)

Log Message:
-----------


Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2009-12-01 16:18:16 UTC (rev 22301)
+++ nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2009-12-02 15:49:32 UTC (rev 22302)
@@ -387,17 +387,17 @@
     }
   }
   
-   private Point3i getMidEdgePointScreen() {return getMidEdgePointScreen(edge);}
+   private Point3i getMidEdgePointScreen() {return getMidMultiEdgePointScreen(edge);}
    /** Edge actually caches midpt from last calc - so uses that if still valid
     * (nodes in same place)
     * @return mid pt to use for bent 2-line multi edge
     * midPt is not the mid point between 2 nodes, but for multiedge is bent off
     * that so edges arent on top of each other. multi edge is 2 lines that meet
     * at midpt */
-  private Point3i getMidEdgePointScreen(Edge e) {
+  private Point3i getMidMultiEdgePointScreen(Edge e) {
     if (e.hasValidMidEdgePoint()) return e.getMidEdgePoint();
     // edge.getMidEdgePoint?? should edge know how to gets its midpoint?
-    Point3i mp = jmolToScreen(getMidEdgePoint(e));
+    Point3i mp = jmolToScreen(getMidMultiEdgePoint(e));
     e.setMidEdgePoint(mp);
     return mp;
    
@@ -408,14 +408,14 @@
    * "bent" lines connect with - should cache this
    * @return
    */
-  private Point3f getMidEdgePoint(Edge e) {
-    if (is2D()) return get2DMidEdgePoint(e);
+  private Point3f getMidMultiEdgePoint(Edge e) {
+    if (is2D()) return get2DMidMultiEdgePoint(e);
     else return get3DMidEdgePoint();// should take e!! but not using at moment
   }
   
   /** mid edge bend point for 2D edge - in jmol/angstroms
    * do this in screen coords? - should the edge cache this? why not right? */
-  private Point3f get2DMidEdgePoint(Edge e) {
+  private Point3f get2DMidMultiEdgePoint(Edge e) {
     //Node node1 = edge.getNode1();Node node2 = edge.getNode2();
       //Vector3f vector12 = new Vector3f(); Vector3f vectorNormalR = new Vector3f(); Vector3f vectorNormalS = new Vector3f();
 //    Vector3f vector1P = new Vector3f();  Point3f pt = new Point3f();
@@ -501,11 +501,14 @@
 //  private int z2s(){return node2().screenZ;}
   // i think stretch has to do with how big nodes are
   private float edgeSpacingAngstrom() { 
-    float s =  (float) ((viewer.calculateStretch(node2().getScreenRadius())
-    +viewer.calculateStretch(node1().getScreenRadius()))/(1.5*viewer.getZoomPercentFloat()));
+    Node n1 = node1(); Node n2 = node2();
+    if (n1==null || n2==null) return .1f;//?? 
+    float s =  (float) ((viewer.calculateStretch(n2.getScreenRadius())
+    +viewer.calculateStretch(n1.getScreenRadius()))/(1.5*viewer.getZoomPercentFloat()));
     if (s==0) s = .001f; // ?? used to be 1 which seems wrong
     return s;
   }
+  
   /** for mid edge point where edge bends for 3D edge */
   private Point3f get3DMidEdgePoint() {
     Node node1 = edge.getNode1();
@@ -1364,7 +1367,7 @@
     int dis;
     if (pointInRectangle(x,y,r1)) {
       //&& circleLineIntersect2D(x,y,p1,midPoint(e))) return true;
-      midPt = midPoint(e);
+      midPt = midPointMulti(e);
       dis = disFromPtToLine(x,y,p1,midPt);  
       // if dis< ptRad then try the next few and return lowest
       // oh wait this is working on one edge - this should not only return
@@ -1378,7 +1381,7 @@
     Rectangle r2 = halfMultiRect(e,p2);
     if (!pointInRectangle(x,y,r2)) return false; 
         //&& circleLineIntersect2D(x,y,p2,midPoint(e)));
-    if (midPt==null) midPt = midPoint(e);
+    if (midPt==null) midPt = midPointMulti(e);
     dis = disFromPtToLine(x,y,p2,midPt);
     return dis<=POINT_RADIUS;
   }
@@ -1391,12 +1394,13 @@
   /** @param p node point to make rect with mid point with
    * @return rectangle from point p to midEdgePt, expand by POINT_RADIUS */
   private Rectangle halfMultiRect(Edge e,Point p) {
-    Point3i midPt = getMidEdgePointScreen(e); // uses this.edge,cached mp
+    Point3i midPt = getMidMultiEdgePointScreen(e); // uses this.edge,cached mp
     Rectangle r = new Rectangle(p);
     r.add(toPoint(midPt));
     r.grow(POINT_RADIUS,POINT_RADIUS);
     return r;
   }
   private Point toPoint(Point3i p) { return new Point(p.x,p.y); }
-  private Point midPoint(Edge e) { return toPoint(getMidEdgePointScreen(e)); }
+  // i think multi edge should have its own class??
+  private Point midPointMulti(Edge e) { return toPoint(getMidMultiEdgePointScreen(e)); }
 }

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java	2009-12-01 16:18:16 UTC (rev 22301)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java	2009-12-02 15:49:32 UTC (rev 22302)
@@ -19,10 +19,10 @@
 public class NodeMover {
 
   // rename these ATTRAC,REPUL,ALL_FORCE...
-    private final static float REPULSION_MULTIPLIER = 1; // _C1
+    private final static float REPULSION_MULTIPLIER = 1.3f;//1; // _C1 - 50 is nuts
     private final static float ATTRACTION_SUBTRACTOR = 1; // C2
     private final static float ATTRACTION_MULTIPLIER = 1; // _C3
-    private final static float ATT_AND_REP_MULT = 0.006f; // C4
+    private final static float ATT_AND_REP_MULT = .03f;//0.006f; // C4
     // a new/added constant (C5?), to put a cap on repulsion as gets way hi if 2 nodes on
     // top of each other, .1 is way too restrictive, but 1 actually didnt seem too bad
     // surprisingly, 10000 is too lenient/jumpy, 50 is fine
@@ -40,10 +40,10 @@
   }
 
 
-    /**
-     *  Constructor for the NodeMover object 
-     *
+    /**  Constructor for the NodeMover object
      * @param  graph  The GraphData object to be spring embedded
+     * this is only called by NBrowseApplet new dimension 
+     * which is currently mothballed - this should be phased out for above constructor
      */
     public NodeMover(GraphData graph, int layoutDimensionSwitch) {
       this();
@@ -109,10 +109,10 @@
     /**
      *  Apply the spring embedding method to the graph data.
      *
-     * @param  C1  A constant value used in the spring embedding
-     * @param  C2  A constant value used in the spring embedding
-     * @param  C3  A constant value used in the spring embedding
-     * @param  C4  A constant value used in the spring embedding
+     * @param  C1 REPULSION MULTIPLIER CONSTANT
+     * @param  C2  Attraction Subtractor constant
+     * @param  C3  Attraction Multiplier
+     * @param  C4  Attraction & repulsion multiplier
      * @param  M   The number of calculations to perform during the spring embedding
      */
   private void move(float C1, float C2, float C3, float C4, long iterations) {

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2009-12-01 16:18:16 UTC (rev 22301)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2009-12-02 15:49:32 UTC (rev 22302)
@@ -618,6 +618,8 @@
         status().normal();
         return; // empty graph, nothing to lay out
       }
+      
+      // maybe nodeMover should do all this figuring - not jnet man
       int graphIterations = LAYOUT_NODE_ITERATIONS / edgeAndNodeCount;
       if (graphIterations < MINIMUM_GRAPH_ITERS) graphIterations = MINIMUM_GRAPH_ITERS;
 


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Revision: 22559
          http://gmod.svn.sourceforge.net/gmod/?rev=22559&view=rev
Author:   montys9
Date:     2010-01-15 22:03:10 +0000 (Fri, 15 Jan 2010)

Log Message:
-----------
Committing work in progress for using raw screen data to load up screen.  useRawData boolean flag is used to disable/enable this code.  Still need to re-enable transforming of x,y,z screen coordinates when done loading, as well as handle mult-edges in this case.  Looking to into various options.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
    nbrowse/trunk/src/org/jnet/modelset/Node.java
    nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -44,6 +44,7 @@
 import java.util.Properties;
 import java.util.Vector;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.JnetManager;
 
 /* 
  * 
@@ -62,7 +63,7 @@
   //  System.out.println("ModelLoader " + this + " finalized");
   //}
   
-
+  private static final boolean useRawData = false; // debug flag to use against useRawData - MS
   private ModelLoader mergeModelSet;
   private boolean merging;
   private boolean isMultiFile;
@@ -561,6 +562,12 @@
           alternateLocation, iterNode.getClientNodeReference(), iterNode.getRadius(),
           iterNode.getEncodedColix(), iterNode.getNodeStep(), iterNode.getNodeStepTranslucencyFlag());
       // return node back to iterator in case they want it
+      
+     if (useRawData)
+     {
+      // add raw screen x,y,z coordinates and use them.       	 
+      JnetManager.inst().checkRawNodeData(iterNode.getNodeName(), node);    	 
+     }
       iterNode.setJnetNode(node);
     }
     

Modified: nbrowse/trunk/src/org/jnet/modelset/Node.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -34,6 +34,7 @@
 import org.jnet.util.Quaternion;
 import org.jnet.util.TextFormat;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.JnetManager;
 
 import java.util.BitSet;
 
@@ -45,6 +46,8 @@
 
 final public class Node extends Point3fi {
 
+  private static final boolean useRawData = false; // debug flag to use against useRawData - MS
+	
   final static byte VIBRATION_VECTOR_FLAG = 0x01;
   final static byte IS_HETERO_FLAG = 0x02;
   final static byte FORMAL_CHARGE_MASK = 0x1C;
@@ -586,9 +589,26 @@
        screen = viewer.transformPoint(this);
      else 
        screen = viewer.transformPoint(this, vibrationVectors[nodeIndex]);
-     screenX = screen.x;
-     screenY = screen.y;
-     screenZ = screen.z;
+     // try changing this
+     if (useRawData)
+     {
+       if (!JnetManager.inst().getUseRawLoadData())
+       {
+         screenX = screen.x;
+    	 screenY = screen.y;
+    	 screenZ = screen.z;    	   
+       }
+    	   
+     }
+     else
+     {
+         screenX = screen.x;
+    	 screenY = screen.y;
+    	 screenZ = screen.z;      	 
+     }
+     //screenX = screen.x;
+     //screenY = screen.y;
+     //screenZ = screen.z;
      screenDiameter = viewer.scaleToScreen(screenZ, Math.abs(madNode));
      //ErrorUtil.debug(this,"new node screen radius "+screenDiameter/2);
    }

Modified: nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -42,9 +42,12 @@
 import javax.vecmath.Vector3f; //Victor Chest
 import org.jnet.g3d.Graphics3D; //Victor Chest
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.JnetManager;
 
 public final class SticksRenderer extends ShapeRenderer {
 
+  private static final boolean useRawData = false; // debug flag to use against useRawData - MS	
+  
   /** pixels away from edge for overlap */
   private static final int POINT_RADIUS = 3; // 7??
   protected boolean showMultipleEdges;
@@ -425,6 +428,22 @@
 //    vectorNormalR.cross(vector1P, vector12); if (!is2D()) vectorNormalS.cross(vectorNormalR, vector12);
 //    vectorNormalR.normalize();if (!is2D()) vectorNormalS.normalize();
 //    float midPtx = node1.x+(node2.x - node1.x)/2;float midPty = node1.y+(node2.y - node1.y)/2;float midPtz = node1.z+(node2.z - node1.z)/2;
+	if (useRawData) // for testing - so far not working yet - need to handle mid edge for multi edges to same nodes when using raw screen data-MS
+	{
+	  JnetManager jnet = JnetManager.inst();
+	  if (jnet.getUseRawLoadData()) // can't use mid point in angstroms unless we use something else
+	  {
+		
+		  Node node1 = e.getNode1();
+		  Node node2 = e.getNode2();
+		  Point3f point = new Point3f();
+		  int midX = node1.screenX + node2.screenX / 2;
+		  int midY = node2.screenX + node2.screenX / 2;
+		  point.x = midX;
+		  point.y = midY;
+		  return point;
+	  }
+	}
     Point3f mp = e.exactMidPointJmol();//exactMidPointJmol(e);
     //double b = (double)(node2.getScreenRadius()+node1.getScreenRadius())/(1.5*viewer.getZoomPercentFloat());
     // stretch is in angstroms and does the spacing between edges
@@ -709,11 +728,36 @@
         Point3i ptXY1 = new Point3i();
         Point3i ptXY2 = new Point3i();
 
-        v.set(node1);
-        viewer.transformPoint(v, ptXY1);
-        v.set(node2);
-        viewer.transformPoint(v, ptXY2);
-
+        if (useRawData)
+        {
+          JnetManager jnet = JnetManager.inst();
+          if (jnet.getUseRawLoadData())
+          {
+            v.set(node1);
+            ptXY1.x = node1.screenX;
+            ptXY1.y = node1.screenY;
+            ptXY1.z = node1.screenZ;
+            v.set(node2);
+            ptXY2.x = node2.screenX;
+            ptXY2.y = node2.screenY;
+            ptXY2.z = node2.screenZ;            
+          }
+          else
+          {
+            v.set(node1);
+            viewer.transformPoint(v, ptXY1);
+            v.set(node2);
+            viewer.transformPoint(v, ptXY2);        	  
+          }
+        }
+        else
+        {
+          v.set(node1);
+          viewer.transformPoint(v, ptXY1);
+          v.set(node2);
+          viewer.transformPoint(v, ptXY2);
+        }
+        
         Vector3f vector12 = new Vector3f();
         Vector3f vectorNormalR = new Vector3f();
         Vector3f vectorNormalS = new Vector3f();

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -30,7 +30,7 @@
  */
 class FileDialog {
   
-  private static final boolean useRawXYZ = false; // debug flag to use against useRawXYZ - MS
+  private static final boolean useRawData = false; // debug flag to use against useRawData - MS
   
   private DataLoader dataLoader;
   private JDialog dlg;
@@ -141,7 +141,7 @@
       }
       dataLoader.setNewGraph(g);
       
-      if (useRawXYZ) // new way
+      if (useRawData) // new way
       {
         if (dbCoordCheckBox.isSelected()) // if selected do usual with layout
           StatusManager.inst().newDataDoneLoading();          

Modified: nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -28,6 +28,7 @@
 import org.nbrowse.layouts.spring.vrmlgraph.GraphData;
 import org.nbrowse.layouts.spring.vrmlgraph.NodeView;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.NodeViewI;
 
 /**
@@ -37,7 +38,7 @@
  */
 class TabFileAdapter implements DataAdapterI {
 
-  private static final boolean useRawXYZ = false; // debug flag to use against useRawXYZ -MS
+  private static final boolean useRawData = false; // debug flag to use against useRawData -MS
   
   private static TabFileAdapter singleton;
   private File file;
@@ -80,6 +81,11 @@
     // set RamAdapter as expansion adapter
     //DataAdapterManager.inst().setExpansionAdapter(RamAdapter.inst());
     newGraph = null; // null out old graph
+    
+    if (useRawData) // we clear raw data node info in case we use it-MS
+    {
+      JnetManager.inst().clearRawNodeData();	
+    }
     try { initReader(); }
     catch (FileNotFoundException ex) {
       ErrorUtil.exception(this,ex,"Can not access file "+file); // throw?
@@ -218,6 +224,12 @@
         }
         edgeDatasets.add(new EdgeDataset(type, dataset, value)); // edge datasets
       }
+      if (useRawData) // parse and store raw data just in case we use it
+      {
+        parseRawNodeData(fromName, fromX, fromY, fromZ);
+        parseRawNodeData(toName, toX, toY, toZ);
+      }
+    	        
     }
 
     private final static String USER_PREFIX = "USER_";
@@ -226,6 +238,40 @@
       return USER_PREFIX + u;
     }
 
+    /**
+     * This method will parse the node info along with screen information
+     * @param name
+     * @param sz_X
+     * @param sz_Y
+     * @param sz_Z
+     */
+    private void parseRawNodeData(String name, String sz_X, String sz_Y, String sz_Z)
+    {
+      JnetManager jnet = JnetManager.inst();
+      int screenX = 0;
+      int screenY = 0;
+      int screenZ = 0;
+      
+      try
+      {
+    	screenX = Integer.parseInt(sz_X);  
+      }
+      catch(NumberFormatException ex) {}
+      try
+      {
+      	screenY = Integer.parseInt(sz_Y); 
+      }
+      catch(NumberFormatException ex) {}
+      try
+      {
+      	screenZ = Integer.parseInt(sz_Z); 
+      	
+      }
+      catch(NumberFormatException ex) {}      
+      
+      jnet.setRawNodeData(name, screenX, screenY, screenZ);  	
+    }
+    
     /** Create from to nodes & edge and add to graph */
     private void addToGraph() {
       NBNode from = getNode(fromName); // if new creates & adds to graph

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -401,7 +401,8 @@
     NodeView nodeView =  (NodeView) new NodeView(nodeModel,x,y,z);
     
     // we try adding node objects with x,y,z settings for screen - set no layout on them. - MS
-    nodeView.createRawJnetNode();
+    //nodeView.createRawJnetNode();
+    
     // for initial query but doesnt work for expanded, as already made
     if (nodeView.isQueryNode()) queryNodes.add(nodeView); //=nodeView;
     addNode(nodeView);

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-15 21:53:48 UTC (rev 22558)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-15 22:03:10 UTC (rev 22559)
@@ -4,6 +4,7 @@
 import java.awt.event.MouseEvent;
 import java.util.ArrayList;
 import java.util.BitSet;
+import java.util.HashMap;
 import java.util.List;
 import javax.swing.JButton;
 import javax.swing.JToolBar;
@@ -42,6 +43,98 @@
 
   private static JnetManager singleton;
 
+  /** 
+   * This class uses raw screen data for use when loading directly
+   * @author Monty
+   *
+   */
+  private class RawNodeProperties
+  {
+	 private String name;
+	 private int screenX;
+	 private int screenY;
+	 private int screenZ;
+	 //private short screenDiameter;
+	 
+	 public RawNodeProperties()
+	 {}
+	 
+	 public RawNodeProperties(String name, int screenX, int screenY, int screenZ)
+	 {
+		this.name = name;
+	    this.screenX = screenX;
+	    this.screenY = screenY;
+	    this.screenZ = screenZ;
+	    //this.screenDiameter = screenDiameter;
+	 }
+	 
+	 public String getName()
+	 {
+		 return name;
+	 }
+	 public int getScreenX()
+	 {
+		 return screenX;
+	 }
+
+	 public int getScreenY()
+	 {
+        return screenY;
+	 }
+
+	 public int getScreenZ()
+	 {
+		 return screenZ;
+	 }
+
+	 //public short getScreenDiameter()
+	 //{
+	//	 return screenDiameter;
+	 //}
+	 
+	 public void setName(String name)
+	 {
+        this.name = name;        
+	 }
+	 
+	 public void setScreenX(int screenX)
+	 {
+        this.screenX = screenX;        
+	 }
+
+	 public void setScreenY(int screenY)
+	 {
+        this.screenY = screenY;        
+	 }
+
+	 public void setScreenZ(int screenZ)
+	 {
+        this.screenZ = screenZ;        
+	 }
+	 //public void setScreenDiameter(short screenDiameter)
+	 //{
+     //   this.screenDiameter = screenDiameter;        
+	 //}	 
+	 	 	  
+  }
+  
+  private HashMap rawNodeData = new HashMap(); // new HashMap stores raw screen data for nodes
+
+  private boolean useRawLoadData = false; // false by default
+  
+  public boolean getUseRawLoadData()
+  {
+    return useRawLoadData;
+  }
+  
+  /** use flag to use raw screen positions
+   * 
+   * @param useRawData
+   */
+  public void setUseRawData(boolean useRawLoadData)
+  {
+	  this.useRawLoadData = useRawLoadData;
+  }
   /** oddly Viewer is a subclass of JnetViewer - refactor! */
   private Viewer jnetViewer;
   /** this should be migrated from NBrowseApplet, and changed to an enum? */
@@ -93,7 +186,23 @@
   void increaseNodeSize() { getJnetViewer().increaseNodeSize(); }
   void decreaseNodeSize() { getJnetViewer().decreaseNodeSize(); }
 
-
+  /**
+   * clears RawNodeData Hashmap for new raw screen data to use instead of using layout
+   */
+  public void clearRawNodeData()
+  {
+	  rawNodeData.clear(); // clear the data for new entries
+  }
+  
+  /**
+   * fill rawDataHashMap with raw screen info to use for loading purposes
+   */
+  public void setRawNodeData(String name, int screenX, int screenY, int screenZ)
+  {
+	  RawNodeProperties rawNode = new RawNodeProperties(name, screenX, screenY, screenZ);
+	  rawNodeData.put(name, rawNode); // adds data here for use later if need be
+  }
+  
   /** clear out jnet & navigator */
   private void clear() {
     getJnetViewer().clear();
@@ -119,22 +228,45 @@
     return createRawViewerNode(false,nv);
   }
   
+  public void checkRawNodeData(String label, Node node)
+  {
+	  RawNodeProperties rawNode = null;
+	  if (useRawLoadData)
+	  {
+         rawNode = (RawNodeProperties) rawNodeData.get(label);
+         if (rawNode != null)
+         {
+           node.screenX = rawNode.getScreenX();
+           node.screenY = rawNode.getScreenY();
+           node.screenZ = rawNode.getScreenZ(); //  check to ensue save
+           //node.screenDiameter = rawNode.getScreenDiameter();
+         }
+	  }
+  }
+  
   private Node createRawViewerNode(boolean isNav,NodeView nv) { // handles raw screen x,y,z
     Viewer v = getViewer(isNav);
     // jnet creates random coords
     Node n = v.addJnetNode(nv.getID(), nv.getLabel(),
       nv.getStep(), nv.getJnetColix(), nv.isTranslucent(), is3D());
     
-    // here we assign raw x,y,z values
+    // add raw screen x,y,z coordinates and use them.
+    RawNodeProperties rawNode = (RawNodeProperties) rawNodeData.get(nv.getLabel());
+    n.screenX = rawNode.getScreenX();
+    n.screenY = rawNode.getScreenY();
+    n.screenZ = rawNode.getScreenZ(); //  check to ensue svae
+
     
     if (isNav) { // set navigator to jnets random init coords
       Node jn = nv.getJnetNode();
       n.x = jn.x; n.y = jn.y; n.z = jn.z;
     }
+              	
     v.synchShapesWithModelSet();//could also probably call this after all nodes?
+ 
     v.setTainted(true); // jnet setup new nodes vis flags & such
     // or just set BALLS flag???
-    //redrawJnet(); // happens after all nodes done
+    //redrawJnet(); // happens after all nodes done  - try
     return n;
   }  
 
@@ -372,6 +504,9 @@
 
 
   }
+
+  /** Draw jnet using current display step from Step/TabManager - using raw screen data */
+  void loadRawJnetFiltered() { loadRawJnetFiltered(getDisplayStep()); }
   
   /** Draw jnet using current display step from Step/TabManager */
   void loadJnetFiltered() { loadJnetFiltered(getDisplayStep()); }
@@ -398,11 +533,44 @@
     loadJnet(filteredGraph);
   }
 
+  /**
+   * used for loading raw screen data
+   * @param step
+   */
+  private void loadRawJnetFiltered(int step) {
+	    GraphViewI fullGraph = GraphViewManager.current();
+	    // sets edge widths as well - funny?
+	    GraphViewI filteredGraph = fullGraph.getSubgraph(EdgeFilterState.inst(), step);
+	    loadRawJnet(filteredGraph);
+	  }  
+  
   private void goToStep(int step){
       jnetScript.goToStep(step);
   }
 
 
+
+  private void loadRawJnet(GraphViewI graphView) {        	  
+	    jnetScript.clearEvals();	    
+//	    if (DO_PJM) { // old way jnetScript.loadGraph(graphView); }
+	    //else { // new way
+	    nbJnetAdap().setLoadingJnet();
+	    getJnetViewer().loadDataViaAdapter(nbJnetAdap(), graphView);
+	    nbJnetAdap().setLoadingNavigator();
+	    getNavigationViewer().loadDataViaAdapter(nbJnetAdap(), graphView);
+	    //}
+	    // select query node - nodes? possible with setModelSet?
+	    // orange - query select, red user find ??
+	    // selectionManager.select - normal select - not red/find?
+	    // probably should fire this to sel man though for now only jnetman
+	    // listening so not a big deal
+	    if (graphView().hasQueryNodes())
+	      selectJnetNodes(graphView().getQueryNodes()); // for n : queryNodes select(n) ??
+	    // step buttons?
+	    drawLabels(); // ??
+	    jnetInfoMessage();
+	  }
+  
   private void loadJnet(GraphViewI graphView) {
     jnetScript.clearEvals();
 //    if (DO_PJM) { // old way jnetScript.loadGraph(graphView); }
@@ -431,15 +599,17 @@
    *    
    */
   private void loadRawData() {
-    StatusManager.inst().layout(); // .loadingNbrowseView()??
+	useRawLoadData = true;  
+	// why do a layout here - try not to  
+    //StatusManager.inst().layout(); // .loadingNbrowseView()??
     //ErrorUtil.debug(this, "Loading new nbrowse graph view");
     graphView().loadNewRawData(); // this filters
     try {
-      loadJnetFiltered();
-      //doLayout(true); // works directly on jnet nodes, threaded, true->fit
-      doLayout(false); // don't do layout here
-      createJnetLineBarStepButton(1);
+      loadRawJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
+      doLayout(true); // works directly on jnet nodes, threaded, true->fit      
+      createJnetLineBarStepButton(1);      
       //StatusManager.inst().newDataDoneLayout(); // normal? take out?
+      GraphViewI fullGraph = GraphViewManager.current();
     }
     catch (Exception e) { ErrorUtil.urgent(this, "Load failed "+e, e); }
   }


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Revision: 22578
          http://gmod.svn.sourceforge.net/gmod/?rev=22578&view=rev
Author:   montys9
Date:     2010-01-19 21:35:27 +0000 (Tue, 19 Jan 2010)

Log Message:
-----------
Made changes affecting how edges are converted to angstroms in generating edge bends.  Reverted SticksRenderer back - no need for mid point conversion there - done in edge object instead via angstrom conversion.  This loading of raw screen data is still work in progress.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/Edge.java
    nbrowse/trunk/src/org/jnet/modelset/Node.java
    nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/modelset/Edge.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-01-19 20:03:11 UTC (rev 22577)
+++ nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-01-19 21:35:27 UTC (rev 22578)
@@ -35,9 +35,12 @@
 
 import org.jnet.util.TextFormat;
 import org.jnet.viewer.JnetConstants;
+import org.nbrowse.views.JnetManager;
 
 public final class Edge {
   /** these fields can not be made private at moment they are accessed externally*/
+  private static final boolean useRawData = false;
+  
   Node node1;
   Node node2;
   short order;
@@ -229,9 +232,37 @@
   // convenience...
   /** calc/return exact midpoint in joml/angstroms */
   public Point3f exactMidPointJmol() {
-    Point3f m = new Point3f(node1);
-    m.add(node2);
-    m.scale(.5f);
+    Point3f m = null;
+    if (useRawData)
+    {
+      JnetManager jnet = JnetManager.inst();
+      if (jnet.getUseRawLoadData())
+      {
+        Point3f screenpt1 = new Point3f();
+        screenpt1.x = node1.screenX;
+        screenpt1.y = node1.screenY;
+        screenpt1.z = node1.screenZ;        
+        Point3f ang1 =  new Point3f();
+        Point3f screenpt2 = new Point3f();
+        screenpt2.x = node2.screenX;
+        screenpt2.y = node2.screenY;
+        screenpt2.z = node2.screenZ;        
+        Point3f ang2 =  new Point3f();        
+        jnet.getJnetViewer().unTransformPoint(screenpt1, ang1);
+        jnet.getJnetViewer().unTransformPoint(screenpt2, ang2);
+        m = new Point3f(ang1);
+        m.add(ang2);
+        m.scale(.5f);
+        //return m;
+      }
+    }
+    else
+    {
+      m = new Point3f(node1);
+      m.add(node2);
+      m.scale(.5f);
+      //return m;
+    }
     return m;
   }
   public float x1(){return node1.x;} public float y1(){ return node1.y;}

Modified: nbrowse/trunk/src/org/jnet/modelset/Node.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-19 20:03:11 UTC (rev 22577)
+++ nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-19 21:35:27 UTC (rev 22578)
@@ -595,16 +595,16 @@
        if (!JnetManager.inst().getUseRawLoadData())
        {
          screenX = screen.x;
-    	 screenY = screen.y;
-    	 screenZ = screen.z;    	   
+    	   screenY = screen.y;
+    	   screenZ = screen.z;    	   
        }
     	   
      }
      else
      {
          screenX = screen.x;
-    	 screenY = screen.y;
-    	 screenZ = screen.z;      	 
+    	   screenY = screen.y;
+    	   screenZ = screen.z;      	 
      }
      //screenX = screen.x;
      //screenY = screen.y;

Modified: nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2010-01-19 20:03:11 UTC (rev 22577)
+++ nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2010-01-19 21:35:27 UTC (rev 22578)
@@ -45,9 +45,7 @@
 import org.nbrowse.views.JnetManager;
 
 public final class SticksRenderer extends ShapeRenderer {
-
-  private static final boolean useRawData = false; // debug flag to use against useRawData - MS	
-  
+	  
   /** pixels away from edge for overlap */
   private static final int POINT_RADIUS = 3; // 7??
   protected boolean showMultipleEdges;
@@ -428,22 +426,7 @@
 //    vectorNormalR.cross(vector1P, vector12); if (!is2D()) vectorNormalS.cross(vectorNormalR, vector12);
 //    vectorNormalR.normalize();if (!is2D()) vectorNormalS.normalize();
 //    float midPtx = node1.x+(node2.x - node1.x)/2;float midPty = node1.y+(node2.y - node1.y)/2;float midPtz = node1.z+(node2.z - node1.z)/2;
-	if (useRawData) // for testing - so far not working yet - need to handle mid edge for multi edges to same nodes when using raw screen data-MS
-	{
-	  JnetManager jnet = JnetManager.inst();
-	  if (jnet.getUseRawLoadData()) // can't use mid point in angstroms unless we use something else
-	  {
-		
-		  Node node1 = e.getNode1();
-		  Node node2 = e.getNode2();
-		  Point3f point = new Point3f();
-		  int midX = node1.screenX + node2.screenX / 2;
-		  int midY = node2.screenX + node2.screenX / 2;
-		  point.x = midX;
-		  point.y = midY;
-		  return point;
-	  }
-	}
+
     Point3f mp = e.exactMidPointJmol();//exactMidPointJmol(e);
     //double b = (double)(node2.getScreenRadius()+node1.getScreenRadius())/(1.5*viewer.getZoomPercentFloat());
     // stretch is in angstroms and does the spacing between edges
@@ -728,35 +711,10 @@
         Point3i ptXY1 = new Point3i();
         Point3i ptXY2 = new Point3i();
 
-        if (useRawData)
-        {
-          JnetManager jnet = JnetManager.inst();
-          if (jnet.getUseRawLoadData())
-          {
-            v.set(node1);
-            ptXY1.x = node1.screenX;
-            ptXY1.y = node1.screenY;
-            ptXY1.z = node1.screenZ;
-            v.set(node2);
-            ptXY2.x = node2.screenX;
-            ptXY2.y = node2.screenY;
-            ptXY2.z = node2.screenZ;            
-          }
-          else
-          {
-            v.set(node1);
-            viewer.transformPoint(v, ptXY1);
-            v.set(node2);
-            viewer.transformPoint(v, ptXY2);        	  
-          }
-        }
-        else
-        {
-          v.set(node1);
-          viewer.transformPoint(v, ptXY1);
-          v.set(node2);
-          viewer.transformPoint(v, ptXY2);
-        }
+        v.set(node1);
+        viewer.transformPoint(v, ptXY1);
+        v.set(node2);
+        viewer.transformPoint(v, ptXY2);        
         
         Vector3f vector12 = new Vector3f();
         Vector3f vectorNormalR = new Vector3f();

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-19 20:03:11 UTC (rev 22577)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-19 21:35:27 UTC (rev 22578)
@@ -8,6 +8,7 @@
 import java.util.List;
 import javax.swing.JButton;
 import javax.swing.JToolBar;
+import javax.vecmath.Point3f;
 
 import org.jnet.viewer.Viewer;
 import org.jnet.modelset.Edge;
@@ -240,6 +241,19 @@
            node.screenY = rawNode.getScreenY();
            node.screenZ = rawNode.getScreenZ(); //  check to ensue save
            //node.screenDiameter = rawNode.getScreenDiameter();
+           // try putting into x,y,z unTransformPoint from screen conversion
+           // using default angstrom seems to make edges thinner
+           /*
+           Point3f screenpt = new Point3f();
+           screenpt.x = node.screenX;
+           screenpt.y = node.screenY;
+           screenpt.z = node.screenZ;        
+           Point3f ang =  new Point3f();
+           getJnetViewer().unTransformPoint(screenpt, ang); // transform point here 
+           node.x = ang.x;
+           node.y = ang.y;
+           node.z = ang.z;
+           */
          }
 	  }
   }


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Revision: 22591
          http://gmod.svn.sourceforge.net/gmod/?rev=22591&view=rev
Author:   montys9
Date:     2010-01-20 22:08:37 +0000 (Wed, 20 Jan 2010)

Log Message:
-----------
Code has been set to load model from flat file with graph in same places (except perspective/zoom off a little). working on null description bug in loading from file (from database-in progress.)

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/Edge.java
    nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
    nbrowse/trunk/src/org/jnet/modelset/Node.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
    nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/modelset/Edge.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -39,6 +39,7 @@
 
 public final class Edge {
   /** these fields can not be made private at moment they are accessed externally*/
+  //use this variable only to ignore transformation of angstroms to screen coordinates  
   private static final boolean useRawData = false;
   
   Node node1;

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -63,7 +63,7 @@
   //  System.out.println("ModelLoader " + this + " finalized");
   //}
   
-  private static final boolean useRawData = false; // debug flag to use against useRawData - MS
+  private static final boolean useRawData = true; // debug flag to use against useRawData - MS
   private ModelLoader mergeModelSet;
   private boolean merging;
   private boolean isMultiFile;
@@ -578,6 +578,11 @@
         models[iLast].firstNodeIndex = i;
         models[iLast].bsNodes = null;
       }
+    if (useRawData)
+    {
+      JnetManager.inst().setUseRawData(false); // hopefully done with using this mode
+      //JnetManager.inst().getJnetViewer().reset();
+    }
   }
 
   public Node addNode(String id, String name, short step, short colix, boolean transluc,int size,

Modified: nbrowse/trunk/src/org/jnet/modelset/Node.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -46,6 +46,7 @@
 
 final public class Node extends Point3fi {
 
+  // use this variable only to ignore transformation of angstroms to screen coordinates
   private static final boolean useRawData = false; // debug flag to use against useRawData - MS
 	
   final static byte VIBRATION_VECTOR_FLAG = 0x01;

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -30,7 +30,7 @@
  */
 class FileDialog {
   
-  private static final boolean useRawData = false; // debug flag to use against useRawData - MS
+  private static final boolean useRawData = true; // debug flag to use against useRawData - MS
   
   private DataLoader dataLoader;
   private JDialog dlg;

Modified: nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -2,8 +2,11 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.util.Iterator;
 import java.util.List;
 import java.util.TreeSet;
+import java.util.Vector;
+
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.NodeInfoRetriever;
 import org.nbrowse.dataset.MetaData;
@@ -12,6 +15,7 @@
 import org.nbrowse.dataset.NBNode;
 import org.nbrowse.dataset.NodeAttrMetaData;
 import org.nbrowse.dataset.Species;
+import org.nbrowse.io.database.NodeInfoJdbc;
 import org.nbrowse.utils.ErrorUtil;
 
 /**
@@ -29,6 +33,7 @@
  */
 public class RamAdapter implements DataAdapterI {
 
+  private static final boolean useRawData = false; // debug flag to use against useRawData -MS  
   private boolean coordFileWithDb = false;//true; // come from gui
   private String startingPoint;
 
@@ -52,7 +57,31 @@
   }
 
   private GraphEltSet loadJustFile() throws Exception {
+    if (useRawData)
+    {
+      MetaDataManager.inst().loadDbMetaData(dbAdapter(), taxon());
+      // fire meta changed? let file adapter add types to it?
+      StatusManager.inst().metaDataChanged();        
+    }
     GraphEltSet g = fileAdapter().load();
+    //test
+    if (useRawData)
+    { // do db just for existing nodes only
+      
+      NodeInfoRetriever nodeInfoRetriever = new NodeInfoJdbc();
+      Vector<NBNode> vect = g.getAllNodes();
+      Iterator<NBNode> it = vect.iterator();
+      while (it.hasNext())
+      {
+        NBNode node = it.next();
+        node.setInfoRetriever(nodeInfoRetriever);
+      }      
+      
+      dbAdapter().setGraphToAddTo(g); // setGraphToAdd/MergeTo
+      dbAdapter().setNodeFactory(new FileDbMergeNodeFactory(g));
+      //dbAdapter().load();       
+    }
+   
     if (haveStartingPoint()) activateStartPointNeighbors(g);
     return g;
   }

Modified: nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -38,7 +38,7 @@
  */
 class TabFileAdapter implements DataAdapterI {
 
-  private static final boolean useRawData = false; // debug flag to use against useRawData -MS
+  private static final boolean useRawData = true; // debug flag to use against useRawData -MS
   
   private static TabFileAdapter singleton;
   private File file;
@@ -102,7 +102,7 @@
       ErrorUtil.exception(this, ex,file+"read failed at line "+reader.getLineNumber());
     }
     //doSecondPassCheckForActiveEdges();
-    return newGraph();
+    return newGraph();    
   }
 
   /** first pass of setting up active graph, if edge is connected to starting node

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-20 22:03:31 UTC (rev 22590)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-20 22:08:37 UTC (rev 22591)
@@ -243,7 +243,7 @@
            //node.screenDiameter = rawNode.getScreenDiameter();
            // try putting into x,y,z unTransformPoint from screen conversion
            // using default angstrom seems to make edges thinner
-           /*
+           
            Point3f screenpt = new Point3f();
            screenpt.x = node.screenX;
            screenpt.y = node.screenY;
@@ -253,7 +253,7 @@
            node.x = ang.x;
            node.y = ang.y;
            node.z = ang.z;
-           */
+           
          }
 	  }
   }
@@ -616,6 +616,7 @@
 	useRawLoadData = true;  
 	// why do a layout here - try not to  
     //StatusManager.inst().layout(); // .loadingNbrowseView()??
+	  StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
     //ErrorUtil.debug(this, "Loading new nbrowse graph view");
     graphView().loadNewRawData(); // this filters
     try {


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Revision: 22599
          http://gmod.svn.sourceforge.net/gmod/?rev=22599&view=rev
Author:   montys9
Date:     2010-01-21 22:07:25 +0000 (Thu, 21 Jan 2010)

Log Message:
-----------
work in progress to save ramadapter database data from file .
Includes more updates on loading saved data and current issues.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
    nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
    nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
    nbrowse/trunk/src/org/nbrowse/io/database/NbrowseJdbcAdapter.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-21 18:12:04 UTC (rev 22598)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-21 22:07:25 UTC (rev 22599)
@@ -580,7 +580,9 @@
       }
     if (useRawData)
     {
-      JnetManager.inst().setUseRawData(false); // hopefully done with using this mode
+      JnetManager.inst().setUseRawData(false); // hopefully done with using this mode      
+      //JnetManager.inst().clearRawNodeData(); // remove remnants
+      //JnetManager.inst().getJnetViewer().synchShapesWithModelSet(); // try this-MS      
       //JnetManager.inst().getJnetViewer().reset();
     }
   }

Modified: nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-21 18:12:04 UTC (rev 22598)
+++ nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-21 22:07:25 UTC (rev 22599)
@@ -15,6 +15,7 @@
 import org.nbrowse.dataset.NBNode;
 import org.nbrowse.dataset.NodeAttrMetaData;
 import org.nbrowse.dataset.Species;
+import org.nbrowse.io.database.NbrowseJdbcAdapter;
 import org.nbrowse.io.database.NodeInfoJdbc;
 import org.nbrowse.utils.ErrorUtil;
 
@@ -33,7 +34,7 @@
  */
 public class RamAdapter implements DataAdapterI {
 
-  private static final boolean useRawData = false; // debug flag to use against useRawData -MS  
+  private static final boolean useRawData = true; // debug flag to use against useRawData -MS  
   private boolean coordFileWithDb = false;//true; // come from gui
   private String startingPoint;
 
@@ -67,7 +68,30 @@
     //test
     if (useRawData)
     { // do db just for existing nodes only
+      // load from database, merge (&activate) nodes with file nodes
+      //dbAdapter().setStartingPoint(getStartingPoint());
+      try
+      {
+      if (getStartingPoint() == null)
+        return g;
+      dbAdapter().setGraphToAddTo(g); // setGraphToAdd/MergeTo
+      dbAdapter().setNodeFactory(new FileDbMergeNodeFactory(g));
+      /*
+      Vector<NBNode> vect = g.getAllNodes();
+      Iterator<NBNode> it = vect.iterator();
+      String[] nodeList = new String[vect.size()];
+      int index = 0;
+      while (it.hasNext())
+      {
+        NBNode node = it.next();
+        nodeList[index] = node.getID();
+        index++;
+      }      
       
+      ((NbrowseJdbcAdapter) dbAdapter()).loadNodeNames(nodeList);
+      */
+      
+      /*
       NodeInfoRetriever nodeInfoRetriever = new NodeInfoJdbc();
       Vector<NBNode> vect = g.getAllNodes();
       Iterator<NBNode> it = vect.iterator();
@@ -79,7 +103,24 @@
       
       dbAdapter().setGraphToAddTo(g); // setGraphToAdd/MergeTo
       dbAdapter().setNodeFactory(new FileDbMergeNodeFactory(g));
-      //dbAdapter().load();       
+      */
+      
+      dbAdapter().setStartingPoint(getStartingPoint());
+      dbAdapter().setGraphToAddTo(g); // setGraphToAdd/MergeTo
+      dbAdapter().setNodeFactory(new FileDbMergeNodeFactory(g));
+      dbAdapter().load();
+      // Activate file nodes(if any) and edges, keep track of nodes activated!
+      if (haveStartingPoint())
+      {
+        NBNode startNode = g.findNodeByIdOrName(getStartingPoint());      
+        firstPassActivateNeighbors(startNode,1); // need to track non db actives
+        secondPassActivateNeighborEdges(g,1);
+      }
+      }
+      catch (Exception ex)
+      {
+        
+      }      
     }
    
     if (haveStartingPoint()) activateStartPointNeighbors(g);

Modified: nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-21 18:12:04 UTC (rev 22598)
+++ nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-21 22:07:25 UTC (rev 22599)
@@ -42,6 +42,7 @@
   
   private static TabFileAdapter singleton;
   private File file;
+  private boolean coordWithDb;  // keep this to be informed
   private String startingPoint;
   private GraphEltSet newGraph;
   public static TabFileAdapter inst() {
@@ -234,6 +235,13 @@
 
     private final static String USER_PREFIX = "USER_";
     private String makeUserString(String u) {
+      if (useRawData)
+      {
+        if (!coordWithDb) // try this
+        {
+          return u;
+        }
+      }
       if (u.startsWith(USER_PREFIX)) return u;
       return USER_PREFIX + u;
     }
@@ -470,7 +478,9 @@
     throw new UnsupportedOperationException("Not supported yet.");
   }
   public void setMergeFileAndDb(boolean coordWithDb) {
-    throw new UnsupportedOperationException("Not applicable");
+    //throw new UnsupportedOperationException("Not applicable");
+    // store this variable instead
+    this.coordWithDb = coordWithDb;
   }
   public void setGraphToAddTo(GraphEltSet g) {
     throw new UnsupportedOperationException("Not supported yet.");

Modified: nbrowse/trunk/src/org/nbrowse/io/database/NbrowseJdbcAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/database/NbrowseJdbcAdapter.java	2010-01-21 18:12:04 UTC (rev 22598)
+++ nbrowse/trunk/src/org/nbrowse/io/database/NbrowseJdbcAdapter.java	2010-01-21 22:07:25 UTC (rev 22599)
@@ -534,6 +534,13 @@
     return g;
   }
 
+  /** this is experimental in loading list of nodes */
+  public GraphEltSet loadNodeNames(String[] nodeNames) throws Exception {
+    clearCache();
+    GraphEltSet g = xmlAdap.loadNewData(nodeNames, taxon());
+    return g;
+  }
+  
   private int taxon() { return MetaDataManager.inst().getTaxonId(); }
 
   /** this is a scandal - for now jdbc adapter calling xml adapter as dont yet

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-21 18:12:04 UTC (rev 22598)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-21 22:07:25 UTC (rev 22599)
@@ -240,11 +240,17 @@
            node.screenX = rawNode.getScreenX();
            node.screenY = rawNode.getScreenY();
            node.screenZ = rawNode.getScreenZ(); //  check to ensue save
+           
            //node.screenDiameter = rawNode.getScreenDiameter();
            // try putting into x,y,z unTransformPoint from screen conversion
            // using default angstrom seems to make edges thinner
            
            Point3f screenpt = new Point3f();
+           // try this
+           //screenpt.x = rawNode.getScreenX();
+           //screenpt.y = rawNode.getScreenY();
+           //screenpt.z = rawNode.getScreenZ();
+           
            screenpt.x = node.screenX;
            screenpt.y = node.screenY;
            screenpt.z = node.screenZ;        
@@ -269,8 +275,22 @@
     n.screenX = rawNode.getScreenX();
     n.screenY = rawNode.getScreenY();
     n.screenZ = rawNode.getScreenZ(); //  check to ensue svae
-
+// set angstroms as well
+    Point3f screenpt = new Point3f();
+    // try this
+    //screenpt.x = rawNode.getScreenX();
+    //screenpt.y = rawNode.getScreenY();
+    //screenpt.z = rawNode.getScreenZ();
     
+    screenpt.x = rawNode.screenX;
+    screenpt.y = rawNode.screenY;
+    screenpt.z = rawNode.screenZ;        
+    Point3f ang =  new Point3f();
+    getJnetViewer().unTransformPoint(screenpt, ang); // transform point here 
+    n.x = ang.x;
+    n.y = ang.y;
+    n.z = ang.z;    
+    
     if (isNav) { // set navigator to jnets random init coords
       Node jn = nv.getJnetNode();
       n.x = jn.x; n.y = jn.y; n.z = jn.z;
@@ -622,14 +642,16 @@
 	  	  
     //ErrorUtil.debug(this, "Loading new nbrowse graph view");
     graphView().loadNewRawData(); // this filters
-    graphView().setDoLayout(false); //this prevents expansions from having lines into nodes    
+    //graphView().setDoLayout(false); //this prevents expansions from having lines into nodes    
     try {
       loadRawJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
+      //doLayout(true); // try this - hope it helps expansion problem-MS
       // don't do layout here - no need to
       //doLayout(true); // works directly on jnet nodes, threaded, true->fit      
       createJnetLineBarStepButton(1);      
       //StatusManager.inst().newDataDoneLayout(); // normal? take out?
       GraphViewI fullGraph = GraphViewManager.current();
+      //StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode - try again      
     }
     catch (Exception e) { ErrorUtil.urgent(this, "Load failed "+e, e); }
   }
@@ -735,7 +757,11 @@
   private GraphViewI graphView() { return GraphViewManager.current(); }
   
   private void handleExpansion() {
-    StatusManager.inst().layout();
+    // try for help 
+    //StatusManager.inst().layoutDone();  // say done first before next layout?-try MS 
+    //System.out.println("expanding");        
+    // end try       
+    StatusManager.inst().layout();    
     int expandedStep = graphModel().getStepDepth();
     // deletes node/edges in step & above and flags layout to false for prev nodes
     // and adds expanded nodes/edges from model - with no regard for filtering
@@ -745,8 +771,8 @@
     // addExpandedNodesToJnet(); // hmmmmmmmmmmmmm  // OR
     // expandedStep overrides StepMan displayStep which isnt updated yet & out of synch
     try { 
-      loadJnetFiltered(expandedStep); // can fire ex, null ptr...
-      doLayout(true); // true->fitToScreen ???
+      loadJnetFiltered(expandedStep); // can fire ex, null ptr...        
+      doLayout(true); // true->fitToScreen ???      
       jnetStepButtonExpansion(expandedStep);
       // strScripts
       StatusManager.inst().normal(); // doneExpansionLayout() ?


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Revision: 22603
          http://gmod.svn.sourceforge.net/gmod/?rev=22603&view=rev
Author:   montys9
Date:     2010-01-22 22:19:04 +0000 (Fri, 22 Jan 2010)

Log Message:
-----------
Added use of implements Serializable for GraphEltSet and GraphData objects.  Attempting to use serializable objects to load the data.  Flag useSerialBinary is used to test using the default save/open file menus (using the same save/load dialogs).  Since this code is being tested, the flag is currently set on.  Also, the flag for useRawData (using open file non-cooperate with database option to load raw data) is also still set to on for testing purposes.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/Chain.java
    nbrowse/trunk/src/org/jnet/modelset/Edge.java
    nbrowse/trunk/src/org/jnet/modelset/Group.java
    nbrowse/trunk/src/org/jnet/modelset/Model.java
    nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
    nbrowse/trunk/src/org/jnet/modelset/Node.java
    nbrowse/trunk/src/org/jnet/modelset/Polymer.java
    nbrowse/trunk/src/org/jnet/viewer/StateManager.java
    nbrowse/trunk/src/org/nbrowse/dataset/AttrValueRangeSet.java
    nbrowse/trunk/src/org/nbrowse/dataset/DoubleValue.java
    nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataSetMetaData.java
    nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataset.java
    nbrowse/trunk/src/org/nbrowse/dataset/EdgeTypeMetaData.java
    nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java
    nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
    nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java
    nbrowse/trunk/src/org/nbrowse/dataset/NodeConnection.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
    nbrowse/trunk/src/org/nbrowse/io/StatusEvent.java
    nbrowse/trunk/src/org/nbrowse/io/StatusManager.java
    nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
    nbrowse/trunk/src/org/nbrowse/io/database/EdgeInfoJdbc.java
    nbrowse/trunk/src/org/nbrowse/io/database/NodeInfoJdbc.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java

Modified: nbrowse/trunk/src/org/jnet/modelset/Chain.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Chain.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/Chain.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -23,12 +23,15 @@
  */
 package org.jnet.modelset;
 
+import java.io.Serializable;
 import java.util.BitSet;
 
 import org.jnet.util.BitSetUtil;
 
-public final class Chain {
+public final class Chain implements Serializable {
 
+  static final long serialVersionUID = 1L;	
+	
   ModelSet modelSet;
   Model model;
   char chainID;

Modified: nbrowse/trunk/src/org/jnet/modelset/Edge.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -28,6 +28,7 @@
 import org.jnet.g3d.Graphics3D;
 
 import java.awt.Point;
+import java.io.Serializable;
 import java.util.BitSet;
 
 import javax.vecmath.Point3f;
@@ -37,10 +38,13 @@
 import org.jnet.viewer.JnetConstants;
 import org.nbrowse.views.JnetManager;
 
-public final class Edge {
+public final class Edge implements Serializable {
   /** these fields can not be made private at moment they are accessed externally*/
+
+  static final long serialVersionUID = 1L;	
+	  
   //use this variable only to ignore transformation of angstroms to screen coordinates  
-  private static final boolean useRawData = false;
+  private static final boolean useRawData = false; // PLEASE LEAVE OFF - turning on is used with node where we calculate edge mid point using screen coordinates
   
   Node node1;
   Node node2;
@@ -361,7 +365,8 @@
    * midPt is specifically a multi edge midpoint where the midpoint
    * is offset from true midpoint so multis dont overlap, and edge
    * is really 2 lines bent at midpt */
-  private class MidPtCache {
+  private class MidPtCache implements Serializable {
+	static final long serialVersionUID = 1L;		  
     private Point3i midEdgePoint;
     private int x1,y1,x2,y2;
     private void recordNodePointsForMidPtCache() {

Modified: nbrowse/trunk/src/org/jnet/modelset/Group.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Group.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/Group.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -28,11 +28,13 @@
 import org.jnet.util.Quaternion;
 import org.jnet.viewer.JnetConstants;
 
+import java.io.Serializable;
 import java.util.Hashtable;
 import java.util.BitSet;
 
-public class Group {
-
+public class Group implements Serializable {
+	
+  static final long serialVersionUID = 1L;	
   protected Chain chain;
   int seqcode;
   protected short groupID;

Modified: nbrowse/trunk/src/org/jnet/modelset/Model.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Model.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/Model.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -23,6 +23,7 @@
  */
 package org.jnet.modelset;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Properties;
@@ -30,8 +31,8 @@
 import org.jnet.util.BitSetUtil;
 import org.jnet.viewer.StateManager.Orientation;
 
-public final class Model {
-
+public final class Model implements Serializable {
+  static final long serialVersionUID = 1L;	
   /*
    * In Jnet all nodes and edges are kept as a set of arrays in 
    * the NodeCollection and EdgeCollection objects. 

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -39,6 +39,8 @@
 
 import javax.vecmath.Point3f;
 import javax.vecmath.Vector3f;
+
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Properties;
@@ -57,13 +59,14 @@
  *  
  */
 
-public final class ModelLoader extends ModelSet {
+public final class ModelLoader extends ModelSet implements Serializable {
 
   //public void finalize() {
   //  System.out.println("ModelLoader " + this + " finalized");
   //}
-  
-  private static final boolean useRawData = true; // debug flag to use against useRawData - MS
+  static final long serialVersionUID = 1L;	
+	  
+  private static final boolean useRawData = true; // debug flag to use against useRawData - use to copy saved loaded data from file over node coord info
   private ModelLoader mergeModelSet;
   private boolean merging;
   private boolean isMultiFile;

Modified: nbrowse/trunk/src/org/jnet/modelset/Node.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -36,6 +36,7 @@
 import org.nbrowse.utils.ErrorUtil;
 import org.nbrowse.views.JnetManager;
 
+import java.io.Serializable;
 import java.util.BitSet;
 
 import javax.vecmath.Point2f;
@@ -44,10 +45,10 @@
 import javax.vecmath.Vector3f;
 import javax.vecmath.Point3i;
 
-final public class Node extends Point3fi {
-
+final public class Node extends Point3fi implements Serializable {
+  static final long serialVersionUID = 1L;	
   // use this variable only to ignore transformation of angstroms to screen coordinates
-  private static final boolean useRawData = false; // debug flag to use against useRawData - MS
+  private static final boolean useRawData = false; // debug flag to use against useRawData - PLEASE LEAVE OFF - turning on will prevent screen data updates
 	
   final static byte VIBRATION_VECTOR_FLAG = 0x01;
   final static byte IS_HETERO_FLAG = 0x02;

Modified: nbrowse/trunk/src/org/jnet/modelset/Polymer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Polymer.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/modelset/Polymer.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -23,6 +23,7 @@
  */
 package org.jnet.modelset;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Vector;
 import java.util.Hashtable;
@@ -30,8 +31,8 @@
 import javax.vecmath.Point3f;
 import javax.vecmath.Vector3f;
 
-abstract public class Polymer {
-
+abstract public class Polymer implements Serializable {
+  static final long serialVersionUID = 1L;	
   /*
    * this is a new class of "polymer" that does not necessarily have anything
    * created from it. Jnet can use it instead of any bioPolymer subclass, since

Modified: nbrowse/trunk/src/org/jnet/viewer/StateManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/StateManager.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/jnet/viewer/StateManager.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -26,6 +26,7 @@
 import javax.vecmath.Point3f;
 import javax.vecmath.Matrix3f;
 
+import java.io.Serializable;
 import java.util.Hashtable;
 import java.util.BitSet;
 import java.util.Enumeration;
@@ -253,8 +254,8 @@
     return true;
   }
 
-  public class Orientation {
-
+  public class Orientation implements Serializable {
+	static final long serialVersionUID = 1L;	
     String saveName;
 
     Matrix3f rotationMatrix = new Matrix3f();

Modified: nbrowse/trunk/src/org/nbrowse/dataset/AttrValueRangeSet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/AttrValueRangeSet.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/AttrValueRangeSet.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,5 +1,6 @@
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -7,7 +8,8 @@
  * @author mgibson
  */
    /** ATTR VALUE RANGE SET CLASS */
-final class AttrValueRangeSet implements NodeAttrValueI {
+final class AttrValueRangeSet implements NodeAttrValueI, Serializable {
+  static final long serialVersionUID = 1L;		
   private final String name;
   private Map<String, ValueRange> valToValRange = new HashMap<String, ValueRange>(7);
   AttrValueRangeSet(String n) { name = n; }
@@ -48,7 +50,7 @@
 
     /** Trying this out, inner class for AttrValueRangeSet values
    * its a value string and optional min max range*/
-  private class ValueRange {
+  private class ValueRange implements Serializable {
     private String value;
     private double min,  max;
     private boolean rangeSet = false; // needed?

Modified: nbrowse/trunk/src/org/nbrowse/dataset/DoubleValue.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/DoubleValue.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/DoubleValue.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -5,13 +5,16 @@
 
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
+
 import org.nbrowse.utils.ErrorUtil;
 
 /**
  *
  * @author mgibson
  */
-final class DoubleValue implements NodeAttrValueI {
+final class DoubleValue implements NodeAttrValueI, Serializable {
+  static final long serialVersionUID = 1L;		
   final private String name;
   DoubleValue(String n) { name = n; }
       private double doubleValue; private boolean valueHasBeenSet = false;

Modified: nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataSetMetaData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataSetMetaData.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataSetMetaData.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,5 +1,7 @@
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
+
 /** From Huey-Lings nbrowse 1.0. MetaData about a dataset.
  * A dataset is part of a type. Has description, name and range
  * range is optional
@@ -7,8 +9,8 @@
  * formerly called EdgeDataSetAttr
  */
 
-public class EdgeDataSetMetaData {
-
+public class EdgeDataSetMetaData implements Serializable {
+static final long serialVersionUID = 1L;	
 private String name=null;
 private boolean hasRange=false;
 private double max=0;

Modified: nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataset.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataset.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/EdgeDataset.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,10 +1,12 @@
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
+
 import org.nbrowse.utils.ErrorUtil;
 
 /** dataset values - type,name,cut_off_vals for a specific edge */
-public class EdgeDataset{
-
+public class EdgeDataset implements Serializable {
+  static final long serialVersionUID = 1L;	
   private final static EdgeDataset DEFAULT_DATASET = new EdgeDataset(null,null);
   private String name = MetaDataManager.getDefaultDataset(); // default
   private boolean hasCutoffValue;

Modified: nbrowse/trunk/src/org/nbrowse/dataset/EdgeTypeMetaData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/EdgeTypeMetaData.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/EdgeTypeMetaData.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,5 +1,6 @@
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import org.nbrowse.io.StatusManager;
@@ -10,8 +11,8 @@
  * protein-protein interactions
  */
 
-public class EdgeTypeMetaData {
-
+public class EdgeTypeMetaData implements Serializable {
+  static final long serialVersionUID = 1L;	
   private String name;
   // no need to be a hash
   //private Hashtable<String,EdgeDataSetMetaData> dataSets;

Modified: nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/GraphEltSet.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -4,6 +4,7 @@
  */
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.List;
@@ -32,8 +33,8 @@
  * not immutable! nodes & aedges can be added & deleted
  * MG - ive really reshpaed this into a datamodel and away from view/graphic data
  */
-public final class GraphEltSet implements ImmutableGraphEltSet {
-
+public final class GraphEltSet implements ImmutableGraphEltSet, Serializable {
+  static final long serialVersionUID = 1L;	
   /** Vector of NBNodes */
   private Vector<NBNode> nodes;
   /** vector of NBEdges */

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,6 +1,7 @@
 package org.nbrowse.dataset;
 
 import java.awt.Color;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -11,11 +12,13 @@
  * @author Victor Chest
  */
 
-public class NBEdge {
+public class NBEdge implements Serializable{
+  static final long serialVersionUID = 1L;		
   public NBNode fromNode;
   public NBNode toNode;
+  private static final boolean useSerialBinary = true;
   //public int order; // not used - is this for direction?? i think so
-
+  
   /** Set in XMLio - move to Edge(view)? hmmmm unclear what Edge's (view) fate is
   with victors changes coming ??? is it funny to have color in model? yes it is */
   //public Color color;
@@ -35,6 +38,8 @@
   private boolean linksRetrieved=false;
   private Iterable<String> links;
   
+  private int hashValue;
+  
   public NBEdge(NBNode fromNode, NBNode toNode) {
     this.fromNode = fromNode;
     this.toNode = toNode;
@@ -43,12 +48,20 @@
     this.id = "Edge from "+fromNode+" to "+toNode+" type "+type; // save id for comparison of NBEdge objects
     // we set 
   //order = -1;
+    if (useSerialBinary)
+    {
+    	hashValue = fromNode.hashCode() + toNode.hashCode() + type.hashCode();
+    }
   }
 
   public NBEdge(NBNode from, NBNode to, String type) {
     this(from,to);
     setType(type);
     this.id = "Edge from "+fromNode+" to "+toNode+" type "+type; // save id for comparison of NBEdge objects    
+    if (useSerialBinary)
+    {
+    	hashValue = fromNode.hashCode() + toNode.hashCode() + type.hashCode();    	
+    }
   }
   /** factory method for basic edge, from to type */
   public static NBEdge makeEdge(NBNode from, NBNode to, String type) {
@@ -93,8 +106,14 @@
   }
   /** if override .equals have to do hashcode - edges not currently
    * hashed - improve if needed */
+  // if using own hashcode - causes problems for serialization
   public int hashCode() {
-    return getFrom().hashCode() + getTo().hashCode() + getType().hashCode();
+	if (useSerialBinary)
+	{
+	  return hashValue;	
+	}
+	else
+      return getFrom().hashCode() + getTo().hashCode() + getType().hashCode();
   }
 
   /** return true if from or to node have name or id string */

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,5 +1,6 @@
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.StringTokenizer;
@@ -15,7 +16,8 @@
  * @author Victor Chest
  */
 
-public final class NBNode {
+public final class NBNode implements Serializable {
+  static final long serialVersionUID = 1L;		
   private static final String AUTO_ID_STRING = "AutoID "; // ??
   //String NodeGOTerms = null;
   //HashMap GOTermMap; -- no reason to be a hash - list? set? bag?
@@ -135,7 +137,7 @@
     //int hash = 7;
     // this is auto generated by netBeans - cant just do node.hashCode()?
     //hash = 83 * hash + (this.nodeId != null ? this.nodeId.hashCode() : 0);
-    //return hash;
+    //return hash;	
     return nodeId.hashCode();
   }
 

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NodeConnection.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NodeConnection.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NodeConnection.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -5,6 +5,7 @@
 
 package org.nbrowse.dataset;
 
+import java.io.Serializable;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -14,7 +15,8 @@
  * than one edge between them.
  * @author mgibson
  */
-class NodeConnection {
+class NodeConnection implements Serializable {
+  static final long serialVersionUID = 1L;		
   private NBNode from;
   private NBNode to;
   private Set<NBEdge> edges = new HashSet<NBEdge>(4);

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -13,16 +13,26 @@
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JDialog;
 import javax.swing.JFileChooser;
 import javax.swing.JLabel;
 import javax.swing.JTextField;
+
+import org.jnet.util.Escape;
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.MetaData;
 import org.nbrowse.dataset.MetaDataManager;
+import org.nbrowse.layouts.spring.vrmlgraph.GraphData;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.JnetManager;
+import org.nbrowse.views.Navigation;
 
 /**
  * singleton? should this be in gui?
@@ -30,7 +40,8 @@
  */
 class FileDialog {
   
-  private static final boolean useRawData = true; // debug flag to use against useRawData - MS
+  private static final boolean useRawData = true; // debug flag to use against useRawData - used in sending status msg to load raw screen data
+  private static final boolean useSerialBinary = true; // used for testing - overides save/open to just use serialized binary files for testing
   
   private DataLoader dataLoader;
   private JDialog dlg;
@@ -94,6 +105,7 @@
         } catch (NoFile ex) {} // do nothing, user cancelled
       }
     }
+    
     private class Load implements ActionListener {
       public void actionPerformed(ActionEvent e) { loadFile(); }
     }
@@ -115,6 +127,42 @@
     }
 
   private void loadFile() {
+	if (useSerialBinary)
+	{
+		File sFile;
+		try { sFile = getFile(); } catch (NoFile n) { return; }
+		try
+		{
+		// Read from disk using FileInputStream
+		FileInputStream f_in = new 
+			FileInputStream(sFile.getAbsolutePath());
+
+		// Read object using ObjectInputStream
+		ObjectInputStream obj_in = 
+			new ObjectInputStream (f_in);
+
+		// Read an object
+		Object ges_obj = obj_in.readObject();
+		if (ges_obj instanceof GraphEltSet){
+		   GraphEltSet.getCurrentGraph().clearAll();
+           GraphEltSet.setCurrentGraph((GraphEltSet) ges_obj);
+		}
+		Object gd_obj = obj_in.readObject();
+		if (gd_obj instanceof GraphData) {
+		   GraphData.getCurrentGraphData().clear();
+		   GraphData.setCurrentGraphData((GraphData) gd_obj);
+		}
+		
+		}
+		catch(Exception ex)
+		{
+			ex.printStackTrace();
+		}
+		StatusManager.inst().newSerialDataDoneLoading(); // use with saving    
+	      dlg.dispose();
+	      return;
+	}
+	  
     if (getCoordWithDb() && !haveStartingPoint()) {
       ErrorUtil.urgent(this, "Starting point required to coord with DB");
       return;
@@ -125,6 +173,11 @@
     if (haveStartingPoint()) d.setStartingPoint(getStartingPoint());
     else d.setStartingPoint(null); // for null and whitespace
     d.setMergeFileAndDb(getCoordWithDb());
+    // testing with jmol scripts
+    //String script = "load " + file.getAbsolutePath() + ".sav";
+    //JnetManager.inst().getJnetViewer().script(script);
+    //Navigation.viewer.script(script);    
+    // end test
     // clears out old meta data, creates new empty one that gets populated on load
     StatusManager.inst().newMetaDataLoading(); // loads with data
     // for now, eventually have taxon chooser in file chooser i think
@@ -178,7 +231,40 @@
   public void saveFile() {
     try {
       File file = getFileFromUser(true); // throws NoFile -> cancel
+      
+      if (useSerialBinary) // save as .ser extension too
+      {
+    	  GraphEltSet currGraph = GraphEltSet.getCurrentGraph();
+    	  GraphData graphData = GraphData.getCurrentGraphData();
+    	// Write to disk with FileOutputStream
+    	  try{
+    	  FileOutputStream f_out = new 
+    	  	FileOutputStream(file.getAbsoluteFile());
+
+    	  // Write object with ObjectOutputStream
+    	  ObjectOutputStream obj_out = new
+    	  	ObjectOutputStream (f_out);
+
+    	  // Write GraphEltSet object out to file
+    	  obj_out.writeObject ( currGraph );
+    	  // Write GraphData object to file
+    	  obj_out.writeObject(graphData);
+    	  obj_out.flush();
+    	  }
+    	  catch(Exception ex)
+    	  {
+    		  ex.printStackTrace();
+    	  }
+    	  return;
+      }
+      
       getFileAdapter(file).save();
+
+      // jmol test
+      //String script = "save " + file.getAbsolutePath() + ".sav";
+      //JnetManager.inst().getJnetViewer().script(script);
+      //Navigation.viewer.script(script);
+      // end test
     } catch (NoFile ex) {} // do nothing
   }
   private DataAdapterManager dataMan() { return DataAdapterManager.inst(); }

Modified: nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -34,7 +34,7 @@
  */
 public class RamAdapter implements DataAdapterI {
 
-  private static final boolean useRawData = true; // debug flag to use against useRawData -MS  
+  private static final boolean useRawData = true; // debug flag to use against useRawData - turn this on to test with database
   private boolean coordFileWithDb = false;//true; // come from gui
   private String startingPoint;
 

Modified: nbrowse/trunk/src/org/nbrowse/io/StatusEvent.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/StatusEvent.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/StatusEvent.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -20,7 +20,7 @@
     NEW_DATASOURCE("Changing database"),
     META_LOADING("Loading Edge Type Info"),
     META_DONE(false), META_CHANGED(false),
-    LOADING("Loading"), NEW_SPECIES_LIST(false), NEW_RAW_LOADED_DONE(true); // added NEW_RAW_LOADED_DONE for no layout-MS
+    LOADING("Loading"), NEW_SPECIES_LIST(false), NEW_RAW_LOADED_DONE(true), NEW_SERIAL_LOADED_DONE(true); // added NEW_RAW_LOADED_DONE for no layout-MS
     boolean isChurning = true;
     private String msg;
     private Status(boolean churn,String m) {isChurning=churn; msg=m; }
@@ -55,6 +55,7 @@
   static StatusEvent loadingNewData() { return new StatusEvent(Status.LOADING_NEW); }
   /** done loading new data (not expansion) */
   static StatusEvent newDataDone() { return new StatusEvent(Status.NEW_LOAD_DONE); }
+  static StatusEvent newSerialDataDone() { return new StatusEvent(Status.NEW_SERIAL_LOADED_DONE); }
   static StatusEvent newRawDataDone() { return new StatusEvent(Status.NEW_RAW_LOADED_DONE); }
   public static StatusEvent layout() { return new StatusEvent(Status.LAYOUT);  }
   /** for both new & expansion, this is used to shut down layout from button so oddly
@@ -90,6 +91,7 @@
   public boolean isLoading() { return isLoadingNewData() || isExpansion(); }
   public boolean newDataLoadDone() { return status==Status.NEW_LOAD_DONE; }
   public boolean newRawLoadedDone() { return status==Status.NEW_RAW_LOADED_DONE; }
+  public boolean newSerialLoadedDone() { return status==Status.NEW_SERIAL_LOADED_DONE; }
   public boolean isNewDataLayoutDone() {
     return status==Status.LAYOUT_DONE && type==LoadType.NEW_DATA;
   }

Modified: nbrowse/trunk/src/org/nbrowse/io/StatusManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/StatusManager.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/StatusManager.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -82,6 +82,7 @@
 
   void expansionLoadDone() { fire(StatusEvent.expansionLoadDone()); }
 
+  public void newSerialDataDoneLoading() { fire(StatusEvent.newSerialDataDone()); } // used with loading raw screen data  
   public void newRawDataDoneLoading() { fire(StatusEvent.newRawDataDone()); } // used with loading raw screen data
   public void newDataDoneLoading() { fire(StatusEvent.newDataDone()); }
 

Modified: nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -38,7 +38,7 @@
  */
 class TabFileAdapter implements DataAdapterI {
 
-  private static final boolean useRawData = true; // debug flag to use against useRawData -MS
+  private static final boolean useRawData = true; // debug flag to use against useRawData - used in parsing raw data in file to jnet mgr for storage, removes user defined edges
   
   private static TabFileAdapter singleton;
   private File file;

Modified: nbrowse/trunk/src/org/nbrowse/io/database/EdgeInfoJdbc.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/database/EdgeInfoJdbc.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/database/EdgeInfoJdbc.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,14 +1,15 @@
 package org.nbrowse.io.database;
 
+import java.io.Serializable;
 import java.util.List;
 
 import org.nbrowse.dataset.EdgeInfoRetriever;
 import org.nbrowse.dataset.NBEdge;
 
-public class EdgeInfoJdbc implements EdgeInfoRetriever {
+public class EdgeInfoJdbc implements EdgeInfoRetriever, Serializable {
   
   //private NBEdge edge; // ??
-  
+  static final long serialVersionUID = 1L;	
   private static EdgeInfoJdbc singleton; // ???
   private EdgeInfoJdbc() {}
   public static EdgeInfoJdbc inst() {

Modified: nbrowse/trunk/src/org/nbrowse/io/database/NodeInfoJdbc.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/database/NodeInfoJdbc.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/io/database/NodeInfoJdbc.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,6 +1,7 @@
 package org.nbrowse.io.database;
 
 //import java.sql.*;
+import java.io.Serializable;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.sql.Statement;
@@ -25,7 +26,8 @@
 /** this talks directly to database - refactor! should talk to data adapter
  actually this should be part of the dataadapter - dataadapter should talk to this
  and html should not be produced here - just populate Node */
-public final class NodeInfoJdbc implements NodeInfoRetriever {
+public final class NodeInfoJdbc implements NodeInfoRetriever, Serializable {
+  static final long serialVersionUID = 1L;		
   //private String gene_acc;private HashMap locusMap = new HashMap();
   //private int taxon_id; // phase out //int step;
   /** node_id in node table of nbrowse db, internal table id used for joins, im now feeling like this

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,6 +1,7 @@
 package org.nbrowse.layouts.spring.vrmlgraph;
 
 import java.awt.Color;
+import java.io.Serializable;
 import java.util.List;
 import org.jnet.g3d.Colix3D;
 import org.jnet.modelset.Edge;
@@ -26,8 +27,8 @@
  * this has been modified alot from pjm
  * should probably be moved to nbrowse.views package
  */
-public class EdgeView implements EdgeViewI {
-
+public class EdgeView implements EdgeViewI, Serializable {
+	static final long serialVersionUID = 1L;	
     private NodeViewI _from, _to;
     private int _step;
     private EdgeSize edgeSize = EdgeSize.defaultSize();

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,5 +1,6 @@
 package org.nbrowse.layouts.spring.vrmlgraph;
 
+import java.io.Serializable;
 import java.util.*;
 // not sure if this belongs here - but both are view
 import java.util.logging.Level;
@@ -24,7 +25,8 @@
  * move to views package i think
  * rename GraphView?
  */
-public class GraphData implements GraphViewI {
+public class GraphData implements GraphViewI, Serializable {
+  static final long serialVersionUID = 1L;		
   private static GraphData currentGraphData = new GraphData();
   // why linked list? more efficient?
   private LinkedList<NodeViewI> _nodes = new LinkedList<NodeViewI>();
@@ -59,7 +61,12 @@
   public static GraphData getCurrentGraphData() {
     return currentGraphData;
   }
-    
+
+  /** This is available to replace with loaded GraphData */
+  public static void setCurrentGraphData(GraphData graphData) {
+	    currentGraphData = graphData;
+	  }
+  
   /** get a GraphData for temporary operations */
   public static GraphData getTempGraphData() { return new GraphData(); }
 

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,6 +1,7 @@
 package org.nbrowse.layouts.spring.vrmlgraph;
 
 import java.awt.Color;
+import java.io.Serializable;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -28,8 +29,8 @@
  * for deleting from step expansion, or could del via edge
  * rename to NodeView or NbrowseNode for disambiguation?
  */
-public class NodeView implements NodeViewI {
-
+public class NodeView implements NodeViewI, Serializable {
+  static final long serialVersionUID = 1L;	
   private static Color HILIGHT_COLOR = Color.ORANGE;//Color.decode("#ffb200"); // altheim: new(?) from 1.0 Node
    // attributes
   private float _x,  _y,  _z; // was doubles

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -628,6 +628,28 @@
 
   private NbrowseJnetAdapter nbJnetAdap() { return NbrowseJnetAdapter.inst(); }
 
+  private void loadSerialData() {
+	//clear();
+	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
+	//clearAll(); // try this  
+	//ErrorUtil.debug(this, "Loading new nbrowse graph view");
+	//graphView().loadNewRawData(); // this filters
+	//graphView().setDoLayout(false); //this prevents expansions from having lines into nodes    
+	try {
+	  for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor(); // will this help color index issue with serializing
+	  loadJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
+		
+	  //doLayout(true); // try this - hope it helps expansion problem-MS
+	  // don't do layout here - no need to
+      //doLayout(true); // works directly on jnet nodes, threaded, true->fit      
+	  createJnetLineBarStepButton(1);      
+	  //StatusManager.inst().newDataDoneLayout(); // normal? take out?
+	  GraphViewI fullGraph = GraphViewManager.current();
+	  //StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode - try again      
+	 }
+	 catch (Exception e) { ErrorUtil.urgent(this, "Load failed "+e, e); }	  
+  }
+  
   /**
    * loadRawData will load data using raw screen x,y,z coordinates
    *    
@@ -727,6 +749,11 @@
         //loadNewData();
         //loadedSavedData(); // using x,y,z coordinates      
       }
+      else if (e.newSerialLoadedDone()) { // event for new loaded serial data keeping GraphEltSet and GraphData)
+    	  //loadJnetFiltered();
+    	  //graphView().setDoLayout(true); //see
+    	  loadSerialData(); // will invoke from serialized binary data
+      }
       else if (e.expansionLoaded()) {
         getJnetViewer().clearNodeInfoHoverShape();// clear out hover shape for realloc with new model
          handleExpansion();

Modified: nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-01-22 22:13:05 UTC (rev 22602)
+++ nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-01-22 22:19:04 UTC (rev 22603)
@@ -1,6 +1,7 @@
 package org.nbrowse.views.edgecontrol;
 
 //import org.nbrowse.views.*;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import javax.swing.tree.TreePath;
@@ -41,8 +42,8 @@
  *
  * @author mgibson
  */
-public class EdgeFilterState implements EdgeFilter {
-
+public class EdgeFilterState implements EdgeFilter, Serializable {
+  static final long serialVersionUID = 1L;	
   /** Should these 2 be merged into 1? */
   //private HashMap<String,Boolean> datasetToState = new HashMap<String,Boolean>();
   //private HashMap<String,Double> datasetToCutoff = new HashMap<String,Double>();
@@ -325,7 +326,7 @@
   /** DATASET FILTER INNER CLASS for both display(checkbox) and cutoff?
    and edge size - its tempting to put this in metadata object, but technically
    this is view and meta is model, so in theory may want diff filts for diff views */
-  private class DatasetFilter {
+  private class DatasetFilter implements Serializable {
     private boolean show = true;
     private double cutoff = -1;
     private boolean hasCutoff = false;


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Revision: 22611
          http://gmod.svn.sourceforge.net/gmod/?rev=22611&view=rev
Author:   montys9
Date:     2010-01-25 21:22:56 +0000 (Mon, 25 Jan 2010)

Log Message:
-----------
Turned off usage of raw x,y,z parsing file for now (useRawData flag) - since we are going database route.
Also added comments as well. JNetManager has use of rawNode hash map for initializing attributes of node view objects.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
    nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
    nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -66,7 +66,7 @@
   //}
   static final long serialVersionUID = 1L;	
 	  
-  private static final boolean useRawData = true; // debug flag to use against useRawData - use to copy saved loaded data from file over node coord info
+  private static final boolean useRawData = false; // debug flag to use against useRawData - use to copy saved loaded data from file over node coord info
   private ModelLoader mergeModelSet;
   private boolean merging;
   private boolean isMultiFile;

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -16,7 +16,7 @@
   static final long serialVersionUID = 1L;		
   public NBNode fromNode;
   public NBNode toNode;
-  private static final boolean useSerialBinary = true;
+  private static final boolean useSerialBinary = false; // stopped using for now
   //public int order; // not used - is this for direction?? i think so
   
   /** Set in XMLio - move to Edge(view)? hmmmm unclear what Edge's (view) fate is

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -40,8 +40,8 @@
  */
 class FileDialog {
   
-  private static final boolean useRawData = true; // debug flag to use against useRawData - used in sending status msg to load raw screen data
-  private static final boolean useSerialBinary = true; // used for testing - overides save/open to just use serialized binary files for testing
+  private static final boolean useRawData = false; // debug flag to use against useRawData - used in sending status msg to load raw screen data
+  private static final boolean useSerialBinary = false; // used for testing - overides save/open to just use serialized binary files for testing
   
   private DataLoader dataLoader;
   private JDialog dlg;

Modified: nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/nbrowse/io/RamAdapter.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -34,7 +34,7 @@
  */
 public class RamAdapter implements DataAdapterI {
 
-  private static final boolean useRawData = true; // debug flag to use against useRawData - turn this on to test with database
+  private static final boolean useRawData = false; // debug flag to use against useRawData - turn this on to test with database
   private boolean coordFileWithDb = false;//true; // come from gui
   private String startingPoint;
 

Modified: nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/nbrowse/io/TabFileAdapter.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -38,7 +38,7 @@
  */
 class TabFileAdapter implements DataAdapterI {
 
-  private static final boolean useRawData = true; // debug flag to use against useRawData - used in parsing raw data in file to jnet mgr for storage, removes user defined edges
+  private static final boolean useRawData = false; // debug flag to use against useRawData - used in parsing raw data in file to jnet mgr for storage, removes user defined edges
   
   private static TabFileAdapter singleton;
   private File file;

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -14,6 +14,7 @@
 import org.nbrowse.views.edgecontrol.EdgeFilterState;
 import org.nbrowse.views.EdgeViewI;
 import org.nbrowse.views.GraphViewI;
+import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.NodeViewI;
         
 /**
@@ -398,15 +399,17 @@
    * adds node to node list, adds node to modToVw cache for edge iterating
    * used by expansion and new load
    * Note - this will generate Node objects using screen x,y,z,coordinates.
+   * This version is used for making node view from flat file
    * @param nodeModel
    * @param is3D
    */
   private NodeViewI makeRawNodeView(NBNode nodeModel,boolean is3D) {
+        
     float x = random();
     float y = random();
     float z = is3D ? random() : 0;
     NodeView nodeView =  (NodeView) new NodeView(nodeModel,x,y,z);
-    
+    JnetManager.inst().checkRawNodeViewData(nodeModel.getID(), nodeView); // try change - didn't do this yet
     // we try adding node objects with x,y,z settings for screen - set no layout on them. - MS
     //nodeView.createRawJnetNode();
     

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-25 18:39:22 UTC (rev 22610)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-25 21:22:56 UTC (rev 22611)
@@ -121,6 +121,7 @@
   
   private HashMap rawNodeData = new HashMap(); // new HashMap stores raw screen data for nodes
 
+  // used for flag when trying to use raw screen x,y,z coordinate file.
   private boolean useRawLoadData = false; // false by default
   
   public boolean getUseRawLoadData()
@@ -229,6 +230,30 @@
     return createRawViewerNode(false,nv);
   }
   
+  public void checkRawNodeViewData(String label, NodeView nv)
+  {
+    RawNodeProperties rawNode = null;
+    if (useRawLoadData)
+    {
+         rawNode = (RawNodeProperties) rawNodeData.get(label);
+         if (rawNode != null)
+         {
+           float x = rawNode.getScreenX();
+           float y = rawNode.getScreenY();
+           float z = rawNode.getScreenZ();
+           Point3f screenpt = new Point3f();
+           screenpt.x = x;
+           screenpt.y = y;
+           screenpt.z = z;        
+           Point3f ang =  new Point3f();
+           getJnetViewer().unTransformPoint(screenpt, ang); // transform point here 
+           nv.setX(ang.x);
+           nv.setY(ang.y);
+           nv.setZ(ang.z);           
+         }
+    }
+  }
+  
   public void checkRawNodeData(String label, Node node)
   {
 	  RawNodeProperties rawNode = null;


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Revision: 22620
          http://gmod.svn.sourceforge.net/gmod/?rev=22620&view=rev
Author:   montys9
Date:     2010-01-26 21:56:56 +0000 (Tue, 26 Jan 2010)

Log Message:
-----------
Serializing more objects for testing.  use_serial flag is turned on now for testing.  filtering objects as needed when loading serialized data,etc. work in progress.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/api/JnetAdapter.java
    nbrowse/trunk/src/org/jnet/api/JnetSimpleViewer.java
    nbrowse/trunk/src/org/jnet/api/JnetViewer.java
    nbrowse/trunk/src/org/jnet/api/LayouterInterface.java
    nbrowse/trunk/src/org/jnet/applet/Jnet.java
    nbrowse/trunk/src/org/jnet/collapse/Collapser.java
    nbrowse/trunk/src/org/jnet/g3d/Circle3D.java
    nbrowse/trunk/src/org/jnet/g3d/Cylinder3D.java
    nbrowse/trunk/src/org/jnet/g3d/Font3D.java
    nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java
    nbrowse/trunk/src/org/jnet/g3d/Hermite3D.java
    nbrowse/trunk/src/org/jnet/g3d/Line3D.java
    nbrowse/trunk/src/org/jnet/g3d/Normix3D.java
    nbrowse/trunk/src/org/jnet/g3d/Platform3D.java
    nbrowse/trunk/src/org/jnet/g3d/Rgb16.java
    nbrowse/trunk/src/org/jnet/g3d/Sphere3D.java
    nbrowse/trunk/src/org/jnet/g3d/Triangle3D.java
    nbrowse/trunk/src/org/jnet/layouts/Layouter.java
    nbrowse/trunk/src/org/jnet/modelset/BoxInfo.java
    nbrowse/trunk/src/org/jnet/modelset/EdgeCollection.java
    nbrowse/trunk/src/org/jnet/modelset/ModelCollection.java
    nbrowse/trunk/src/org/jnet/modelset/ModelSet.java
    nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java
    nbrowse/trunk/src/org/jnet/popup/JnetPopup.java
    nbrowse/trunk/src/org/jnet/popup/JnetPopupSwing.java
    nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java
    nbrowse/trunk/src/org/jnet/util/CommandHistory.java
    nbrowse/trunk/src/org/jnet/util/TempArray.java
    nbrowse/trunk/src/org/jnet/viewer/ColorManager.java
    nbrowse/trunk/src/org/jnet/viewer/Compiler.java
    nbrowse/trunk/src/org/jnet/viewer/DataManager.java
    nbrowse/trunk/src/org/jnet/viewer/Eval.java
    nbrowse/trunk/src/org/jnet/viewer/FileManager.java
    nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java
    nbrowse/trunk/src/org/jnet/viewer/ModelManager.java
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/jnet/viewer/PickingManager.java
    nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java
    nbrowse/trunk/src/org/jnet/viewer/ScriptManager.java
    nbrowse/trunk/src/org/jnet/viewer/SelectionManager.java
    nbrowse/trunk/src/org/jnet/viewer/StateManager.java
    nbrowse/trunk/src/org/jnet/viewer/StatusManager.java
    nbrowse/trunk/src/org/jnet/viewer/TransformManager.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java
    nbrowse/trunk/src/org/nbrowse/views/EdgeInfoMaker.java
    nbrowse/trunk/src/org/nbrowse/views/EdgeInfoView.java
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java
    nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java
    nbrowse/trunk/src/org/nbrowse/views/Navigation.java
    nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java
    nbrowse/trunk/src/org/nbrowse/views/NodeInfoView.java

Modified: nbrowse/trunk/src/org/jnet/api/JnetAdapter.java
===================================================================
--- nbrowse/trunk/src/org/jnet/api/JnetAdapter.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/api/JnetAdapter.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -26,6 +26,7 @@
 
 import java.io.BufferedReader;
 import java.io.InputStream;
+import java.io.Serializable;
 import java.util.Properties;
 import java.util.Hashtable;
 import java.util.BitSet;
@@ -53,8 +54,8 @@
  * covalent edgeing radius. 
  * @see org.jnet.api.JnetViewer
  ****************************************************************/
-public abstract class JnetAdapter {
-
+public abstract class JnetAdapter implements Serializable {
+  static final long serialVersionUID = 1L;  
   // These are not used in jnet - should probably comment out
 //  public final static short ORDER_COVALENT_SINGLE = JnetConstants.EDGE_COVALENT_SINGLE;
 //  public final static short ORDER_COVALENT_DOUBLE = JnetConstants.EDGE_COVALENT_DOUBLE;

Modified: nbrowse/trunk/src/org/jnet/api/JnetSimpleViewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/api/JnetSimpleViewer.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/api/JnetSimpleViewer.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -27,6 +27,7 @@
 import java.awt.Graphics;
 import java.awt.Dimension;
 import java.awt.Rectangle;
+import java.io.Serializable;
 
 import org.jnet.viewer.Viewer;
 
@@ -34,8 +35,8 @@
  * This is the high-level API for the JnetViewer for simple access.
  **/
 
-abstract public class JnetSimpleViewer {
-
+abstract public class JnetSimpleViewer implements Serializable {
+  static final long serialVersionUID = 1L;
   /**
    *  This is the main access point for creating an application
    *  or applet viewer. After allocation it is MANDATORY that one of 

Modified: nbrowse/trunk/src/org/jnet/api/JnetViewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/api/JnetViewer.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/api/JnetViewer.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -35,6 +35,8 @@
 import java.util.Properties;
 import java.util.Hashtable;
 import java.io.Reader;
+import java.io.Serializable;
+
 import javax.vecmath.Matrix4f;
 import javax.vecmath.Point3f;
 import javax.vecmath.Point3i;
@@ -50,8 +52,8 @@
  *
  **/
 
-abstract public class JnetViewer extends JnetSimpleViewer {
-
+abstract public class JnetViewer extends JnetSimpleViewer implements Serializable {
+  static final long serialVersionUID = 1L;
   /**
    *  This is the main access point for creating an application
    *  or applet viewer. After allocation it is MANDATORY that one of 

Modified: nbrowse/trunk/src/org/jnet/api/LayouterInterface.java
===================================================================
--- nbrowse/trunk/src/org/jnet/api/LayouterInterface.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/api/LayouterInterface.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -2,6 +2,8 @@
 
 import java.util.BitSet;
 
+import org.jnet.viewer.Viewer;
+
 public interface LayouterInterface { //vc spring layout
 
   public void fitToScreen(); // move somewhere else?
@@ -12,4 +14,5 @@
   public abstract int getProperty(String propertyName);
   public abstract boolean getStatus(String propertyName);
   public abstract void interruptLayout();
+  public abstract void setViewer(Viewer viewer);
 }

Modified: nbrowse/trunk/src/org/jnet/applet/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/jnet/applet/Jnet.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/applet/Jnet.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -36,6 +36,7 @@
 import org.jnet.util.Parser;
 
 import java.awt.*;
+import java.io.Serializable;
 import java.net.URL;
 import java.net.MalformedURLException;
 import java.util.Hashtable;
@@ -797,8 +798,8 @@
     }
   }
 
-  class MyStatusListener implements JnetStatusListener {
-
+  class MyStatusListener implements JnetStatusListener, Serializable {
+    static final long serialVersionUID = 1L;
     public boolean notifyEnabled(int type) {
       switch (type) {
       case JnetConstants.CALLBACK_ANIMFRAME:

Modified: nbrowse/trunk/src/org/jnet/collapse/Collapser.java
===================================================================
--- nbrowse/trunk/src/org/jnet/collapse/Collapser.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/collapse/Collapser.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -1,5 +1,6 @@
 package org.jnet.collapse;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Vector;
@@ -18,8 +19,8 @@
 
 import javax.vecmath.Point3f;
 
-public class Collapser implements CollapserInterface {
-
+public class Collapser implements CollapserInterface, Serializable {
+    static final long serialVersionUID = 1L;
     public Viewer viewer;
     public Node[] nodes;
     public int nodeCount;
@@ -106,7 +107,7 @@
 
   boolean collapseOn;
 
-  private CollapseThread collapseThread;
+  private transient CollapseThread collapseThread; // don't serialize thread will create when setCollapseOn called
 
   private void setCollapseOn(boolean collapseOn) {
     if (!collapseOn) {

Modified: nbrowse/trunk/src/org/jnet/g3d/Circle3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Circle3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Circle3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -23,6 +23,8 @@
  */
 package org.jnet.g3d;
 
+import java.io.Serializable;
+
 /**
  *<p>
  * Implements flat circle drawing/filling routines.
@@ -30,8 +32,9 @@
  *
  * @author Miguel, miguel@...
  */
-final class Circle3D {
-
+final class Circle3D implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   Graphics3D g3d;
 
   Circle3D(Graphics3D g3d) {

Modified: nbrowse/trunk/src/org/jnet/g3d/Cylinder3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Cylinder3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Cylinder3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -24,6 +24,8 @@
 
 package org.jnet.g3d;
 
+import java.io.Serializable;
+
 /**
  *<p>
  * Draws shaded cylinders in 3D.
@@ -34,8 +36,8 @@
  *
  * @author Miguel, miguel@...
  */
-public class Cylinder3D {
-
+public class Cylinder3D implements Serializable {
+  static final long serialVersionUID = 1L;  
   final Graphics3D g3d;
   final Line3D line3d;
 

Modified: nbrowse/trunk/src/org/jnet/g3d/Font3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Font3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Font3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -27,6 +27,7 @@
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.font.TextAttribute;
+import java.io.Serializable;
 import java.util.Hashtable;
 
 import org.jnet.util.Logger;
@@ -41,8 +42,8 @@
  *
  * @author Miguel, miguel@...
  */
-final public class Font3D {
-
+final public class Font3D implements Serializable {
+  static final long serialVersionUID = 1L;  
   public final byte fid;
   public final String fontFace;
   public final String fontStyle;

Modified: nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -26,6 +26,7 @@
 import java.awt.Color;
 import java.awt.Component;
 import java.awt.Image;
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
@@ -143,9 +144,9 @@
  * 
  */
 
-/*final*/ public class Graphics3D implements JnetRendererInterface {
+/*final*/ public class Graphics3D implements JnetRendererInterface, Serializable {
 
-
+  static final long serialVersionUID = 1L;
   Platform3D platform;
   Line3D line3d;
   Circle3D circle3d;

Modified: nbrowse/trunk/src/org/jnet/g3d/Hermite3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Hermite3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Hermite3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -28,6 +28,8 @@
 import javax.vecmath.Tuple3f;
 import javax.vecmath.Point3f;
 import javax.vecmath.Vector3f;
+
+import java.io.Serializable;
 import java.util.Vector;
 
 import org.jnet.api.JnetRendererInterface;
@@ -53,8 +55,8 @@
  *
  * @author Miguel, miguel@...
  */
-public class Hermite3D {
-
+public class Hermite3D implements Serializable {
+  static final long serialVersionUID = 1L;  
   /* really a private class to g3d and export3d */
   
   private JnetRendererInterface g3d;

Modified: nbrowse/trunk/src/org/jnet/g3d/Line3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Line3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Line3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -42,13 +42,15 @@
   * added line bitset option for rockets. Rendering times for edges done this way are a bit slower.
   */
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
 import org.jnet.util.Logger;
 
-public final class Line3D {
-
+public final class Line3D implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   Graphics3D g3d;
 
   Line3D(Graphics3D g3d) {

Modified: nbrowse/trunk/src/org/jnet/g3d/Normix3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Normix3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Normix3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -29,6 +29,8 @@
 
 import javax.vecmath.Vector3f;
 import javax.vecmath.Matrix3f;
+
+import java.io.Serializable;
 import java.util.Random;
 import java.util.BitSet;
 import org.jnet.util.Logger;
@@ -41,8 +43,8 @@
  *
  * @author Miguel, miguel@...
  */
-class Normix3D {
-
+class Normix3D implements Serializable {
+  static final long serialVersionUID = 1L;  
   final static int NORMIX_GEODESIC_LEVEL = Geodesic.standardLevel;
 
   private final static int normixCount = Geodesic.getVertexCount(NORMIX_GEODESIC_LEVEL);

Modified: nbrowse/trunk/src/org/jnet/g3d/Platform3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Platform3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Platform3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -26,6 +26,7 @@
 import java.awt.Component;
 import java.awt.Graphics;
 import java.awt.Image;
+import java.io.Serializable;
 
 /**
  *<p>
@@ -35,8 +36,8 @@
  *
  * @author Miguel, miguel@...
  */ 
-abstract class Platform3D {
-
+abstract class Platform3D implements Serializable {
+  static final long serialVersionUID = 1L;  
   int windowWidth, windowHeight, windowSize;
   int bufferWidth, bufferHeight, bufferSize, bufferSizeT;
 
@@ -53,7 +54,8 @@
   final static boolean desireClearingThread = false;
   boolean useClearingThread = true;
 
-  ClearingThread clearingThread;
+  // made transient if serialized - flag to use ClearingThread is not even used-MS
+  transient ClearingThread clearingThread;
 
   static Platform3D createInstance(Component awtComponent) {
     boolean jvm12orGreater =

Modified: nbrowse/trunk/src/org/jnet/g3d/Rgb16.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Rgb16.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Rgb16.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -24,7 +24,10 @@
 
 package org.jnet.g3d;
 
-final class Rgb16 {
+import java.io.Serializable;
+
+final class Rgb16 implements Serializable {
+  static final long serialVersionUID = 1L;    
   int rScaled;
   int gScaled;
   int bScaled;

Modified: nbrowse/trunk/src/org/jnet/g3d/Sphere3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Sphere3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Sphere3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -24,6 +24,8 @@
 
 package org.jnet.g3d;
 
+import java.io.Serializable;
+
 import javax.vecmath.Matrix3f;
 import javax.vecmath.Matrix4f;
 import javax.vecmath.Point3f;
@@ -54,8 +56,9 @@
  *
  * @author Miguel, miguel@...
  */
-public class Sphere3D {
-
+public class Sphere3D implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   Graphics3D g3d;
   
   protected Sphere3D(Graphics3D g3d) {

Modified: nbrowse/trunk/src/org/jnet/g3d/Triangle3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Triangle3D.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/g3d/Triangle3D.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -24,6 +24,8 @@
 
 package org.jnet.g3d;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 import javax.vecmath.Point3i;
 
@@ -38,8 +40,9 @@
  *
  * @author Miguel, miguel@...
  */
-class Triangle3D {
-
+class Triangle3D implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   final Graphics3D g3d;
   final Line3D line3d;
 

Modified: nbrowse/trunk/src/org/jnet/layouts/Layouter.java
===================================================================
--- nbrowse/trunk/src/org/jnet/layouts/Layouter.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/layouts/Layouter.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -36,6 +36,10 @@
   public Layouter() {
   }
 
+  /** this update/replaces the viewer used */
+  public void setViewer(Viewer viewer) {
+    this.viewer = viewer; 
+  }
   public void setProperty(String propertyName, Object value) {
     if (propertyName.equals("cancel")) {
       stopLayout(false);

Modified: nbrowse/trunk/src/org/jnet/modelset/BoxInfo.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/BoxInfo.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/modelset/BoxInfo.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -25,13 +25,15 @@
 
 package org.jnet.modelset;
 
+import java.io.Serializable;
 import java.util.Hashtable;
 
 import javax.vecmath.Point3f;
 import javax.vecmath.Vector3f;
 
-public class BoxInfo {
-
+public class BoxInfo implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   private final Point3f bbCorner0 = new Point3f(-10, -10, -10);
   private final Point3f bbCorner1 = new Point3f(10, 10, 10);
   private final Point3f bbCenter = new Point3f();

Modified: nbrowse/trunk/src/org/jnet/modelset/EdgeCollection.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/EdgeCollection.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/modelset/EdgeCollection.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -25,6 +25,7 @@
 
 package org.jnet.modelset;
 
+import java.io.Serializable;
 import java.util.BitSet;
 
 import org.jnet.bspt.CubeIterator;
@@ -34,8 +35,9 @@
 import org.jnet.viewer.JnetConstants;
 import org.jnet.viewer.Token;
 
-abstract public class EdgeCollection extends NodeCollection {
-
+abstract public class EdgeCollection extends NodeCollection implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   protected void releaseModelSet() {
     edges = null;
     freeEdges = null;

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelCollection.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelCollection.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelCollection.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -54,8 +54,9 @@
 import org.jnet.viewer.Viewer;
 import org.jnet.viewer.StateManager.Orientation;
 
-abstract public class ModelCollection extends EdgeCollection {
-
+abstract public class ModelCollection extends EdgeCollection implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   /**
    * initial transfer of model data from old to new model set.
    * Note that all new models are added later, AFTER the old ones. This is 

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelSet.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelSet.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelSet.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -36,6 +36,7 @@
 import org.jnet.shape.Shape; // model should technically not know shape
 import org.jnet.shape.Sticks;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Vector;
@@ -65,8 +66,8 @@
  * Bob Hanson, 5/2007, 10/2007
  * 
  */
-abstract public class ModelSet extends ModelCollection {
-
+abstract public class ModelSet extends ModelCollection implements Serializable {
+  static final long serialVersionUID = 1L;
   ////////////////////////////////////////////////////////////////
 
   protected void releaseModelSet() {

Modified: nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -26,6 +26,7 @@
 package org.jnet.modelset;
 
 import java.awt.Rectangle;
+import java.io.Serializable;
 import java.util.BitSet;
 
 import javax.vecmath.AxisAngle4f;
@@ -49,7 +50,9 @@
 import org.jnet.viewer.Token;
 import org.jnet.viewer.Viewer;
 
-abstract public class NodeCollection {
+abstract public class NodeCollection implements Serializable {
+  static final long serialVersionUID = 1L;
+  
 
   protected void releaseModelSet() {
     nodes = null;
@@ -86,7 +89,7 @@
   }
   
   public Viewer viewer; //TESTING ONLY
-  Graphics3D g3d;
+  transient Graphics3D g3d;
 
   final protected static boolean showReedgeTimes = true;
 

Modified: nbrowse/trunk/src/org/jnet/popup/JnetPopup.java
===================================================================
--- nbrowse/trunk/src/org/jnet/popup/JnetPopup.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/popup/JnetPopup.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -34,6 +34,7 @@
 import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
+import java.io.Serializable;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.Hashtable;
@@ -42,8 +43,9 @@
 
 
 /** Pulldown menu for jnet */
-abstract public class JnetPopup {
-
+abstract public class JnetPopup implements Serializable {
+  static final long serialVersionUID = 1L; 
+  
   private final static boolean forceAwt = false;
 
   //list is saved in http://www.stolaf.edu/academics/chemapps/jnet/docs/misc
@@ -62,7 +64,7 @@
   Hashtable htMenus = new Hashtable();
   Properties menuText = new Properties();
   
-  Object frankPopup;
+  transient Object frankPopup;
 
   int aboutComputedMenuBaseCount;
   String nullModelSetName, modelSetName;
@@ -822,7 +824,8 @@
 
   String currentMenuItemId = null;
 
-  class MenuItemListener implements ActionListener {
+  class MenuItemListener implements ActionListener, Serializable {
+    static final long serialVersionUID = 1L;     
     public void actionPerformed(ActionEvent e) {
       restorePopupMenu();
       String script = e.getActionCommand();
@@ -841,7 +844,8 @@
     }
   }
 
-  class CheckboxMenuItemListener implements ItemListener {
+  class CheckboxMenuItemListener implements ItemListener, Serializable {
+    static final long serialVersionUID = 1L;     
     public void itemStateChanged(ItemEvent e) {
       restorePopupMenu();
       setCheckBoxValue(e.getSource());

Modified: nbrowse/trunk/src/org/jnet/popup/JnetPopupSwing.java
===================================================================
--- nbrowse/trunk/src/org/jnet/popup/JnetPopupSwing.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/popup/JnetPopupSwing.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -34,9 +34,10 @@
 import javax.swing.JCheckBoxMenuItem;
 
 import java.awt.Component;
+import java.io.Serializable;
 
-public class JnetPopupSwing extends JnetPopup {
-
+public class JnetPopupSwing extends JnetPopup implements Serializable {
+  static final long serialVersionUID = 1L;  
   JPopupMenu swingPopup;
   JMenu elementComputedMenu;
   JMenu mainMenu;

Modified: nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -24,6 +24,7 @@
 
 package org.jnet.symmetry;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Vector;
@@ -48,7 +49,8 @@
  *
  */
 
-class PointGroup {
+class PointGroup implements Serializable {
+  static final long serialVersionUID = 1L;  
 
   private final static int[] axesMaxN = new int[] { 
      15, // used for plane count

Modified: nbrowse/trunk/src/org/jnet/util/CommandHistory.java
===================================================================
--- nbrowse/trunk/src/org/jnet/util/CommandHistory.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/util/CommandHistory.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -23,12 +23,13 @@
  */
 package org.jnet.util;
 
+import java.io.Serializable;
 import java.util.Vector;
 /**
  * Implements a queue for a bash-like command history.
  */
-final public class CommandHistory {
-
+final public class CommandHistory implements Serializable {
+  static final long serialVersionUID = 1L;  
   
   public final static String ERROR_FLAG = "#??";
   public final static String NOHISTORYLINE_FLAG = "#--";

Modified: nbrowse/trunk/src/org/jnet/util/TempArray.java
===================================================================
--- nbrowse/trunk/src/org/jnet/util/TempArray.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/util/TempArray.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -23,10 +23,13 @@
  */
 package org.jnet.util;
 
+import java.io.Serializable;
+
 import javax.vecmath.*;
 
-public class TempArray {
-
+public class TempArray implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   public TempArray() {
   }
 

Modified: nbrowse/trunk/src/org/jnet/viewer/ColorManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ColorManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/ColorManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -25,16 +25,19 @@
 
 import org.jnet.util.ArrayUtil;
 import org.jnet.util.Logger;
+
+import java.io.Serializable;
 import java.util.BitSet;
 import org.jnet.g3d.*;
 import org.jnet.modelset.Node;
 import org.jnet.modelset.ModelSet;
 import org.jnet.util.ColorEncoder;
 
-class ColorManager {
-
+class ColorManager implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   private Viewer viewer;
-  private Graphics3D g3d;
+  private transient Graphics3D g3d;
   private int[] argbsCpk;
   private int[] altArgbsCpk;
   private float colorHi, colorLo;

Modified: nbrowse/trunk/src/org/jnet/viewer/Compiler.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Compiler.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/Compiler.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -196,6 +196,14 @@
     this.viewer = viewer;
   }
 
+  /**
+   * used for viewer replacement
+   * @param viewer
+   */
+  void setViewer(Viewer viewer) {
+    this.viewer = viewer;  
+  }
+  
   boolean compile(String filename, String script, boolean isPredefining,
                   boolean isSilent, boolean debugScript, boolean isCheckOnly) {
     this.isCheckOnly = isCheckOnly;

Modified: nbrowse/trunk/src/org/jnet/viewer/DataManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/DataManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/DataManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -23,6 +23,7 @@
  */
 package org.jnet.viewer;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -39,8 +40,8 @@
  * 
  */
 
-class DataManager {
-
+class DataManager implements Serializable {
+  static final long serialVersionUID = 1L;
   private Hashtable dataValues = new Hashtable();
 
   DataManager() {

Modified: nbrowse/trunk/src/org/jnet/viewer/Eval.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Eval.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/Eval.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -158,6 +158,14 @@
       clearDefinitionsAndLoadPredefined();
   }
 
+  /**
+   * replace viewer used for object
+   * @param viewer
+   */
+  public void setViewer(Viewer viewer) {
+    this.viewer = viewer;  
+  }
+  
   private Object getParameter(String var, boolean asToken) {
     Token token = getContextVariableAsToken(var);
     return (token == null ? viewer.getParameter(var) : asToken ? token : Token

Modified: nbrowse/trunk/src/org/jnet/viewer/FileManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/FileManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/FileManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -49,6 +49,7 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.Serializable;
 import java.io.StringReader;
 import java.io.Reader;
 import java.util.zip.GZIPInputStream;
@@ -64,8 +65,9 @@
 import org.openscience.jnet.io.ReaderFactory;
 */
 
-public class FileManager {
-
+public class FileManager implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   private Viewer viewer;
   private String openErrorMessage;
  
@@ -91,9 +93,9 @@
 
   private String loadScript; 
 
-  FileOpenThread fileOpenThread;
-  FilesOpenThread filesOpenThread;
-  private DOMOpenThread aDOMOpenThread;
+  transient FileOpenThread fileOpenThread; // made transient if serializing
+  transient FilesOpenThread filesOpenThread;// made transient if serializing
+  private transient DOMOpenThread aDOMOpenThread;// made transient if serializing
 
 
   FileManager(Viewer viewer, JnetAdapter modelAdapter) {

Modified: nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -48,6 +48,15 @@
     this.viewer = viewer;
   }
 
+  /**
+   * Viewer is set to replace existing.
+   * @param viewer
+   */
+  public void setViewer(Viewer viewer)
+  {
+    this.viewer = viewer;
+  }
+  
   void render(Graphics3D g3d, ModelSet modelSet) {  //, Rectangle rectClip
 
     if (modelSet == null || !viewer.mustRenderFlag())

Modified: nbrowse/trunk/src/org/jnet/viewer/ModelManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ModelManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/ModelManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -24,12 +24,15 @@
  */
 package org.jnet.viewer;
 
+import java.io.Serializable;
+
 import org.jnet.modelset.ModelLoader;
 import org.jnet.modelset.ModelSet;
 import org.jnet.api.JnetAdapter;
 
-class ModelManager {
-
+class ModelManager implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   private final Viewer viewer;
   private ModelLoader modelLoader;
 

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -169,6 +169,14 @@
         addPopupMenu(); // add popup menu to this	    
   }
 
+  /**
+   * updates viewer with replacement
+   * @param viewer
+   */
+  public void setViewer(Viewer viewer) {
+    this.viewer = viewer;  
+  }
+  
   void clear() {
     startHoverWatcher(false);
   }

Modified: nbrowse/trunk/src/org/jnet/viewer/PickingManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/PickingManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/PickingManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -56,6 +56,11 @@
     clear();
   }
 
+  /** sets the viewer for replacement */
+  public void setViewer(Viewer viewer) {
+  this.viewer = viewer;  
+  }
+  
   void clear() {
     pickingMode = JnetConstants.PICKING_IDENT;
     drawHover = false;

Modified: nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -48,6 +48,15 @@
 
   FrameRenderer getFrameRenderer() { return frameRenderer; }
   
+  /**
+   * sets replacement of viewer
+   * @param viewer
+   */
+  public void setViewer(Viewer viewer) {
+    this.viewer = viewer;  
+    frameRenderer.setViewer(viewer);
+  }
+  
   void setCurrentModelIndex(int modelIndex) {
     setCurrentModelIndex(modelIndex, true);  
   }

Modified: nbrowse/trunk/src/org/jnet/viewer/ScriptManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ScriptManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/ScriptManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -45,6 +45,12 @@
     startCommandWatcher(false);
   }
 
+  /** reset viewer for replacement */
+  public void setViewer(Viewer viewer)
+  {
+    this.viewer = viewer;  
+  }
+  
   public void setQueue(boolean TF) {
     useQueue = TF;
     if (!TF)

Modified: nbrowse/trunk/src/org/jnet/viewer/SelectionManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/SelectionManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/SelectionManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -31,6 +31,7 @@
 import org.jnet.i18n.GT;
 import org.jnet.modelset.ModelSet;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
@@ -38,8 +39,8 @@
 /** make this a singleton? 
  * this is just for nodes - no edge selection in jmol
  * all done with BitSets - not sure how much nb uses this? */
-class SelectionManager {
-
+class SelectionManager implements Serializable {
+  static final long serialVersionUID = 1L;
   private Viewer viewer;
 
   private JnetSelectionListener[] listeners = new JnetSelectionListener[4];

Modified: nbrowse/trunk/src/org/jnet/viewer/StateManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/StateManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/StateManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -42,8 +42,9 @@
 
 import java.util.Arrays;
 
-public class StateManager {
-
+public class StateManager implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   /* steps in adding a global variable:
    
    In Viewer:
@@ -389,8 +390,8 @@
         "angstroms;au;bohr;nanometers;nm;picometers;pm");
   }
 
-  class GlobalSettings {
-
+  class GlobalSettings implements Serializable {
+    static final long serialVersionUID = 1L;
     /*
      *  Mostly these are just saved and restored directly from Viewer.
      *  They are collected here for reference and to ensure that no 

Modified: nbrowse/trunk/src/org/jnet/viewer/StatusManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/StatusManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/StatusManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -26,6 +26,7 @@
 import org.jnet.util.Logger;
 import org.jnet.util.TextFormat;
 
+import java.io.Serializable;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.Vector;
@@ -67,8 +68,9 @@
  * 
  */
 
-class StatusManager {
-
+class StatusManager implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   private boolean allowStatusReporting = true;
   
   void setAllowStatusReporting(boolean TF){
@@ -99,6 +101,12 @@
     viewer.setStatusFileLoaded(0, null, null, null, null);
   }
   
+  /** used for replacing current viewer */
+  public void setViewer(Viewer viewer)
+  {
+    this.viewer = viewer;
+  }
+  
   private synchronized boolean resetMessageQueue(String statusList) {
     boolean isRemove = (statusList.length() > 0 && statusList.charAt(0) == '-');
     boolean isAdd = (statusList.length() > 0 && statusList.charAt(0) == '+');

Modified: nbrowse/trunk/src/org/jnet/viewer/TransformManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/TransformManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/TransformManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -37,9 +37,11 @@
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.awt.Rectangle;
+import java.io.Serializable;
 
-abstract class TransformManager {
-
+abstract class TransformManager implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   Viewer viewer;
 
   final static float twoPI = (float) (2 * Math.PI);

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -77,6 +77,7 @@
 import java.net.URL;
 import java.io.ByteArrayOutputStream;
 import java.io.Reader;
+import java.io.Serializable;
 import java.io.UnsupportedEncodingException;
 
 /*
@@ -107,8 +108,9 @@
 import org.jnet.shape.Hover;
 
 /** Viewer and JnetViewer should maybe have their names switched? */
-public class Viewer extends JnetViewer implements NodeDataServer {
-
+public class Viewer extends JnetViewer implements NodeDataServer, Serializable {
+  static final long serialVersionUID = 1L;  
+  
   /** if false then selection is disabled -- MG*/
   private boolean selectionEnabled = true;
   private boolean hoverVisibility=false; // default false?
@@ -129,24 +131,24 @@
   // being accesed by any other classes
 
   private Component display;
-  private Graphics3D g3d;
+  private transient Graphics3D g3d;
   private JnetAdapter modelAdapter;
 
   private CommandHistory commandHistory = new CommandHistory();
   private ColorManager colorManager;
-  private Compiler compiler;
+  private transient Compiler compiler; // don't serialize - just reset if load serialized
   
   private boolean freezing = false;
-  private Eval eval;
+  private transient Eval eval; // don't serialize - just reset if load serialized
   private DataManager dataManager;
   private FileManager fileManager;
   private ModelManager modelManager;
   //private ModelSet modelSet;
-  private ModelLoader modelSet;
-  public MouseManager mouseManager;
-  private PickingManager pickingManager;
-  private RepaintManager repaintManager;
-  private ScriptManager scriptManager;
+  private ModelLoader modelSet; 
+  public transient MouseManager mouseManager; // dont' serialize - just reset if serialized
+  private transient PickingManager pickingManager; // dont't serialize - juset reset if serialized
+  private transient RepaintManager repaintManager; // dont't serialize - juset reset if serialized
+  private transient ScriptManager scriptManager; // dont't serialize - juset reset if serialized
   private SelectionManager selectionManager;
   private StateManager stateManager;
   private StateManager.GlobalSettings global;
@@ -172,7 +174,7 @@
   private boolean jvm12orGreater = false;
   private boolean jvm14orGreater = false;
 
-  private Hashtable evalVariables;
+  private transient Hashtable evalVariables; // don't serialize since used with Eval object
 
   Compiler getCompiler() {
     return compiler;
@@ -246,7 +248,7 @@
   }
   public boolean is2D() { return getDimensionMode() == 2; }
   
-  private LayouterInterface layouter;
+  private transient LayouterInterface layouter; // do not serialize layoutinterface use default
   
   public void setLayouter(LayouterInterface layouter) { 
     this.layouter = layouter;
@@ -284,7 +286,7 @@
       return freezing;
   }
 
-  private MinimizerInterface minimizer;
+  transient private MinimizerInterface minimizer; // don't serialize this - no implementation for this yet
 
   public void setMinimizer(MinimizerInterface minimizer) {
     this.minimizer = minimizer;
@@ -421,6 +423,39 @@
     return (htmlName.length() > 0);
   }
 
+  public static Viewer reallocateViewer(Viewer newViewer, Viewer oldViewer) 
+  {
+  // need to copy display, compiler, mouse manager, etc. from old viewer to newViewer object
+    newViewer.evalVariables = oldViewer.evalVariables;
+    newViewer.compiler = oldViewer.compiler;
+    newViewer.compiler.setViewer(newViewer); // replace viewer
+    newViewer.display = oldViewer.display; // awt display
+    newViewer.eval = oldViewer.eval;
+    newViewer.eval.setViewer(newViewer);
+    newViewer.g3d = oldViewer.g3d;
+    
+    newViewer.mouseManager = oldViewer.mouseManager;
+    if (newViewer.mouseManager != null)
+      newViewer.mouseManager.setViewer(newViewer);
+    newViewer.pickingManager = oldViewer.pickingManager;
+    if (newViewer.pickingManager != null)    
+    newViewer.pickingManager.setViewer(newViewer);
+    //newViewer.statusManager = oldViewer.statusManager; // test this
+    //newViewer.statusManager.setViewer(newViewer);
+    newViewer.repaintManager = oldViewer.repaintManager;
+    if (newViewer.repaintManager != null)     
+      newViewer.repaintManager.setViewer(newViewer);
+    newViewer.scriptManager = oldViewer.scriptManager;
+    if (newViewer.scriptManager != null)       
+      newViewer.scriptManager.setViewer(newViewer);
+    newViewer.layouter = oldViewer.layouter;
+    if (newViewer.layouter != null)       
+      newViewer.layouter.setViewer(newViewer);
+    newViewer.minimizer = oldViewer.minimizer;
+    newViewer.modelSet = null; // try nulling to hopefully set
+    return newViewer;
+  }
+  
   public void setAppletContext(String fullName, URL documentBase, URL codeBase,
                                String commandOptions) {
     this.fullName = fullName = (fullName == null ? "" : fullName);
@@ -2436,7 +2471,7 @@
   }
 
 
-  private ModelSet savedModelSet;
+  private transient ModelSet savedModelSet; // seems to always be null - no point in serializing
   private TransformManager savedTransfManager = new TransformManager11();
   Point3f fixedRotationCenter;
 

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -16,7 +16,7 @@
   static final long serialVersionUID = 1L;		
   public NBNode fromNode;
   public NBNode toNode;
-  private static final boolean useSerialBinary = false; // stopped using for now
+  private static final boolean useSerialBinary = true; // stopped using for now
   //public int order; // not used - is this for direction?? i think so
   
   /** Set in XMLio - move to Edge(view)? hmmmm unclear what Edge's (view) fate is

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -26,12 +26,14 @@
 import javax.swing.JTextField;
 
 import org.jnet.util.Escape;
+import org.jnet.viewer.Viewer;
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.MetaData;
 import org.nbrowse.dataset.MetaDataManager;
 import org.nbrowse.layouts.spring.vrmlgraph.GraphData;
 import org.nbrowse.utils.ErrorUtil;
 import org.nbrowse.views.JnetManager;
+import org.nbrowse.views.JnetPanel;
 import org.nbrowse.views.Navigation;
 
 /**
@@ -41,7 +43,7 @@
 class FileDialog {
   
   private static final boolean useRawData = false; // debug flag to use against useRawData - used in sending status msg to load raw screen data
-  private static final boolean useSerialBinary = false; // used for testing - overides save/open to just use serialized binary files for testing
+  private static final boolean useSerialBinary = true; // used for testing - overides save/open to just use serialized binary files for testing
   
   private DataLoader dataLoader;
   private JDialog dlg;
@@ -142,6 +144,7 @@
 			new ObjectInputStream (f_in);
 
 		// Read an object
+		
 		Object ges_obj = obj_in.readObject();
 		if (ges_obj instanceof GraphEltSet){
 		   GraphEltSet.getCurrentGraph().clearAll();
@@ -155,7 +158,14 @@
 		   GraphData.setCurrentGraphData((GraphData) gd_obj);
 		}
 		
+		Object viewer = obj_in.readObject();
+		if (viewer instanceof Viewer)
+		{
+	    //JnetPanel panel = JnetPanel.inst();
+		  JnetManager.inst().loadJnetViewer((Viewer) viewer);
+		  
 		}
+		}
 		catch(Exception ex)
 		{
 			ex.printStackTrace();
@@ -236,9 +246,12 @@
       
       if (useSerialBinary) // save as .ser extension too
       {
+        
     	  GraphEltSet currGraph = GraphEltSet.getCurrentGraph();
         //GraphEltSet currGraph = GraphEltSet.getCurrentGraph().getFilteredGraph(); // save filtered?
-    	  GraphData graphData = GraphData.getCurrentGraphData();
+    	  GraphData graphData = GraphData.getCurrentGraphData();    	  
+    	  
+        Viewer viewer = JnetManager.inst().getJnetViewer();
     	// Write to disk with FileOutputStream
     	  try{
     	  FileOutputStream f_out = new 
@@ -247,11 +260,14 @@
     	  // Write object with ObjectOutputStream
     	  ObjectOutputStream obj_out = new
     	  	ObjectOutputStream (f_out);
+    	  
+        // Write GraphEltSet object out to file
+        obj_out.writeObject ( currGraph );
+        // Write GraphData object to file
+        obj_out.writeObject(graphData);
+    	  
+        obj_out.writeObject(viewer);
 
-    	  // Write GraphEltSet object out to file
-    	  obj_out.writeObject ( currGraph );
-    	  // Write GraphData object to file
-    	  obj_out.writeObject(graphData);
     	  obj_out.flush();
     	  }
     	  catch(Exception ex)

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -1,5 +1,6 @@
 package org.nbrowse.layouts.spring.vrmlgraph;
 
+import java.io.Serializable;
 import java.util.*;
 import org.nbrowse.io.StatusEvent;
 import org.nbrowse.views.NodeViewI;
@@ -16,8 +17,9 @@
  * @author     Paul James Mutton, paul@...
  * @created    18 December 2000 
  */
-public class NodeMover {
-
+public class NodeMover implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   // higher makes layout faster, but 1.5 made small (par-4) graph get stuck
   private final static float REPULSION_MULTIPLIER = 1.3f;//1; // _C1 - 50 is nuts
   private final static float ATTRACTION_SUBTRACTOR = 1; // C2

Modified: nbrowse/trunk/src/org/nbrowse/views/EdgeInfoMaker.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/EdgeInfoMaker.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/EdgeInfoMaker.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -5,6 +5,7 @@
 
 package org.nbrowse.views;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import org.jnet.viewer.JnetMouseEvent;
@@ -23,8 +24,9 @@
  * as it becomes available
  * @author mgibson
  */
-final class EdgeInfoMaker {
-
+final class EdgeInfoMaker implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   private List<EdgeInfoObserver> observers = new ArrayList<EdgeInfoObserver>(2);
   private EdgeViewI edge;
   private StringBuilder edgeInfoNoLinks=new StringBuilder();
@@ -64,7 +66,9 @@
 //      makeEdgeInfo(e.getJnetEdgeIndex());//e.getJnetNodeIndex());
 //    }
 //  }
-  private class EdgeSel implements SelectionListener {
+  private class EdgeSel implements SelectionListener, Serializable  {
+    static final long serialVersionUID = 1L;
+    
     public void selectEdge(EdgeViewI e) {
       makeEdgeInfo(e);
     }

Modified: nbrowse/trunk/src/org/nbrowse/views/EdgeInfoView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/EdgeInfoView.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/EdgeInfoView.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -3,6 +3,8 @@
 import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.Rectangle;
+import java.io.Serializable;
+
 import org.nbrowse.api.AbstractView;
 import javax.swing.event.HyperlinkListener;
 import javax.swing.JEditorPane;
@@ -43,7 +45,8 @@
 
   private EdgeInfoMaker infoMaker() { return EdgeInfoMaker.inst(); }
 
-  private class EdgeInfoObs implements EdgeInfoObserver {
+  private class EdgeInfoObs implements EdgeInfoObserver, Serializable {
+    static final long serialVersionUID = 1L;    
     public void edgeInfoChanged() { updateDisplay(); }
   }
 

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -7,6 +7,7 @@
 import java.awt.BorderLayout;
 import java.awt.Image;
 import java.awt.Toolkit;
+import java.io.Serializable;
 import java.net.URL;
 import java.awt.Insets;
 import java.awt.Font;
@@ -166,7 +167,8 @@
 //    zoomSlider.setValue(value);
 //  }
 
-  private class ZoomObs implements ZoomObserver {
+  private class ZoomObs implements ZoomObserver, Serializable {
+    static final long serialVersionUID = 1L;    
     public void zoomChanged() { synchZoombar(); }
   }
 
@@ -186,7 +188,8 @@
     return zoombar;
   }
 
-  class ZoomSliderListener implements AdjustmentListener {
+  class ZoomSliderListener implements AdjustmentListener, Serializable {
+    static final long serialVersionUID = 1L;   
     public void adjustmentValueChanged(AdjustmentEvent e) {
         int fr = JnetPanel.viewer.getZoomPercent()-e.getValue();
         //JnetPanel.viewer.script("zoom " + e.getValue());

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -2,6 +2,7 @@
 
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.HashMap;
@@ -38,8 +39,9 @@
  * or something - not sure how this will pan out
  * @author mgibson
  */
-public final class JnetManager {
-
+public final class JnetManager implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   public final static boolean DO_PJM = false;
 
   private static JnetManager singleton;
@@ -49,8 +51,9 @@
    * @author Monty
    *
    */
-  private class RawNodeProperties
+  private class RawNodeProperties implements Serializable 
   {
+   static final long serialVersionUID = 1L;    
 	 private String name;
 	 private int screenX;
 	 private int screenY;
@@ -147,7 +150,7 @@
    * bypassing Jnet, which is a nbrowse view, refactor? Jnet also has the toolbar
    with step buttons */
   private Jnet jnet;
-  private final JNetScript jnetScript;
+  private transient final JNetScript jnetScript; // should use jnet from new - jnetscript uses new eval
   
   private boolean jnetStepButtonClicked=false; // dont think this is used
   // enum Dimension { 2D, 2_5D, 3D }; // ??
@@ -372,6 +375,16 @@
     return StepManager.inst().getDisplayStep();
   }
 
+
+  /**
+   * replaces the jnet viewer being used. invokes JnetPanel to rest of restore
+   */
+  public void loadJnetViewer(Viewer viewer)
+  {
+    JnetPanel panel = JnetPanel.inst();
+    panel.loadViewer(viewer);        
+  }
+  
   /** @param node to query jnet with its label
    * @return jnet node number for node's label, -1 if not found */
   public int getJnetNodeNumber(NodeViewI node) {
@@ -591,7 +604,7 @@
     GraphViewI filteredGraph = fullGraph.getSubgraph(EdgeFilterState.inst(), step);
     loadJnet(filteredGraph);
   }
-
+  
   /**
    * used for loading raw screen data
    * @param step
@@ -654,8 +667,12 @@
   private NbrowseJnetAdapter nbJnetAdap() { return NbrowseJnetAdapter.inst(); }
 
   private void loadSerialData() {
+    GraphViewI fullGraph = GraphViewManager.current();
+    //redrawJnet();    
 	//clear();
+    
 	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
+	
 	//clearAll(); // try this  
 	//ErrorUtil.debug(this, "Loading new nbrowse graph view");
 	//graphView().loadNewRawData(); // this filters
@@ -667,9 +684,9 @@
 	  //doLayout(true); // try this - hope it helps expansion problem-MS
 	  // don't do layout here - no need to
       //doLayout(true); // works directly on jnet nodes, threaded, true->fit      
-	  createJnetLineBarStepButton(1);      
+	  //createJnetLineBarStepButton(1);      
 	  //StatusManager.inst().newDataDoneLayout(); // normal? take out?
-	  GraphViewI fullGraph = GraphViewManager.current();
+	  //GraphViewI fullGraph = GraphViewManager.current();
 	  //StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode - try again      
 	 }
 	 catch (Exception e) { ErrorUtil.urgent(this, "Load failed "+e, e); }	  
@@ -1078,7 +1095,9 @@
   }
 
   /** listen for selection from NBrowse(locate gene) and select jnet */
-  private class JnetSelListener implements SelectionListener {
+  private class JnetSelListener implements SelectionListener, Serializable {
+    static final long serialVersionUID = 1L;
+    
     public void selectNode(NodeViewI sel) {
       selectJnetNode(sel);
     }
@@ -1147,7 +1166,9 @@
     info().addNodeInfoObserver(new NodeInfoObs());
   }
 
-  private class NodeInfoObs implements NodeInfoObserver {
+  private class NodeInfoObs implements NodeInfoObserver, Serializable {
+    static final long serialVersionUID = 1L;
+    
     public void nodeInfoChanged() { nodeInfoPopup(); }
     private void nodeInfoPopup() {
       if (!getJnetViewer().hoverIsEnabled()) return;
@@ -1155,6 +1176,7 @@
       getJnetViewer().showNodeHoverText(ni,info().getJnetNodeId());
     }
   }
+
 }
 
 //  private boolean selectionInitialized=false;

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -4,6 +4,7 @@
 
 import java.awt.*;
 import java.awt.print.*;
+import java.io.Serializable;
 import java.util.Hashtable;
 
 import org.jnet.api.*;
@@ -55,6 +56,18 @@
         viewer.setJnetStatusListener(myStatusListener);
     }
 
+    /** used to reset listener in jpanel to new viewer */
+    public void loadViewer(Viewer newViewer) 
+    {
+      newViewer = Viewer.reallocateViewer(newViewer, viewer); // copy from      
+      viewer = newViewer;
+      JnetManager.inst().setJnetViewer(viewer); //resetViewer
+      myStatusListener = new MyStatusListener();
+      viewer.setJnetStatusListener(myStatusListener);   
+      // do we need to call initApp afterwards?
+      viewer.popHoldRepaint(); // try      
+    }
+    
   Viewer getViewer() { return viewer; }
     
     
@@ -89,8 +102,9 @@
     }
   }
     
-  class MyStatusListener implements JnetStatusListener {
-
+  class MyStatusListener implements JnetStatusListener, Serializable {
+    static final long serialVersionUID = 1L;
+    
         protected void finalize() throws Throwable {
             Logger.debug("MyStatusListener finalize " + this);
             super.finalize();

Modified: nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -5,6 +5,7 @@
 
 package org.nbrowse.views;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.BitSet;
 import java.util.HashSet;
@@ -23,7 +24,8 @@
  * to nbrowse nodes (to be used by nbrowse, like GO)
  * @author mgibson
  */
-public class NBSelectionManager {
+public class NBSelectionManager implements Serializable {
+  static final long serialVersionUID = 1L;  
   private static NBSelectionManager singleton=new NBSelectionManager();
   private Set<SelectionListener> listeners = new HashSet<SelectionListener>(3);
   private BitSet jnetSelection;
@@ -87,7 +89,8 @@
   /** hmmmm - should we listen for sel events from jnet and construct nbrowse
    * selection state - should this be push or pull, on demand or select driven?
    */
-  private class JnetSelLis implements JnetSelectionListener {
+  private class JnetSelLis implements JnetSelectionListener, Serializable  {
+    static final long serialVersionUID = 1L;    
     public void selectionChanged(BitSet selection) { jnetSelection = selection; }
     public void select(JnetSelection s) {
       if (!s.isEdge()) return;

Modified: nbrowse/trunk/src/org/nbrowse/views/Navigation.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Navigation.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/Navigation.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -3,6 +3,7 @@
 import org.nbrowse.api.AbstractView;
 
 import java.awt.*;
+import java.io.Serializable;
 import java.util.Hashtable;
 
 import org.jnet.api.*;
@@ -99,8 +100,9 @@
     }
   }
     
-  class MyStatusListener implements JnetStatusListener {
-
+  class MyStatusListener implements JnetStatusListener, Serializable {
+        static final long serialVersionUID = 1L;
+    
         protected void finalize() throws Throwable {
             Logger.debug("MyStatusListener finalize " + this);
             super.finalize();

Modified: nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -5,6 +5,7 @@
 
 package org.nbrowse.views;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import org.jnet.viewer.JnetMouseEvent;
@@ -22,8 +23,9 @@
  * as it becomes available
  * @author mgibson
  */
-final class NodeInfoMaker {
-
+final class NodeInfoMaker implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   private List<NodeInfoObserver> observers = new ArrayList<NodeInfoObserver>(2);
   private NodeViewI displayNode;
   private StringBuilder nodeInfoNoLinks=new StringBuilder();
@@ -75,7 +77,8 @@
     previousJnetNodeIndex = jnetNodeIndex;
     return isNew;
   }
-  private class EdgeInfoObs implements EdgeInfoObserver {
+  private class EdgeInfoObs implements EdgeInfoObserver, Serializable {
+    static final long serialVersionUID = 1L;
     public void edgeInfoChanged() { edgeInfoCurrentlyShowing = true; }
   }
 

Modified: nbrowse/trunk/src/org/nbrowse/views/NodeInfoView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NodeInfoView.java	2010-01-26 21:37:44 UTC (rev 22619)
+++ nbrowse/trunk/src/org/nbrowse/views/NodeInfoView.java	2010-01-26 21:56:56 UTC (rev 22620)
@@ -3,6 +3,8 @@
 import java.awt.Dimension;
 import java.awt.Graphics;
 import java.awt.Rectangle;
+import java.io.Serializable;
+
 import org.nbrowse.api.AbstractView;
 import javax.swing.event.HyperlinkListener;
 import javax.swing.JEditorPane;
@@ -44,13 +46,15 @@
   private NodeInfoMaker infoMaker() { return NodeInfoMaker.inst(); }
   private EdgeInfoMaker edgeInfo() { return EdgeInfoMaker.inst(); }
   
-  private class NodeInfoObs implements NodeInfoObserver {
+  private class NodeInfoObs implements NodeInfoObserver, Serializable {
+    static final long serialVersionUID = 1L;
     public void nodeInfoChanged() { updateDisplay(); }
   }
   
   /** experimenting with doing node & edge info in same
    * view - if ok then obviously rename this class */
-  private class EdgeInfoObs implements EdgeInfoObserver {
+  private class EdgeInfoObs implements EdgeInfoObserver, Serializable {
+    static final long serialVersionUID = 1L;    
     public void edgeInfoChanged(){updateDisplay(edgeInfo().getEdgeInfo());}
   }
 


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22631
          http://gmod.svn.sourceforge.net/gmod/?rev=22631&view=rev
Author:   montys9
Date:     2010-01-27 21:10:43 +0000 (Wed, 27 Jan 2010)

Log Message:
-----------
added more serializing and handling of null data - ie rebuild objects.. work in progress

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/g3d/Font3D.java
    nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java
    nbrowse/trunk/src/org/jnet/modelset/ModelSet.java
    nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java
    nbrowse/trunk/src/org/jnet/shape/Balls.java
    nbrowse/trunk/src/org/jnet/shape/Bbcage.java
    nbrowse/trunk/src/org/jnet/shape/Echo.java
    nbrowse/trunk/src/org/jnet/shape/FontLineShape.java
    nbrowse/trunk/src/org/jnet/shape/Frank.java
    nbrowse/trunk/src/org/jnet/shape/Hover.java
    nbrowse/trunk/src/org/jnet/shape/Measures.java
    nbrowse/trunk/src/org/jnet/shape/NodeShape.java
    nbrowse/trunk/src/org/jnet/shape/Object2d.java
    nbrowse/trunk/src/org/jnet/shape/Object2dShape.java
    nbrowse/trunk/src/org/jnet/shape/Shape.java
    nbrowse/trunk/src/org/jnet/shape/Sticks.java
    nbrowse/trunk/src/org/jnet/shape/Text.java
    nbrowse/trunk/src/org/jnet/shape/Uccage.java
    nbrowse/trunk/src/org/jnet/viewer/ColorManager.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/g3d/Font3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Font3D.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/g3d/Font3D.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -42,8 +42,7 @@
  *
  * @author Miguel, miguel@...
  */
-final public class Font3D implements Serializable {
-  static final long serialVersionUID = 1L;  
+final public class Font3D  {
   public final byte fid;
   public final String fontFace;
   public final String fontStyle;

Modified: nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java
===================================================================
--- nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/g3d/Graphics3D.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -147,7 +147,7 @@
 /*final*/ public class Graphics3D implements JnetRendererInterface, Serializable {
 
   static final long serialVersionUID = 1L;
-  Platform3D platform;
+  transient Platform3D platform;
   Line3D line3d;
   Circle3D circle3d;
   Sphere3D sphere3d;
@@ -196,7 +196,7 @@
   int translucencyMask;
   int argbNoisyUp, argbNoisyDn;
 
-  Font3D font3dCurrent;
+  transient Font3D font3dCurrent;// font 3d should not be serialized
 
   public final static byte ENDCAPS_NONE = 0;
   public final static byte ENDCAPS_OPEN = 1;
@@ -257,6 +257,15 @@
   }
 
   /**
+   * sets platform based on parent component
+   * @param awtComponent
+   */
+  public void setPlatform(Component awtComponent)
+  {
+	  platform = Platform3D.createInstance(awtComponent);	  
+  }
+  
+  /**
    * is full scene / oversampling antialiasing GENERALLY in effect
    *
    * @return the answer

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelSet.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelSet.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelSet.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -517,7 +517,7 @@
         asDraw, false, type, index, scale);
   }
 
-  SymmetryInterface pointGroup;
+  transient SymmetryInterface pointGroup; // not used
   private Object calculatePointGroupForFirstModel(BitSet bsNodes,
                                                   boolean doAll,
                                                   boolean asDraw,

Modified: nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/modelset/NodeCollection.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -89,7 +89,7 @@
   }
   
   public Viewer viewer; //TESTING ONLY
-  transient Graphics3D g3d;
+  Graphics3D g3d;
 
   final protected static boolean showReedgeTimes = true;
 

Modified: nbrowse/trunk/src/org/jnet/shape/Balls.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Balls.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Balls.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -25,6 +25,7 @@
 
 package org.jnet.shape;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import javax.vecmath.Point3f; //Victor Chest
 
@@ -34,8 +35,9 @@
 import org.jnet.viewer.MouseManager; //Victor Chest
 import java.util.Hashtable;
 
-public class Balls extends NodeShape {
-  
+public class Balls extends NodeShape implements Serializable {
+  static final long serialVersionUID = 1L;  
+	  
   public void setSize(int size, BitSet bsSelected) {
     isActive = true;
     if (bsSizeSet == null)

Modified: nbrowse/trunk/src/org/jnet/shape/Bbcage.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Bbcage.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Bbcage.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -23,12 +23,14 @@
  */
 package org.jnet.shape;
 
+import java.io.Serializable;
 import java.util.BitSet;
 
 import org.jnet.viewer.StateManager;
 
-public class Bbcage extends FontLineShape {
+public class Bbcage extends FontLineShape implements Serializable {
 
+  static final long serialVersionUID = 1L; 	
   // by XORing each of the three bits of my index
   final static byte edges[] = {
       0,1, 0,2, 0,4, 1,3, 

Modified: nbrowse/trunk/src/org/jnet/shape/Echo.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Echo.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Echo.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -29,11 +29,12 @@
 import org.jnet.g3d.*;
 
 import java.awt.Image;
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Enumeration;
 
-public class Echo extends TextShape {
-
+public class Echo extends TextShape implements Serializable {
+	static final long serialVersionUID = 1L;
   /*
    * set echo Text.TOP    [Text.LEFT|Text.CENTER|Text.RIGHT]
    * set echo MIDDLE [Text.LEFT|Text.CENTER|Text.RIGHT]

Modified: nbrowse/trunk/src/org/jnet/shape/FontLineShape.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/FontLineShape.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/FontLineShape.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -32,7 +32,7 @@
 
   // Axes, Bbcage, Frank, Uccage
 
-  Font3D font3d;
+  transient Font3D font3d; // not serializable - though only setting
   String myType;
 
   public void initShape() {

Modified: nbrowse/trunk/src/org/jnet/shape/Frank.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Frank.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Frank.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -27,9 +27,10 @@
 import org.jnet.g3d.Font3D;
 
 import java.awt.FontMetrics;
+import java.io.Serializable;
 
-public class Frank extends FontLineShape {
-
+public class Frank extends FontLineShape implements Serializable {
+  static final long serialVersionUID = 1L; 
   // Axes, Bbcage, Frank, Uccage
 
   final static String defaultFontName = "SansSerif";
@@ -38,8 +39,8 @@
   final static int frankMargin = 4;
 
   String frankString = "Jnet";
-  Font3D currentMetricsFont3d;
-  Font3D baseFont3d;
+  transient Font3D currentMetricsFont3d; // not serializable 
+  transient Font3D baseFont3d; // not serializable 
   int frankWidth;
   int frankAscent;
   int frankDescent;
@@ -71,7 +72,16 @@
     frankAscent = fm.getAscent();
   }
 
+  private void setFont3D()
+  {
+	  baseFont3d = font3d = g3d.getFont3D(defaultFontName, defaultFontStyle, defaultFontSize);
+	  calcMetrics();
+  }
+  
   void getFont(float imageFontScaling) {
+	if (font3d == null) // used to reset if baseFont3d becomes null
+		setFont3D();	
+	  
     font3d = g3d.getFont3DScaled(baseFont3d, imageFontScaling);
     calcMetrics();
   }

Modified: nbrowse/trunk/src/org/jnet/shape/Hover.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Hover.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Hover.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -29,13 +29,15 @@
 import org.jnet.modelset.Node; //Victor Chest
 import org.jnet.modelset.Edge;  //Victor Chest
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
 import javax.vecmath.Point3i;
 
-public class Hover extends TextShape {
-
+public class Hover extends TextShape implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   public static short originalColix;   //Victor Chest
   public static Node hoveredNode;      //Victor Chest
   public static int previousNodeIndex = -1;   //Victor Chest
@@ -54,7 +56,7 @@
 
   //public static NodeInfoJdbc info;
 
-  Text hoverText;
+  transient Text hoverText;
   int nodeIndex = -1;
   Point3i xy;
   String text;
@@ -72,7 +74,19 @@
     hoverText.setAdjustForWindow(true);
   }
 
-
+  /**
+   * used for resetting hoverText object if serialized
+   */
+  private void resetHoverText()
+  {
+	Font3D font3d = g3d.getFont3D(FONTFACE, FONTSTYLE, FONTSIZE);
+	short bgcolix = Graphics3D.getColix("#FFFFC3"); // 255, 255, 195
+	short colix = Graphics3D.BLACK;
+	currentObject = hoverText = new Text(g3d, font3d, null, colix, bgcolix, 0, 0,
+	    1, Integer.MIN_VALUE, Object2d.ALIGN_LEFT, 0, true); //VC
+	hoverText.setAdjustForWindow(true);	  
+  }
+  
   // i dont think this is used
   public void setProperty(String propertyName, Object value, //Victor Chest
           BitSet bsSelected, Point3i xy) {
@@ -195,8 +209,17 @@
     + ";\n" + getShapeCommands(temp, null, nodeCount);
   }
 
-  public void setText(String s) { hoverText.setText(s); }
-  public boolean isNewTextDrawn() { return hoverText.isNewTextDrawn(); }
+  public void setText(String s) { 
+	  if (hoverText == null)
+		  resetHoverText();
+	  
+	  hoverText.setText(s); 
+	  }
+  public boolean isNewTextDrawn() {
+	  if (hoverText == null)
+		  resetHoverText();
+	  return hoverText.isNewTextDrawn(); 
+	  }
 
   public void setNodeIndex(int ni) { nodeIndex = ni; }
 }

Modified: nbrowse/trunk/src/org/jnet/shape/Measures.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Measures.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Measures.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -35,14 +35,15 @@
 import org.jnet.viewer.JnetConstants;
 import org.jnet.viewer.Token;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Vector;
 import java.util.Hashtable;
 
 import javax.vecmath.Point3f;
 
-public class Measures extends Shape {
-
+public class Measures extends Shape implements Serializable {
+  static final long serialVersionUID = 1L; 
   private final static int measurementGrowthIncrement = 16;
 
   private BitSet bsColixSet;
@@ -61,7 +62,7 @@
   short mad = (short)-1;
   short colix; // default to none in order to contrast with background
   
-  Font3D font3d;
+  transient Font3D font3d; // graphics not serializable 
   
   protected void initModelSet() {
     for (int i = 0; i < measurements.length; i++)
@@ -76,6 +77,24 @@
     font3d = g3d.getFont3D(JnetConstants.MEASURE_DEFAULT_FONTSIZE);
   }
 
+  /**
+   * used to reset g3d package to shape - over-ridden to rest font3d
+   * @param g3d
+   */
+  public void setGraphics3D(Graphics3D g3d)
+  {
+	this.g3d = g3d;  
+	font3d = g3d.getFont3D(JnetConstants.MEASURE_DEFAULT_FONTSIZE);
+  }
+  
+  /** 
+   * used to reset font3d if null.
+   */
+  public void setFont3D()
+  {
+	  font3d = g3d.getFont3D(JnetConstants.MEASURE_DEFAULT_FONTSIZE);
+  }
+  
   public void setSize(int size, BitSet bsSelected) {
     mad = (short)size;
   }
@@ -577,6 +596,9 @@
   }
   
  public String getShapeState() {
+	// ensure font3d is set
+	 if (font3d == null)
+		setFont3D();
     StringBuffer commands = new StringBuffer("");
     appendCmd(commands, "measures delete");
     for (int i = 0; i < measurementCount; i++)

Modified: nbrowse/trunk/src/org/jnet/shape/NodeShape.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/NodeShape.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/NodeShape.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -25,6 +25,7 @@
 
 package org.jnet.shape;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
@@ -34,8 +35,8 @@
 import org.jnet.util.BitSetUtil;
 import org.jnet.viewer.JnetConstants;
 
-public abstract class NodeShape extends Shape {
-
+public abstract class NodeShape extends Shape implements Serializable {
+  static final long serialVersionUID = 1L; 
   // Balls, Dots, Halos, Labels, Polyhedra, Stars, Vectors
   
   public short[] mads;

Modified: nbrowse/trunk/src/org/jnet/shape/Object2d.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Object2d.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Object2d.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -1,5 +1,6 @@
 package org.jnet.shape;
 
+import java.io.Serializable;
 import java.util.BitSet;
 
 import javax.vecmath.Point3f;
@@ -9,8 +10,9 @@
 import org.jnet.viewer.JnetConstants;
 import org.jnet.viewer.Viewer;
 
-public abstract class Object2d {
-
+public abstract class Object2d implements Serializable {
+	static final long serialVersionUID = 1L; 
+	
   public final static int POINTER_NONE = 0;
   public final static int POINTER_ON = 1;
   public final static int POINTER_BACKGROUND = 2;

Modified: nbrowse/trunk/src/org/jnet/shape/Object2dShape.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Object2dShape.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Object2dShape.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -1,5 +1,6 @@
 package org.jnet.shape;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -11,15 +12,15 @@
 import org.jnet.util.TextFormat;
 import org.jnet.viewer.Viewer;
 
-public class Object2dShape extends Shape {
-
+public class Object2dShape extends Shape implements Serializable {
+  static final long serialVersionUID = 1L;
   // Echo, Hover, JnetImage
 
   Hashtable objects = new Hashtable();
   Object2d currentObject;
-  Font3D currentFont;
-  Object currentColor;
-  Object currentBgColor;
+  transient Font3D currentFont; // needs to be reset if serialized - only used for set it seems
+  transient Object currentColor; // same as above
+  transient Object currentBgColor; // same as above
   float currentTranslucentLevel;
   float currentBgTranslucentLevel;
   protected String thisID;

Modified: nbrowse/trunk/src/org/jnet/shape/Shape.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Shape.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Shape.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -36,6 +36,8 @@
 import org.jnet.modelset.Edge; //Victor Chest
 
 import javax.vecmath.Point3f;
+
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Vector;
 import java.util.Hashtable;
@@ -77,8 +79,7 @@
  *    Echo, Hover
  *    
  */
-public abstract class Shape {
-
+public abstract class Shape  {
   //public Shape () {
   //  System.out.println("Shape " + this + " constructed");
   //}
@@ -89,7 +90,7 @@
   
   public Viewer viewer; //public for now for Backbone
   public ModelSet modelSet;
-  public Graphics3D g3d;
+  public Graphics3D g3d; // need to reassign
   public int shapeID;
   public int myVisibilityFlag;
   protected float translucentLevel;
@@ -112,6 +113,15 @@
 
   }
 
+  /**
+   * used to reset g3d package to shape
+   * @param g3d
+   */
+  public void setGraphics3D(Graphics3D g3d)
+  {
+	this.g3d = g3d;  
+  }
+  
   public void setModelSet(ModelSet modelSet) {
     this.modelSet = modelSet;
     initModelSet();

Modified: nbrowse/trunk/src/org/jnet/shape/Sticks.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Sticks.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Sticks.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -30,6 +30,7 @@
 import org.jnet.util.Logger;
 import org.jnet.viewer.JnetConstants;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
@@ -45,8 +46,9 @@
 import org.jnet.g3d.Graphics3D; //Victor Chest
 import org.nbrowse.utils.ErrorUtil;
 
-public class Sticks extends Shape {
-
+public class Sticks extends Shape implements Serializable {
+  static final long serialVersionUID = 1L; 
+	  
   short myMask;
   boolean reportAll;
   

Modified: nbrowse/trunk/src/org/jnet/shape/Text.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Text.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Text.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -25,6 +25,7 @@
 
 import java.awt.FontMetrics;
 import java.awt.Image;
+import java.io.Serializable;
 
 import java.text.BreakIterator;
 import java.util.ArrayList;
@@ -36,8 +37,8 @@
 import org.jnet.viewer.Viewer;
 import org.jnet.util.TextFormat;
 
-public class Text extends Object2d {
-
+public class Text extends Object2d implements Serializable {
+  static final long serialVersionUID = 1L; 
   
   private float fontScale;
 
@@ -46,7 +47,7 @@
 
   private String[] lines;
 
-  Font3D font;
+  transient Font3D font; // don't store Font Graphics  - not serializable 
   private FontMetrics fm;
   private byte fid;
   private int ascent;

Modified: nbrowse/trunk/src/org/jnet/shape/Uccage.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Uccage.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/shape/Uccage.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -23,8 +23,11 @@
  */
 package org.jnet.shape;
 
-public class Uccage extends FontLineShape {
+import java.io.Serializable;
 
+public class Uccage extends FontLineShape implements Serializable {
+  static final long serialVersionUID = 1L; 
+	
   public String getShapeState() {
     if (modelSet.getCellInfos() == null)
       return "";

Modified: nbrowse/trunk/src/org/jnet/viewer/ColorManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ColorManager.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/viewer/ColorManager.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -37,7 +37,7 @@
   static final long serialVersionUID = 1L;  
   
   private Viewer viewer;
-  private transient Graphics3D g3d;
+  private Graphics3D g3d;
   private int[] argbsCpk;
   private int[] altArgbsCpk;
   private float colorHi, colorLo;
@@ -56,6 +56,15 @@
     //causes problems? flushCaches();
   }
   
+  /**
+   * sets g3d to new version of package
+   * @param g3d
+   */
+  public void setGraphics3D(Graphics3D g3d)
+  {
+	this.g3d = g3d;
+  }
+  
   private boolean isDefaultColorRasmol;
   boolean getDefaultColorRasmol() {
     return isDefaultColorRasmol;

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -130,8 +130,8 @@
   // these are all private now so we are certain they are not 
   // being accesed by any other classes
 
-  private Component display;
-  private transient Graphics3D g3d;
+  private transient Component display;// don't serialize - use new display instead
+  private Graphics3D g3d;
   private JnetAdapter modelAdapter;
 
   private CommandHistory commandHistory = new CommandHistory();
@@ -144,7 +144,7 @@
   private FileManager fileManager;
   private ModelManager modelManager;
   //private ModelSet modelSet;
-  private ModelLoader modelSet; 
+  private ModelLoader modelSet; // important in getting latest
   public transient MouseManager mouseManager; // dont' serialize - just reset if serialized
   private transient PickingManager pickingManager; // dont't serialize - juset reset if serialized
   private transient RepaintManager repaintManager; // dont't serialize - juset reset if serialized
@@ -426,14 +426,18 @@
   public static Viewer reallocateViewer(Viewer newViewer, Viewer oldViewer) 
   {
   // need to copy display, compiler, mouse manager, etc. from old viewer to newViewer object
+	newViewer.jvm11orGreater = oldViewer.jvm11orGreater;
+	newViewer.jvm12orGreater = oldViewer.jvm12orGreater;
+	newViewer.jvm14orGreater = oldViewer.jvm14orGreater;
     newViewer.evalVariables = oldViewer.evalVariables;
     newViewer.compiler = oldViewer.compiler;
     newViewer.compiler.setViewer(newViewer); // replace viewer
     newViewer.display = oldViewer.display; // awt display
     newViewer.eval = oldViewer.eval;
     newViewer.eval.setViewer(newViewer);
-    newViewer.g3d = oldViewer.g3d;
-    
+    //newViewer.g3d = oldViewer.g3d;
+    //newViewer.colorManager.setGraphics3D(newViewer.g3d);
+    newViewer.g3d.setPlatform(newViewer.display);
     newViewer.mouseManager = oldViewer.mouseManager;
     if (newViewer.mouseManager != null)
       newViewer.mouseManager.setViewer(newViewer);
@@ -452,7 +456,20 @@
     if (newViewer.layouter != null)       
       newViewer.layouter.setViewer(newViewer);
     newViewer.minimizer = oldViewer.minimizer;
-    newViewer.modelSet = null; // try nulling to hopefully set
+    
+    for (int i = 0; i < JnetConstants.SHAPE_MAX; i++)
+    {
+    	Shape shape = newViewer.modelSet.getShape(i);
+    	if (shape != null){
+    	  shape.setGraphics3D(newViewer.g3d);
+    	  shape.setModelSet(newViewer.modelSet);
+    	  shape.viewer = newViewer; // try
+    	}
+
+    }
+   
+    //newViewer.modelSet = oldViewer.modelSet; // try this
+    //newViewer.modelSet = null; // try nulling to hopefully set
     return newViewer;
   }
   

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-27 20:21:04 UTC (rev 22630)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-27 21:10:43 UTC (rev 22631)
@@ -149,7 +149,7 @@
   /** Jnet has JnetPanel which has (Jnet)Viewer, so using Viewer directly is
    * bypassing Jnet, which is a nbrowse view, refactor? Jnet also has the toolbar
    with step buttons */
-  private Jnet jnet;
+  private transient Jnet jnet; // should use jnet from new
   private transient final JNetScript jnetScript; // should use jnet from new - jnetscript uses new eval
   
   private boolean jnetStepButtonClicked=false; // dont think this is used
@@ -668,19 +668,22 @@
 
   private void loadSerialData() {
     GraphViewI fullGraph = GraphViewManager.current();
-    //redrawJnet();    
+    //for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
+    
+    redrawJnet();    
 	//clear();
     
 	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
 	
+	
 	//clearAll(); // try this  
 	//ErrorUtil.debug(this, "Loading new nbrowse graph view");
 	//graphView().loadNewRawData(); // this filters
 	//graphView().setDoLayout(false); //this prevents expansions from having lines into nodes    
 	try {
-	  for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor(); // will this help color index issue with serializing
-	  loadJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
-		
+	  //for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor(); // will this help color index issue with serializing
+	  //loadJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
+
 	  //doLayout(true); // try this - hope it helps expansion problem-MS
 	  // don't do layout here - no need to
       //doLayout(true); // works directly on jnet nodes, threaded, true->fit      


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22632
          http://gmod.svn.sourceforge.net/gmod/?rev=22632&view=rev
Author:   montys9
Date:     2010-01-27 21:54:09 +0000 (Wed, 27 Jan 2010)

Log Message:
-----------
made Eval, Token classes serialized,  made instance of JnetManager transient - always use latest instance.  work in progress.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Eval.java
    nbrowse/trunk/src/org/jnet/viewer/Token.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Eval.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Eval.java	2010-01-27 21:10:43 UTC (rev 22631)
+++ nbrowse/trunk/src/org/jnet/viewer/Eval.java	2010-01-27 21:54:09 UTC (rev 22632)
@@ -67,9 +67,11 @@
 
 import org.nbrowse.views.Navigation;
 
-class Eval {
+class Eval implements Serializable {
+static final long serialVersionUID = 1L;
 
-  private static class Context {
+  private static class Context implements Serializable {
+	static final long serialVersionUID = 1L;	  
     String filename;
     String functionName;
     String script;
@@ -94,7 +96,7 @@
 
   private final static int scriptLevelMax = 10;
 
-  private Compiler compiler;
+  private transient Compiler compiler; // reset this if serialized
   private int scriptLevel;
   private int scriptReportingLevel = 0;
   private Context[] stack = new Context[scriptLevelMax];
@@ -166,6 +168,14 @@
     this.viewer = viewer;  
   }
   
+  /**
+   * resets the compiler if load serialized
+   * @param compiler
+   */
+  public void setCompiler(Compiler compiler) {
+	  this.compiler = compiler;
+  }
+  
   private Object getParameter(String var, boolean asToken) {
     Token token = getContextVariableAsToken(var);
     return (token == null ? viewer.getParameter(var) : asToken ? token : Token
@@ -286,7 +296,7 @@
   private Boolean executionPaused = Boolean.FALSE;
   private boolean isExecuting = false;
 
-  private Thread currentThread = null;
+  private transient Thread currentThread = null; // threads are not serialized
 
   void runEval(boolean checkScriptOnly, boolean openFiles,
                boolean historyDisabled, boolean listCommands) {

Modified: nbrowse/trunk/src/org/jnet/viewer/Token.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Token.java	2010-01-27 21:10:43 UTC (rev 22631)
+++ nbrowse/trunk/src/org/jnet/viewer/Token.java	2010-01-27 21:54:09 UTC (rev 22632)
@@ -24,6 +24,7 @@
 
 package org.jnet.viewer;
 
+import java.io.Serializable;
 import java.util.Arrays;
 import java.util.Enumeration;
 import java.util.Hashtable;
@@ -42,8 +43,8 @@
 import org.jnet.modelset.Edge.EdgeSet;
 
 
-public class Token {
-
+public class Token implements Serializable {
+  static final long serialVersionUID = 1L;
   public int tok;
   public Object value;
   public int intValue = Integer.MAX_VALUE;

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-27 21:10:43 UTC (rev 22631)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-27 21:54:09 UTC (rev 22632)
@@ -139,7 +139,7 @@
   private transient Compiler compiler; // don't serialize - just reset if load serialized
   
   private boolean freezing = false;
-  private transient Eval eval; // don't serialize - just reset if load serialized
+  private Eval eval; // don't serialize - just reset if load serialized
   private DataManager dataManager;
   private FileManager fileManager;
   private ModelManager modelManager;
@@ -174,7 +174,7 @@
   private boolean jvm12orGreater = false;
   private boolean jvm14orGreater = false;
 
-  private transient Hashtable evalVariables; // don't serialize since used with Eval object
+  private Hashtable evalVariables; // don't serialize since used with Eval object
 
   Compiler getCompiler() {
     return compiler;
@@ -429,12 +429,13 @@
 	newViewer.jvm11orGreater = oldViewer.jvm11orGreater;
 	newViewer.jvm12orGreater = oldViewer.jvm12orGreater;
 	newViewer.jvm14orGreater = oldViewer.jvm14orGreater;
-    newViewer.evalVariables = oldViewer.evalVariables;
+    //newViewer.evalVariables = oldViewer.evalVariables;
     newViewer.compiler = oldViewer.compiler;
     newViewer.compiler.setViewer(newViewer); // replace viewer
+    newViewer.eval.setCompiler(newViewer.compiler); // replace compiler
     newViewer.display = oldViewer.display; // awt display
-    newViewer.eval = oldViewer.eval;
-    newViewer.eval.setViewer(newViewer);
+    //newViewer.eval = oldViewer.eval;
+    //newViewer.eval.setViewer(newViewer);
     //newViewer.g3d = oldViewer.g3d;
     //newViewer.colorManager.setGraphics3D(newViewer.g3d);
     newViewer.g3d.setPlatform(newViewer.display);
@@ -450,8 +451,10 @@
     if (newViewer.repaintManager != null)     
       newViewer.repaintManager.setViewer(newViewer);
     newViewer.scriptManager = oldViewer.scriptManager;
-    if (newViewer.scriptManager != null)       
-      newViewer.scriptManager.setViewer(newViewer);
+    if (newViewer.scriptManager != null)  
+    {
+      newViewer.scriptManager.setViewer(newViewer);    
+    }
     newViewer.layouter = oldViewer.layouter;
     if (newViewer.layouter != null)       
       newViewer.layouter.setViewer(newViewer);

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-27 21:10:43 UTC (rev 22631)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-27 21:54:09 UTC (rev 22632)
@@ -44,7 +44,7 @@
   
   public final static boolean DO_PJM = false;
 
-  private static JnetManager singleton;
+  private transient static JnetManager singleton; // don't save instance should always use latest
 
   /** 
    * This class uses raw screen data for use when loading directly
@@ -672,7 +672,8 @@
     
     redrawJnet();    
 	//clear();
-    
+    //loadJnet(fullGraph); // generates entire graph again but not centered
+    //drawLabels();
 	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
 	
 	


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22634
          http://gmod.svn.sourceforge.net/gmod/?rev=22634&view=rev
Author:   montys9
Date:     2010-01-28 20:07:06 +0000 (Thu, 28 Jan 2010)

Log Message:
-----------
Serializing more objects - handling null fonts as well - Text/labels objects.  Added broadcastTuple method to NbrowseGoose.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/ModelSet.java
    nbrowse/trunk/src/org/jnet/popup/JnetPopup.java
    nbrowse/trunk/src/org/jnet/shape/Labels.java
    nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java
    nbrowse/trunk/src/org/jnet/shape/Measures.java
    nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java
    nbrowse/trunk/src/org/jnet/shape/Object2dShape.java
    nbrowse/trunk/src/org/jnet/shape/Shape.java
    nbrowse/trunk/src/org/jnet/shape/Text.java
    nbrowse/trunk/src/org/jnet/symmetry/HallInfo.java
    nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java
    nbrowse/trunk/src/org/jnet/symmetry/SpaceGroup.java
    nbrowse/trunk/src/org/jnet/symmetry/Symmetry.java
    nbrowse/trunk/src/org/jnet/symmetry/SymmetryInfo.java
    nbrowse/trunk/src/org/jnet/symmetry/UnitCell.java
    nbrowse/trunk/src/org/jnet/viewer/Compiler.java
    nbrowse/trunk/src/org/jnet/viewer/Eval.java
    nbrowse/trunk/src/org/jnet/viewer/Function.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/io/NbrowseGoose.java

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelSet.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelSet.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelSet.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -517,7 +517,7 @@
         asDraw, false, type, index, scale);
   }
 
-  transient SymmetryInterface pointGroup; // not used
+  SymmetryInterface pointGroup; 
   private Object calculatePointGroupForFirstModel(BitSet bsNodes,
                                                   boolean doAll,
                                                   boolean asDraw,

Modified: nbrowse/trunk/src/org/jnet/popup/JnetPopup.java
===================================================================
--- nbrowse/trunk/src/org/jnet/popup/JnetPopup.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/popup/JnetPopup.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -64,7 +64,7 @@
   Hashtable htMenus = new Hashtable();
   Properties menuText = new Properties();
   
-  transient Object frankPopup;
+  Object frankPopup;
 
   int aboutComputedMenuBaseCount;
   String nullModelSetName, modelSetName;

Modified: nbrowse/trunk/src/org/jnet/shape/Labels.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Labels.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/Labels.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -77,6 +77,16 @@
     translucentAllowed = false;
   }
 
+  /**
+   * Returns default font3d object - used for deserializing
+   * @return
+   */
+  public Font3D getDefaultFont3D()
+  {
+    return g3d.getFont3D(JnetConstants.DEFAULT_FONTFACE,
+        JnetConstants.DEFAULT_FONTSTYLE, JnetConstants.LABEL_DEFAULT_FONTSIZE);
+  }
+  
   public void setProperty(String propertyName, Object value, BitSet bsSelected) {
     isActive = true;
 

Modified: nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -106,6 +106,11 @@
           g3d.setFont(fid);
           fidPrevious = fid;
           font3d = g3d.getFont3DCurrent();
+          // check for null and set it
+          if (font3d == null)
+          {
+            font3d = labels.getDefaultFont3D(); // for deserializing            
+          }
           if (isLeft) {
             FontMetrics fontMetrics = font3d.fontMetrics;
             ascent = fontMetrics.getAscent();

Modified: nbrowse/trunk/src/org/jnet/shape/Measures.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Measures.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/Measures.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -62,7 +62,8 @@
   short mad = (short)-1;
   short colix; // default to none in order to contrast with background
   
-  transient Font3D font3d; // graphics not serializable 
+  // make this private
+  private transient Font3D font3d; // graphics not serializable 
   
   protected void initModelSet() {
     for (int i = 0; i < measurements.length; i++)
@@ -78,6 +79,17 @@
   }
 
   /**
+   * This is added to return font3d - if not defined we redefine
+   * @return
+   */
+  public Font3D getFont3D()
+  {
+    if (font3d == null)
+      font3d = g3d.getFont3D(JnetConstants.MEASURE_DEFAULT_FONTSIZE);
+    return font3d;   
+  }
+  
+  /**
    * used to reset g3d package to shape - over-ridden to rest font3d
    * @param g3d
    */

Modified: nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -47,7 +47,8 @@
     Measures measures = (Measures) shape;
     doJustify = viewer.getJustifyMeasurements();
     measurementMad = measures.mad;
-    font3d = g3d.getFont3DScaled(measures.font3d, imageFontScaling);
+    //font3d = g3d.getFont3DScaled(measures.font3d, imageFontScaling);
+    font3d = g3d.getFont3DScaled(measures.getFont3D(), imageFontScaling);    
     renderPendingMeasurement(measures.measurementPending);
     if (!viewer.getShowMeasurements())
       return;

Modified: nbrowse/trunk/src/org/jnet/shape/Object2dShape.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Object2dShape.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/Object2dShape.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -19,8 +19,8 @@
   Hashtable objects = new Hashtable();
   Object2d currentObject;
   transient Font3D currentFont; // needs to be reset if serialized - only used for set it seems
-  transient Object currentColor; // same as above
-  transient Object currentBgColor; // same as above
+  Object currentColor; // same as above
+  Object currentBgColor; // same as above
   float currentTranslucentLevel;
   float currentBgTranslucentLevel;
   protected String thisID;

Modified: nbrowse/trunk/src/org/jnet/shape/Shape.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Shape.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/Shape.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -79,7 +79,9 @@
  *    Echo, Hover
  *    
  */
-public abstract class Shape  {
+public abstract class Shape implements Serializable {
+  static final long serialVersionUID = 1L; 
+  
   //public Shape () {
   //  System.out.println("Shape " + this + " constructed");
   //}

Modified: nbrowse/trunk/src/org/jnet/shape/Text.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Text.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/shape/Text.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -108,6 +108,7 @@
   }
 
   private void getFontMetrics() {
+    // check if font is null
     fm = font.fontMetrics;
     descent = fm.getDescent();
     ascent = fm.getAscent();
@@ -155,10 +156,16 @@
 
   void setFontScale(float scale) {
     if (fontScale == scale)
-      return;
+      return;    
     fontScale = scale;
     if (fontScale != 0)
+    {
+      // if font is null re-assign it - deserialize
+      if (font == null)
+        font = Font3D.getFont3D(fid);
+      
       setFont(g3d.getFont3DScaled(font, scale));
+    }
   }
 
   String fixText(String text) {

Modified: nbrowse/trunk/src/org/jnet/symmetry/HallInfo.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/HallInfo.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/symmetry/HallInfo.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -52,11 +52,14 @@
  *
  */
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3i;
 import javax.vecmath.Matrix4f;
 import org.jnet.util.Logger;
 
-class HallInfo {
+class HallInfo implements Serializable {
+  static final long serialVersionUID = 1L;
   
   String hallSymbol;
   String primitiveHallSymbol;
@@ -175,8 +178,8 @@
     return name;
   }
   
-  class RotationTerm {
-    
+  class RotationTerm implements Serializable {
+    static final long serialVersionUID = 1L;    
     RotationTerm() {      
     }
     
@@ -351,7 +354,8 @@
   }  
 }
 
-class Translation {
+class Translation implements Serializable {
+  static final long serialVersionUID = 1L;
   
   char translationCode = '\0';
   int rotationOrder;
@@ -491,7 +495,9 @@
   };
 }
 
-class Rotation {
+class Rotation implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   String rotCode;
   //int order;
   Matrix4f seitzMatrix = new Matrix4f();

Modified: nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/symmetry/PointGroup.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -827,7 +827,9 @@
       "center of inversion" };
 
   int nOps = 0;
-  private class Operation {
+  private class Operation implements Serializable {
+    static final long serialVersionUID = 1L;
+    
     int type;
     int order;
     int index;

Modified: nbrowse/trunk/src/org/jnet/symmetry/SpaceGroup.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/SpaceGroup.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/symmetry/SpaceGroup.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -24,6 +24,7 @@
 
 package org.jnet.symmetry;
 
+import java.io.Serializable;
 import java.util.Arrays;
 
 import javax.vecmath.Point3f;
@@ -64,8 +65,9 @@
  *
  */
 
-class SpaceGroup {
-
+class SpaceGroup implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   int index;
   String hallSymbol;
   //String schoenfliesSymbol; //parsed but not read

Modified: nbrowse/trunk/src/org/jnet/symmetry/Symmetry.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/Symmetry.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/symmetry/Symmetry.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -25,6 +25,7 @@
 
 package org.jnet.symmetry;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import java.util.Hashtable;
 
@@ -36,7 +37,7 @@
 import org.jnet.modelset.Node;
 import org.jnet.util.Logger;
 
-public class Symmetry implements SymmetryInterface {
+public class Symmetry implements SymmetryInterface, Serializable {
   
   // NOTE: THIS CLASS IS VERY IMPORTANT.
   // IN ORDER TO MODULARIZE IT, IT IS REFERENCED USING 
@@ -60,6 +61,8 @@
    * The modelSet and modelLoader classes use UnitCell and SymmetryInfo 
    * 
    */
+  static final long serialVersionUID = 1L;
+  
   private PointGroup pointGroup;
   private SpaceGroup spaceGroup;
   private SymmetryInfo symmetryInfo;

Modified: nbrowse/trunk/src/org/jnet/symmetry/SymmetryInfo.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/SymmetryInfo.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/symmetry/SymmetryInfo.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -26,10 +26,13 @@
 package org.jnet.symmetry;
 
 import javax.vecmath.Point3f;
+
+import java.io.Serializable;
 import java.util.Hashtable;
 
-class SymmetryInfo {
-
+class SymmetryInfo implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   boolean coordinatesAreFractional;
   boolean isMultiCell;
   String spaceGroup;

Modified: nbrowse/trunk/src/org/jnet/symmetry/UnitCell.java
===================================================================
--- nbrowse/trunk/src/org/jnet/symmetry/UnitCell.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/symmetry/UnitCell.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -32,6 +32,8 @@
  * 
  *
  */
+import java.io.Serializable;
+
 import javax.vecmath.Matrix4f;
 import javax.vecmath.Point3f;
 import javax.vecmath.Vector3f;
@@ -42,7 +44,8 @@
 
 //import org.jnet.util.Escape;
 
-public class UnitCell {
+public class UnitCell implements Serializable {
+  static final long serialVersionUID = 1L;
   
   final static float toRadians = (float) Math.PI * 2 / 360;
   final static Point3f[] unitCubePoints = { new Point3f(0, 0, 0),

Modified: nbrowse/trunk/src/org/jnet/viewer/Compiler.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Compiler.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/viewer/Compiler.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -30,14 +30,16 @@
 import org.jnet.modelset.Group;
 import org.jnet.modelset.Edge.EdgeSet;
 
+import java.io.Serializable;
 import java.util.Hashtable;
 import java.util.Vector;
 import java.util.BitSet;
 
 import javax.vecmath.Point3f;
 
-class Compiler {
-
+class Compiler implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   Hashtable localFunctions = new Hashtable();
   static Hashtable globalFunctions = new Hashtable();
   boolean isFunction(String name) {
@@ -145,7 +147,9 @@
    * 
    */
   
-  private static class FlowContext {
+  private static class FlowContext implements Serializable {
+    static final long serialVersionUID = 1L;
+    
     Token token;
     int pt0;
     Function function;

Modified: nbrowse/trunk/src/org/jnet/viewer/Eval.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Eval.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/viewer/Eval.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -96,7 +96,7 @@
 
   private final static int scriptLevelMax = 10;
 
-  private transient Compiler compiler; // reset this if serialized
+  private Compiler compiler; // reset this if serialized
   private int scriptLevel;
   private int scriptReportingLevel = 0;
   private Context[] stack = new Context[scriptLevelMax];

Modified: nbrowse/trunk/src/org/jnet/viewer/Function.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Function.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/viewer/Function.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -23,10 +23,13 @@
 
 package org.jnet.viewer;
 
+import java.io.Serializable;
 import java.util.Hashtable;
 import java.util.Vector;
 
-class Function {
+class Function implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   int pt0;
   int chpt0;
   int cmdpt0= -1;

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -136,7 +136,7 @@
 
   private CommandHistory commandHistory = new CommandHistory();
   private ColorManager colorManager;
-  private transient Compiler compiler; // don't serialize - just reset if load serialized
+  private Compiler compiler; // don't serialize - just reset if load serialized
   
   private boolean freezing = false;
   private Eval eval; // don't serialize - just reset if load serialized
@@ -425,14 +425,19 @@
 
   public static Viewer reallocateViewer(Viewer newViewer, Viewer oldViewer) 
   {
-  // need to copy display, compiler, mouse manager, etc. from old viewer to newViewer object
-	newViewer.jvm11orGreater = oldViewer.jvm11orGreater;
-	newViewer.jvm12orGreater = oldViewer.jvm12orGreater;
-	newViewer.jvm14orGreater = oldViewer.jvm14orGreater;
+    // need to copy display, compiler, mouse manager, etc. from old viewer to newViewer object
+	  newViewer.jvm11orGreater = oldViewer.jvm11orGreater;
+  	newViewer.jvm12orGreater = oldViewer.jvm12orGreater;
+	  newViewer.jvm14orGreater = oldViewer.jvm14orGreater;
+	  newViewer.strJavaVendor = oldViewer.strJavaVendor;
+	  newViewer.strJavaVersion = oldViewer.strJavaVersion;
+	  newViewer.strOSName = oldViewer.strOSName;
     //newViewer.evalVariables = oldViewer.evalVariables;
-    newViewer.compiler = oldViewer.compiler;
-    newViewer.compiler.setViewer(newViewer); // replace viewer
-    newViewer.eval.setCompiler(newViewer.compiler); // replace compiler
+	
+    //newViewer.compiler = oldViewer.compiler;
+    //newViewer.compiler.setViewer(newViewer); // replace viewer
+    //newViewer.eval.setCompiler(newViewer.compiler); // replace compiler
+	
     newViewer.display = oldViewer.display; // awt display
     //newViewer.eval = oldViewer.eval;
     //newViewer.eval.setViewer(newViewer);
@@ -463,7 +468,7 @@
     for (int i = 0; i < JnetConstants.SHAPE_MAX; i++)
     {
     	Shape shape = newViewer.modelSet.getShape(i);
-    	if (shape != null){
+    	if (shape != null){ // why does this need to be reset
     	  shape.setGraphics3D(newViewer.g3d);
     	  shape.setModelSet(newViewer.modelSet);
     	  shape.viewer = newViewer; // try

Modified: nbrowse/trunk/src/org/nbrowse/io/NbrowseGoose.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/NbrowseGoose.java	2010-01-28 12:03:53 UTC (rev 22633)
+++ nbrowse/trunk/src/org/nbrowse/io/NbrowseGoose.java	2010-01-28 20:07:06 UTC (rev 22634)
@@ -40,6 +40,7 @@
 import org.systemsbiology.gaggle.core.datatypes.Interaction;
 import org.systemsbiology.gaggle.core.datatypes.Namelist;
 import org.systemsbiology.gaggle.core.datatypes.Network;
+import org.systemsbiology.gaggle.core.datatypes.Single;
 import org.systemsbiology.gaggle.core.datatypes.Tuple;
 import org.systemsbiology.gaggle.core.Boss;
 import org.systemsbiology.gaggle.core.Goose;
@@ -466,6 +467,44 @@
    private String species() { 
      return MetaDataManager.inst().getSpeciesLatinName();
    }
+
+
+   /** broadcast current connected 1 hop nodes as selected, rest as unselected to gaggle */
+   private void broadcastNodeIdTuple() {
+     //String[] nameList = {"YFL036W", "YFL037W", "YLR212C", "YLR213C"};
+     // need to get search-based node and find all connected nodes and send with 0 - then send all rest with 0
+     String[] ids = sel().getSelectedIds(); // starting point
+     //NBNode queryNode = g.findNodeByName(ids[0]);
+     //if (queryNode==null) {
+     //  ErrorUtil.error(this, "query node for file load not found "+startingPoint);
+     //  return;
+     //}     
+     
+     //String species = "Saccharomyces cerevisiae";
+     //Namelist gaggleNameList = new Namelist();
+     GaggleTuple gaggleTuple = new GaggleTuple();
+     gaggleTuple.setName("list of nodes with 1 for foreground/0 for background ");
+     gaggleTuple.setSpecies(species());
+     Single condition = new Single("node", "1/0");// name and foreground/background
+     gaggleTuple.getMetadata().addSingle(condition);
+     /*
+     for (int i = 0; i < rowNames.length; i++) {
+       Tuple tuple = new Tuple();
+       tuple.addSingle(new Single(null, rowNames[i]));
+       tuple.addSingle(new Single(null, "log10 ratios"));
+       tuple.addSingle(new Single(null, values[i]));
+       gaggleTuple.getData().addSingle(new Single(tuple));       
+     }
+     */
+     
+     try {
+       boss.broadcastTuple(myGaggleName, targetGoose, gaggleTuple);
+     }
+     catch (RemoteException rex) {
+       ErrorUtil.error(this,"NbrowseGoose: rmi error calling boss.broadcast (nameList)");
+       rex.printStackTrace();
+     }
+   } // broadcastSampleList
    
    /** broadcast current selected node ids? (names?) to gaggle */
    private void broadcastNodeIdList() {


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22639
          http://gmod.svn.sourceforge.net/gmod/?rev=22639&view=rev
Author:   montys9
Date:     2010-01-29 22:34:44 +0000 (Fri, 29 Jan 2010)

Log Message:
-----------
Lot of work done on serializing and at times not using serialized based on side effects, etc.  Currently trying to get model to load as per each step since the StepManager is not serializable. I can load individual steps though.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/shape/BallsRenderer.java
    nbrowse/trunk/src/org/jnet/shape/EchoRenderer.java
    nbrowse/trunk/src/org/jnet/shape/FontLineShapeRenderer.java
    nbrowse/trunk/src/org/jnet/shape/HalosRenderer.java
    nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java
    nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java
    nbrowse/trunk/src/org/jnet/shape/ShapeRenderer.java
    nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
    nbrowse/trunk/src/org/jnet/util/Point3fi.java
    nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java
    nbrowse/trunk/src/org/jnet/viewer/ModelManager.java
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/jnet/viewer/MouseManager10.java
    nbrowse/trunk/src/org/jnet/viewer/MouseManager11.java
    nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java
    nbrowse/trunk/src/org/jnet/viewer/TransformManager11.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/api/AbstractView.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java
    nbrowse/trunk/src/org/nbrowse/views/Navigation.java
    nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java
    nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java

Modified: nbrowse/trunk/src/org/jnet/shape/BallsRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/BallsRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/BallsRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -36,6 +36,7 @@
 //import javax.vecmath.*;
 import java.awt.Color;  //Victor Chest
 import java.awt.Rectangle;
+import java.io.Serializable;
 
 import javax.vecmath.Matrix3f;
 import javax.vecmath.Matrix4f;
@@ -46,7 +47,8 @@
 import org.jnet.g3d.Graphics3D;
 import org.nbrowse.utils.ErrorUtil;
 
-public class BallsRenderer extends ShapeRenderer {
+public class BallsRenderer extends ShapeRenderer implements Serializable {
+  static final long serialVersionUID = 1L;
   // overlap debug code switch - please note that switch is only used here to remove redundancy using methods getXLeftHand and getXRightHand
   final boolean tryOverlapCode = true;
   //int minX, minY, maxX, maxY; 

Modified: nbrowse/trunk/src/org/jnet/shape/EchoRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/EchoRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/EchoRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -23,11 +23,13 @@
  */
 package org.jnet.shape;
 
+import java.io.Serializable;
 import java.util.Enumeration;
 import javax.vecmath.Point3i;
 
-public class EchoRenderer extends ShapeRenderer {
-
+public class EchoRenderer extends ShapeRenderer implements Serializable {
+	static final long serialVersionUID = 1L;
+	
   float imageFontScaling;
 
   protected void render() {

Modified: nbrowse/trunk/src/org/jnet/shape/FontLineShapeRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/FontLineShapeRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/FontLineShapeRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -23,12 +23,15 @@
  */
 package org.jnet.shape;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 import javax.vecmath.Point3i;
 
 import org.jnet.g3d.Graphics3D;
 
-abstract class FontLineShapeRenderer extends ShapeRenderer {
+abstract class FontLineShapeRenderer extends ShapeRenderer implements Serializable {
+  static final long serialVersionUID = 1L;
 
   float imageFontScaling;
   

Modified: nbrowse/trunk/src/org/jnet/shape/HalosRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/HalosRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/HalosRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -29,11 +29,13 @@
 import org.jnet.modelset.Node;
 import org.jnet.viewer.JnetConstants;
 
+import java.io.Serializable;
 import java.util.BitSet;
 import org.jnet.api.JnetRendererInterface;
 
-public class HalosRenderer extends ShapeRenderer {
-
+public class HalosRenderer extends ShapeRenderer implements Serializable {
+  static final long serialVersionUID = 1L;
+	
   boolean isAntialiased;
   protected void render() {
     Halos halos = (Halos) shape;

Modified: nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/LabelsRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -29,12 +29,14 @@
 import org.jnet.modelset.Group;
 
 import java.awt.FontMetrics;
+import java.io.Serializable;
 
-public class LabelsRenderer extends ShapeRenderer {
+public class LabelsRenderer extends ShapeRenderer implements Serializable {
+	static final long serialVersionUID = 1L;
 
   // offsets are from the font baseline
   byte fidPrevious;
-  protected Font3D font3d;
+  protected transient Font3D font3d;
   protected int ascent;
   protected int descent;
 

Modified: nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/MeasuresRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -24,6 +24,8 @@
 
 package org.jnet.shape;
 
+import java.io.Serializable;
+
 import org.jnet.g3d.*;
 import org.jnet.modelset.Measurement;
 import org.jnet.modelset.MeasurementPending;
@@ -34,10 +36,10 @@
 import javax.vecmath.Matrix3f;
 import javax.vecmath.AxisAngle4f;
 
-public class MeasuresRenderer extends FontLineShapeRenderer {
+public class MeasuresRenderer extends FontLineShapeRenderer implements Serializable {
 
   private short measurementMad;
-  private Font3D font3d;
+  private transient Font3D font3d;
   private Measurement measurement;
   private boolean doJustify;
   protected void render() {
@@ -84,6 +86,16 @@
     return a;
   }
   
+  /**
+   * this method reset the font3d used
+   */
+  private void resetFont3D()
+  {
+    imageFontScaling = viewer.getImageFontScaling();
+	Measures measures = (Measures) shape;	  
+	font3d = g3d.getFont3DScaled(measures.getFont3D(), imageFontScaling); 
+  }
+  
   private void renderMeasurement(int count, Measurement measurement, boolean renderLabel) {
     this.measurement = measurement;
     switch(count) {
@@ -224,6 +236,10 @@
     String strMeasurement = measurement.getString();
     if (strMeasurement == null)
       return;
+    
+    if (font3d == null)
+    	resetFont3D(); // if not defined due to serializing, reset
+    
     int width = font3d.fontMetrics.stringWidth(strMeasurement);
     int height = font3d.fontMetrics.getAscent();
     int xT = x;

Modified: nbrowse/trunk/src/org/jnet/shape/ShapeRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/ShapeRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/ShapeRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -24,6 +24,8 @@
 
 package org.jnet.shape;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 import org.jnet.viewer.Overlap;
 import javax.vecmath.Point3i;
@@ -34,8 +36,9 @@
 import org.jnet.viewer.Viewer;
 //import java.awt.Rectangle;
 
-public abstract class ShapeRenderer {
-
+public abstract class ShapeRenderer implements Serializable {
+	static final long serialVersionUID = 1L;
+	
   //public void finalize() {
   //  System.out.println("ShapeRenderer " + shapeID + " " + this + " finalized");
   //}

Modified: nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/shape/SticksRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -33,6 +33,7 @@
 
 import java.awt.Point;
 import java.awt.Rectangle;
+import java.io.Serializable;
 import java.util.Hashtable; //Victor Chest
 
 import javax.vecmath.Point2f;
@@ -44,8 +45,9 @@
 import org.nbrowse.utils.ErrorUtil;
 import org.nbrowse.views.JnetManager;
 
-public final class SticksRenderer extends ShapeRenderer {
-	  
+public final class SticksRenderer extends ShapeRenderer implements Serializable {
+	static final long serialVersionUID = 1L;
+	
   /** pixels away from edge for overlap */
   private static final int POINT_RADIUS = 3; // 7??
   protected boolean showMultipleEdges;

Modified: nbrowse/trunk/src/org/jnet/util/Point3fi.java
===================================================================
--- nbrowse/trunk/src/org/jnet/util/Point3fi.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/util/Point3fi.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -23,12 +23,16 @@
  */
 
 package org.jnet.util;
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 
 /** strange this seems to be Point3f with int xyz
  * but nothing that relates the floats to ints?? */
 
-public class Point3fi extends Point3f {
+public class Point3fi extends Point3f implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   public int screenX;
   public int screenY;
   public int screenZ;

Modified: nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/FrameRenderer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -24,6 +24,8 @@
 
 package org.jnet.viewer;
 
+import java.io.Serializable;
+
 import org.jnet.api.JnetExportInterface;
 import org.jnet.api.JnetRendererInterface;
 import org.jnet.g3d.*;
@@ -36,8 +38,9 @@
 import org.jnet.viewer.Viewer;
 import org.jnet.util.Logger;
 
-public class FrameRenderer {
-
+public class FrameRenderer implements Serializable {
+  static final long serialVersionUID = 1L;
+  
   boolean logTime;
     
   Viewer viewer;

Modified: nbrowse/trunk/src/org/jnet/viewer/ModelManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ModelManager.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/ModelManager.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -50,6 +50,15 @@
     return null;
   }
 
+  /**
+   * resets the model loader
+   * @param modelLoader
+   */
+  public void setModelLoader(ModelLoader modelLoader)
+  {
+	this.modelLoader = modelLoader;  
+  }
+  
   ModelLoader zap() {
     clear();
     fullPathName = fileName;

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -15,6 +15,7 @@
 
 import java.awt.event.*;
 import java.awt.Component;
+import java.io.Serializable;
 
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -44,8 +45,9 @@
 import org.nbrowse.views.NodeViewI;
 import org.nbrowse.views.StepManager;
 
-public abstract class MouseManager implements KeyListener {
-
+public abstract class MouseManager implements KeyListener, Serializable {
+	static final long serialVersionUID = 1L;
+	
   // overlap debug code switch - this code is set to true for new overlap methodology.
   final boolean tryOverlapCode = true;
   // using new key/mouse mappings
@@ -57,8 +59,9 @@
    * @author monty
    *
    */
-  private class MousePopupMenu
+  private class MousePopupMenu implements Serializable 
   {
+	  static final long serialVersionUID = 1L;
      // Swing and awt based popup-MS
     private JPopupMenu mainPopupMenuSwing = null;
     private PopupMenu mainPopupMenuAwt = null; // legacy version if needed-MS
@@ -130,7 +133,7 @@
   
   Viewer viewer;
 
-  Thread hoverWatcherThread;
+  transient Thread hoverWatcherThread;
 
   int previousDragX, previousDragY;
   int xCurrent = -1000;
@@ -149,6 +152,24 @@
   final static Rectangle rectRubber = new Rectangle();
   Rectangle rectNavigator = new Rectangle();
 
+  public void setMouseManagerProperties(MouseManager mouseManager)
+  {
+	  /*
+	this.previousDragX = mouseManager.previousDragX;  
+	this.previousDragY = mouseManager.previousDragY;
+	this.xCurrent = mouseManager.xCurrent;
+	this.timeCurrent = mouseManager.timeCurrent;
+	this.drawMode = mouseManager.drawMode;
+	this.measuresEnabled = mouseManager.measuresEnabled;
+	this.measurementPending = mouseManager.measurementPending;
+	this.set = mouseManager.set;
+	this.rubberbandSelectionMode = mouseManager.rubberbandSelectionMode;
+	this.xAnchor = mouseManager.xAnchor;
+	this.yAnchor = mouseManager.yAnchor;
+	this.rectNavigator = mouseManager.rectNavigator;
+	*/
+  }
+  
   /** In practice theres only 1 MouseMan, cant enforce the way code is structured i dont
    * think */
   private static MouseManager unenforcedSingleton;
@@ -177,6 +198,18 @@
     this.viewer = viewer;  
   }
   
+  /** used for reseting mouse manager */
+  public void resetMouseManager()
+  {
+	    Component display = viewer.getAwtComponent();
+	    if (display != null)
+	      display.addKeyListener(this);
+		    
+	    if (tryNewMenu) // add popup menu if needed
+	        addPopupMenu(); // add popup menu to this
+	    //clear();
+  }
+  
   void clear() {
     startHoverWatcher(false);
   }

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager10.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager10.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager10.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -26,9 +26,11 @@
 
 import java.awt.Component;
 import java.awt.Event;
+import java.io.Serializable;
 
-class MouseManager10 extends MouseManager {
-
+class MouseManager10 extends MouseManager implements Serializable {
+	static final long serialVersionUID = 1L;
+	
   MouseManager10(Component component, Viewer viewer) {
     super(viewer);
     //Logger.debug("MouseManager10 implemented");

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager11.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager11.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager11.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -29,10 +29,12 @@
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.io.Serializable;
 
 class MouseManager11 extends MouseManager
-  implements MouseListener, MouseMotionListener {
-
+  implements MouseListener, MouseMotionListener, Serializable {
+	static final long serialVersionUID = 1L;
+	
   MouseManager11(Component display, Viewer viewer) {
     super(viewer);
     if (display == null)
@@ -41,7 +43,21 @@
     display.addMouseListener(this);
     display.addMouseMotionListener(this);
   }
-
+  
+  /** resets display
+   * 
+   */
+  public void resetMouseManager()
+  {
+	 super.resetMouseManager();
+	 Component display = viewer.getAwtComponent();
+	 if (display != null)
+	 {
+	   display.addMouseListener(this);
+	   display.addMouseMotionListener(this);
+	 }
+  }
+  
   void removeMouseListeners11() {
     viewer.getAwtComponent().removeMouseListener(this);
     viewer.getAwtComponent().removeMouseMotionListener(this);

Modified: nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/RepaintManager.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -29,13 +29,16 @@
 import org.jnet.modelset.ModelSet;
 
 import java.awt.Rectangle;
+import java.io.Serializable;
 import java.util.Hashtable;
 import java.util.BitSet;
 
 import javax.vecmath.Point3i;
 
-class RepaintManager {
-
+class RepaintManager implements Serializable {
+  static final long serialVersionUID = 1L;
+	
+	
   Viewer viewer;
   FrameRenderer frameRenderer;
   

Modified: nbrowse/trunk/src/org/jnet/viewer/TransformManager11.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/TransformManager11.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/TransformManager11.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -31,10 +31,13 @@
 
 import java.awt.event.KeyEvent;
 import java.awt.event.InputEvent;
+import java.io.Serializable;
+
 import org.jnet.g3d.Graphics3D;
 
-class TransformManager11 extends TransformManager {
-
+class TransformManager11 extends TransformManager implements Serializable {
+  static final long serialVersionUID = 1L; 
+  
   private float navigationSlabOffset;
   private float zoomFactor = Float.MAX_VALUE;
 

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -106,6 +106,7 @@
  */
 import org.jnet.adapter.smarter.Resolver;
 import org.jnet.shape.Hover;
+import org.nbrowse.views.Navigation;
 
 /** Viewer and JnetViewer should maybe have their names switched? */
 public class Viewer extends JnetViewer implements NodeDataServer, Serializable {
@@ -147,7 +148,7 @@
   private ModelLoader modelSet; // important in getting latest
   public transient MouseManager mouseManager; // dont' serialize - just reset if serialized
   private transient PickingManager pickingManager; // dont't serialize - juset reset if serialized
-  private transient RepaintManager repaintManager; // dont't serialize - juset reset if serialized
+  private RepaintManager repaintManager; // dont't serialize - juset reset if serialized
   private transient ScriptManager scriptManager; // dont't serialize - juset reset if serialized
   private SelectionManager selectionManager;
   private StateManager stateManager;
@@ -264,6 +265,7 @@
     return layouter;
   }
 
+  
   /** Fits graph to screen/centers */
   public void fitToScreen() {
     getLayouter(true).fitToScreen();
@@ -444,17 +446,23 @@
     //newViewer.g3d = oldViewer.g3d;
     //newViewer.colorManager.setGraphics3D(newViewer.g3d);
     newViewer.g3d.setPlatform(newViewer.display);
-    newViewer.mouseManager = oldViewer.mouseManager;
+    //newViewer.mouseManager.resetMouseManager(); // resets values
+    // mouse manager copying properties not helping
+    //oldViewer.mouseManager.setMouseManagerProperties(newViewer.mouseManager); // copy properties to current mousemanager
+    //newViewer.mouseManager = oldViewer.mouseManager; // copy over mouse manager instead of using old copy
+    
+    newViewer.mouseManager = oldViewer.mouseManager; // if mouse manager is serialized, hovering on objects no longer work properly right now
     if (newViewer.mouseManager != null)
       newViewer.mouseManager.setViewer(newViewer);
+    
     newViewer.pickingManager = oldViewer.pickingManager;
     if (newViewer.pickingManager != null)    
     newViewer.pickingManager.setViewer(newViewer);
     //newViewer.statusManager = oldViewer.statusManager; // test this
     //newViewer.statusManager.setViewer(newViewer);
-    newViewer.repaintManager = oldViewer.repaintManager;
-    if (newViewer.repaintManager != null)     
-      newViewer.repaintManager.setViewer(newViewer);
+    //newViewer.repaintManager = oldViewer.repaintManager;
+    //if (newViewer.repaintManager != null)     
+    //  newViewer.repaintManager.setViewer(newViewer);
     newViewer.scriptManager = oldViewer.scriptManager;
     if (newViewer.scriptManager != null)  
     {
@@ -465,13 +473,16 @@
       newViewer.layouter.setViewer(newViewer);
     newViewer.minimizer = oldViewer.minimizer;
     
+    // if navaigation is set to different viewer - can't click or move nodes around
+    //Navigation.inst().setViewer(newViewer); // needs to make sure point to correct viewer
+    
     for (int i = 0; i < JnetConstants.SHAPE_MAX; i++)
     {
     	Shape shape = newViewer.modelSet.getShape(i);
     	if (shape != null){ // why does this need to be reset
-    	  shape.setGraphics3D(newViewer.g3d);
-    	  shape.setModelSet(newViewer.modelSet);
-    	  shape.viewer = newViewer; // try
+    	  //shape.setGraphics3D(newViewer.g3d);
+    	  //shape.setModelSet(newViewer.modelSet);
+    	  //shape.viewer = newViewer; // try
     	}
 
     }
@@ -2514,6 +2525,24 @@
       return savedTransfManager;
   }
 
+  /** sets current model manager to model loader
+   * 
+   * @return
+   */
+  public void setModelManagerLoader(ModelLoader modelLoader)
+  {
+	  modelManager.setModelLoader(modelLoader);
+  }
+  
+  /** 
+   * sets to modelset
+   * @param modelset
+   */
+  public void setModelSet(ModelLoader modelset)
+  {
+	this.modelSet = modelset;  
+  }
+  
   public void clear() {
     if (modelSet == null)
       return;

Modified: nbrowse/trunk/src/org/nbrowse/api/AbstractView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/api/AbstractView.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/api/AbstractView.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -37,6 +37,14 @@
         this.parent = parent;
     }
     
+    /**
+     * returns JFrame parent
+     * @return
+     */
+    public javax.swing.JFrame getJParent() {
+    	return parent;    	
+    }
+    
     /** By default make display name out of class name, subclasses override this to give
      * a name other than the name of the subclass */
     protected String getViewDisplayName() {

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -25,7 +25,11 @@
 import javax.swing.JLabel;
 import javax.swing.JTextField;
 
+import org.jnet.modelset.ModelLoader;
+import org.jnet.modelset.ModelSet;
+import org.jnet.shape.Shape;
 import org.jnet.util.Escape;
+import org.jnet.viewer.JnetConstants;
 import org.jnet.viewer.Viewer;
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.MetaData;
@@ -34,8 +38,10 @@
 import org.nbrowse.utils.ErrorUtil;
 import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.JnetPanel;
+import org.nbrowse.views.NBSelectionManager;
 import org.nbrowse.views.Navigation;
 import org.nbrowse.views.StepManager;
+import org.nbrowse.views.edgecontrol.EdgeFilterState;
 
 /**
  * singleton? should this be in gui?
@@ -158,6 +164,27 @@
 		   GraphData.getCurrentGraphData().clear();
 		   GraphData.setCurrentGraphData((GraphData) gd_obj);
 		}
+
+		/*
+		Object modelset = obj_in.readObject();
+		if (modelset instanceof ModelLoader)
+		{
+			ModelLoader modelLoader = (ModelLoader) modelset;
+			Viewer viewer = JnetManager.inst().getJnetViewer();
+			JnetManager.inst().getJnetViewer().setModelSet((ModelLoader) modelset);
+			viewer.setModelManagerLoader(modelLoader); // if doing modelloader add it back in
+		    for (int i = 0; i < JnetConstants.SHAPE_MAX; i++)
+		    {
+		    	Shape shape = modelLoader.getShape(i);
+		    	if (shape != null){ // why does this need to be reset
+		    	  shape.setGraphics3D(viewer.getGraphics3D());
+		    	  shape.setModelSet(viewer.getModelSet());
+		    	  shape.viewer = viewer; // try
+		    	}
+
+		    }			
+		}
+		*/
 		
 		Object viewer = obj_in.readObject();
 		if (viewer instanceof Viewer)
@@ -166,12 +193,41 @@
 		  JnetManager.inst().loadJnetViewer((Viewer) viewer);
 		  
 		}
+
+		Object edgeFilterState = obj_in.readObject();
+		if (edgeFilterState instanceof EdgeFilterState)
+		{
+		  	EdgeFilterState.inst().setEdgeFilterState((EdgeFilterState) edgeFilterState); // use for edge filtering
+		}
 		
+		/*
+		Object navigation = obj_in.readObject();
+		if (navigation instanceof Navigation)
+		{
+			Navigation nav = (Navigation) navigation;
+			nav.setParent(Navigation.inst().getJParent());
+			Navigation.inst().setNavigation((Navigation) navigation);
+		}
+		*/
+		
+		/*
+		Object nbselection = obj_in.readObject();
+		if (nbselection instanceof NBSelectionManager)
+		{
+			NBSelectionManager.inst().setNBSelectionManager((NBSelectionManager) nbselection);
+		}
+		*/
+		
+		
 		Object stepMan = obj_in.readObject();
 		if (stepMan instanceof StepManager)
 		{
-			StepManager.inst().setStepManager((StepManager) stepMan);
+			//StepManager.inst().setStepManager((StepManager) stepMan);
+			//StepManager.inst().getDisplayStep(); // current display step
+			// lastQueryDepth is last expansion done
 		}
+	
+		
 		}
 		catch(Exception ex)
 		{
@@ -258,8 +314,11 @@
         //GraphEltSet currGraph = GraphEltSet.getCurrentGraph().getFilteredGraph(); // save filtered?
     	  GraphData graphData = GraphData.getCurrentGraphData();    	  
     	  StepManager stepMan = StepManager.inst();
-    	  
+    	  ModelSet modelset = JnetManager.inst().getJnetViewer().getModelSet();
+    	  Navigation navigate = Navigation.inst();
+    	  NBSelectionManager nbselection = NBSelectionManager.inst();
         Viewer viewer = JnetManager.inst().getJnetViewer();
+        EdgeFilterState edgeFilterState = EdgeFilterState.inst();
     	// Write to disk with FileOutputStream
     	  try{
     	  FileOutputStream f_out = new 
@@ -273,9 +332,16 @@
         obj_out.writeObject ( currGraph );
         // Write GraphData object to file
         obj_out.writeObject(graphData);
-    	  
+    	
+        //obj_out.writeObject(modelset);
+        
         obj_out.writeObject(viewer);
 
+        obj_out.writeObject(edgeFilterState);
+        //obj_out.writeObject(navigate);
+        
+        //obj_out.writeObject(nbselection);
+        
         obj_out.writeObject(stepMan);
         
     	  obj_out.flush();

Modified: nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -67,7 +67,9 @@
     }
 
   // set of edges changed due to edge filtering, redo tablex
-  private class EdgeLis implements EdgeChangeListener {
+  private class EdgeLis implements EdgeChangeListener, Serializable {
+	  static final long serialVersionUID = 1L;	
+	  
     public void edgeChanged(EdgeChangeEvent e) { redoTable(); }
     public void filterChanged() { redoTable(); }
   }

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -432,8 +432,9 @@
   /** The edge controls/filters have been changed, modify edges and display 
    Make new GraphData with new controls, and make jnet script.
    */
-  private class EdgeChangeLis implements EdgeChangeListener {
-
+  private class EdgeChangeLis implements EdgeChangeListener, Serializable {
+	  static final long serialVersionUID = 1L;	
+	  
     // shold the event be dropped - its doing a little but not a lot
     public void edgeChanged(EdgeChangeEvent e) {
       if (e.isSizeChange()) synchEdgeSizes();
@@ -666,17 +667,49 @@
 
   private NbrowseJnetAdapter nbJnetAdap() { return NbrowseJnetAdapter.inst(); }
 
-  private void loadSerialData() {
+  private void loadSerialData() {	 
     GraphViewI fullGraph = GraphViewManager.current();
-    //for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
-    
-    redrawJnet();    
+    for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
+	
+	
+    redrawJnet();  
+	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
 	//clear();
+    System.out.println("display step = " + getDisplayStep());
+   // loadJnetFiltered(); // this will load current step used in stepmanager    
+    //centerGraph();
     
+    int expandedStep = graphModel().getStepDepth();
+    System.out.println("step depth = " + expandedStep);
+    GraphViewI filteredGraph = null;
+    
+    for (int step = 1; step <= expandedStep; step++)
+    {
+    	filteredGraph = fullGraph.getSubgraph(EdgeFilterState.inst(), step);
+    	if (step == 1) // inital graph
+    	{
+    	   loadJnet(filteredGraph);
+    	   centerGraph();
+    	   //createJnetLineBarStepButton(1);
+    	}
+    	else
+    	{
+    		graphView().doExpansion(step,is3D()); // do we still need this?
+    		loadJnetFiltered(step);
+    		//jnetStepButtonExpansion(step);
+    	}
+    }
+    
+    //int step = 2; // need to utilize number of steps last expanded to re-add steps.
+    //GraphViewI filteredGraph = fullGraph.getSubgraph(EdgeFilterState.inst(), step);
+    //loadJnet(filteredGraph);
+    
     //loadJnet(fullGraph); // generates entire graph again but not centered
+    //centerGraph(); // if using above loadJnet need to center graph
+    
     //drawLabels();
     
-	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
+	//StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
 	
 	
 	//clearAll(); // try this  
@@ -684,8 +717,8 @@
 	//graphView().loadNewRawData(); // this filters
 	//graphView().setDoLayout(false); //this prevents expansions from having lines into nodes    
 	try {
-	  //for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor(); // will this help color index issue with serializing
-	  loadJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
+//	  for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor(); // will this help color index issue with serializing
+	  //loadJnetFiltered(); // is this a problem causing 0,0,0 of coordinates
 
 	  //doLayout(true); // try this - hope it helps expansion problem-MS
 	  // don't do layout here - no need to

Modified: nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/views/NBSelectionManager.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -37,6 +37,12 @@
   }
   public static NBSelectionManager inst() { return singleton; }
 
+  /** sets the instance */
+  public void setNBSelectionManager(NBSelectionManager instance)
+  {
+	  this.singleton = instance;
+  }
+  
   void initJnetSelListener(Viewer jnetViewer) {
     jnetViewer.addSelectionListener(new JnetSelLis());
     //jnetViewer.getMouseManager().addSelectListener(l)

Modified: nbrowse/trunk/src/org/nbrowse/views/Navigation.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Navigation.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/views/Navigation.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -13,8 +13,9 @@
 import org.jnet.viewer.Viewer;
 import org.jnet.util.Logger;
 
-public final class Navigation extends AbstractView {
-
+public final class Navigation extends AbstractView implements Serializable {
+  static final long serialVersionUID = 1L;
+	
   public final static String TITLE = "Birds Eye View"; // Navigator/tion
   private final Dimension currentSize = new Dimension();
   private final Rectangle rectClip = new Rectangle();
@@ -53,7 +54,18 @@
    public static Navigation inst() { return instance; }
    public Viewer getViewer() { return viewer; }
    
+   /**
+    * sets the new instance
+    * @param instance
+    */
+   public void setNavigation(Navigation instance)
+   {
+	   this.instance = instance;
+   }
    
+   public void setViewer(Viewer viewer) {
+	   this.viewer = viewer;
+   }
     public void initWindows() {
         adapter = new SmarterJnetAdapter();
         viewer = JnetViewer.allocateViewer(this, adapter, null, null, null, "", null);

Modified: nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -57,7 +57,9 @@
 
   int getJnetNodeId() { return displayNode.getNodeIndex(); }
 
-  private class NodeHover implements JnetMouseListener {
+  private class NodeHover implements JnetMouseListener, Serializable {
+	  static final long serialVersionUID = 1L;
+	  
     public void mouseChanged(JnetMouseEvent e) {
       if (!e.isHover()) return;
       if (!e.hasNode()) return;

Modified: nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-01-29 20:17:24 UTC (rev 22638)
+++ nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-01-29 22:34:44 UTC (rev 22639)
@@ -51,7 +51,7 @@
 //          new HashMap<String, DatasetFilter>();
   private List<DatasetFilter> filters = new ArrayList<DatasetFilter>();
   private static EdgeFilterState singleton = new EdgeFilterState();
-  private List<EdgeChangeListener> filterListeners = new ArrayList<EdgeChangeListener>(3);
+  private transient List<EdgeChangeListener> filterListeners = new ArrayList<EdgeChangeListener>(3);
   /** if true then only isVisible node connections with more than one edge */
   private boolean showMultiEdgesOnly = false;
 
@@ -64,6 +64,14 @@
 
   public static EdgeFilterState inst() { return singleton; }
 
+  /**
+   * sets the current edgefilterstate
+   * @param instance
+   */
+  public void setEdgeFilterState(EdgeFilterState instance)
+  {
+	  this.singleton = instance;
+  }
 
   /** clear out filter state on meta changes, new filters are loaded
    * via the EdgeFilterTypeGui -> initDataset  */


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Revision: 22645
          http://gmod.svn.sourceforge.net/gmod/?rev=22645&view=rev
Author:   montys9
Date:     2010-02-01 20:04:52 +0000 (Mon, 01 Feb 2010)

Log Message:
-----------
Fixed problem where couldn't load diagram if something is already loaded.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/views/GraphViewManager.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java
    nbrowse/trunk/src/org/nbrowse/views/StepManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -137,18 +137,18 @@
 
   private CommandHistory commandHistory = new CommandHistory();
   private ColorManager colorManager;
-  private Compiler compiler; // don't serialize - just reset if load serialized
+  private Compiler compiler; // currently serialized
   
   private boolean freezing = false;
-  private Eval eval; // don't serialize - just reset if load serialized
+  private Eval eval; // currently serialized
   private DataManager dataManager;
   private FileManager fileManager;
   private ModelManager modelManager;
   //private ModelSet modelSet;
   private ModelLoader modelSet; // important in getting latest
-  public transient MouseManager mouseManager; // dont' serialize - just reset if serialized
+  public transient MouseManager mouseManager; // don't serialize - just reset if serialized
   private transient PickingManager pickingManager; // dont't serialize - juset reset if serialized
-  private RepaintManager repaintManager; // dont't serialize - juset reset if serialized
+  private RepaintManager repaintManager; // serialized now
   private transient ScriptManager scriptManager; // dont't serialize - juset reset if serialized
   private SelectionManager selectionManager;
   private StateManager stateManager;

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NBEdge.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -219,8 +219,9 @@
 
   @Override
   public String toString() { 
-    return id; // id is now same as commented out return statement below-MS
-    //return "Edge from "+fromNode+" to "+toNode+" type "+type; 
+    //return id; // id is now same as commented out return statement below-MS
+    // still so far seems to need to use original and not id - prevent not equal null pointer exception-MS
+    return "Edge from "+fromNode+" to "+toNode+" type "+type; 
     }
 
   /** optional internal db id - convenience for caching for further retrievals - ideally 

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -36,6 +36,7 @@
 import org.nbrowse.dataset.MetaDataManager;
 import org.nbrowse.layouts.spring.vrmlgraph.GraphData;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.GraphViewManager;
 import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.JnetPanel;
 import org.nbrowse.views.NBSelectionManager;
@@ -146,6 +147,9 @@
 		FileInputStream f_in = new 
 			FileInputStream(sFile.getAbsolutePath());
 
+		// try status messages to clear for load
+		//StatusManager.inst().newMetaDataLoading(); // try this		
+		//StatusManager.inst().loadingNewData(); // try this
 		// need to clear everything - especially if model is already loaded
 		JnetManager.inst().clearSerialLoad();
 		// Read object using ObjectInputStream
@@ -153,10 +157,14 @@
 			new ObjectInputStream (f_in);
 
 		// Read an object
+    //GraphEltSet.setCurrentGraph(null); // null it first - then try
+		//GraphData.setCurrentGraphData(null); // null it first
+		//GraphViewManager.getNewGraph();
 		
 		Object ges_obj = obj_in.readObject();
 		if (ges_obj instanceof GraphEltSet){
 		   GraphEltSet.getCurrentGraph().clearAll();
+		   //GraphEltSet.setCurrentGraph(new GraphEltSet()); // try create default
 		   //GraphEltSet graph = (GraphEltSet) ges_obj;
        GraphEltSet.setCurrentGraph((GraphEltSet) ges_obj);
        //GraphEltSet.setCurrentGraph(graph.getFilteredGraph());
@@ -164,9 +172,11 @@
 		Object gd_obj = obj_in.readObject();
 		if (gd_obj instanceof GraphData) {
 		   GraphData.getCurrentGraphData().clear();
+		   //GraphData.setCurrentGraphData(GraphData.getNewGraphData());		  
 		   GraphData.setCurrentGraphData((GraphData) gd_obj);
+		   GraphViewManager.refreshGraphData(); // refresh Graph View Manager
 		}
-
+		 //GraphData graphTest = GraphData.getCurrentGraphData(); // test
 		/*
 		Object modelset = obj_in.readObject();
 		if (modelset instanceof ModelLoader)
@@ -195,13 +205,13 @@
 		  JnetManager.inst().loadJnetViewer((Viewer) viewer);
 		  
 		}
-
+		//graphTest = GraphData.getCurrentGraphData(); 
 		Object edgeFilterState = obj_in.readObject();
 		if (edgeFilterState instanceof EdgeFilterState)
 		{
 		  	EdgeFilterState.inst().setEdgeFilterState((EdgeFilterState) edgeFilterState); // use for edge filtering
 		}
-		
+		//graphTest = GraphData.getCurrentGraphData(); 
 		/*
 		Object navigation = obj_in.readObject();
 		if (navigation instanceof Navigation)
@@ -229,9 +239,10 @@
 			// lastQueryDepth is last expansion done
 			StepManager stepper = (StepManager) stepMan;
 			int dispStep = stepper.getDisplayStep();
-			StepManager.inst().setDisplayStepDepth((short) dispStep); // set only display step for now - issue			
+			int dispDepth = stepper.getStepQueryDepth();
+			StepManager.inst().setDisplayStepDepth((short) dispStep, (short) dispDepth); // set only display step for now - issue			
 		}
-	
+		//graphTest = GraphData.getCurrentGraphData(); 
 		
 		}
 		catch(Exception ex)

Modified: nbrowse/trunk/src/org/nbrowse/views/GraphViewManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/GraphViewManager.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/nbrowse/views/GraphViewManager.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -11,6 +11,10 @@
     return current;
   }
 
+  public static void refreshGraphData() {
+    current = GraphData.getCurrentGraphData();
+  }
+  
   static GraphViewI getNewGraph() {
     current().clear();
     return current();

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -17,6 +17,7 @@
 import org.jnet.modelset.Node;
 import org.jnet.viewer.JnetMouseListener;
 import org.jnet.viewer.MouseManager;
+import org.nbrowse.NBrowseApplet;
 import org.nbrowse.layouts.spring.vrmlgraph.NodeView;
 import org.nbrowse.views.edgecontrol.EdgeChangeEvent;
 import org.nbrowse.views.edgecontrol.EdgeFilterState;
@@ -216,9 +217,22 @@
    */
   public void clearSerialLoad()
   {
+    //NBrowseApplet.inst().init(); // try this for clearing  
+    //NBrowseApplet.inst().stop();
+    //NBrowseApplet.inst().start();
+    //status().normal();  
+    
+    //DataAdapterManager.getDataAdapter().setNodeFactory(null); // try this
+    //StatusManager.inst().newDatasource(); // try this too
+    //getJnetViewer().clear();
+    //getJnetViewer().popHoldRepaint(); // try this  
+    //Jnet cjnet = new Jnet();
+    //this.jnet = cjnet; // try doing this
+    //nodeMover = null; // set to null the node mover
 	  clear();
 	  jnetScript.clearEvals();
 	  StepManager.inst().showInitialQueryDisplay();
+	  //getJnetViewer().releaseScreenImage(); // will this release
   }
   
   /** clear out jnet & navigator */
@@ -695,11 +709,15 @@
     //toggle = 1;
 	
     GraphViewI fullGraph = GraphViewManager.current();
+    GraphData graphTest = GraphData.getCurrentGraphData();
     for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
 	
 	
-    redrawJnet();  
-	StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
+    redrawJnet();
+    if (nodeMover != null)
+      nodeMover.setGraph(fullGraph); // set default
+	 StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode
+    
 	//clear();
     System.out.println("display step = " + getDisplayStep());
    // loadJnetFiltered(); // this will load current step used in stepmanager    
@@ -735,6 +753,8 @@
     //jnetStepButtonExpansion(getDisplayStep()); // uses display step as query depth as well - does not seem to work correctly
     centerGraph(); // still need to center
     
+    // try ensuring visible
+    //getJnetViewer().popHoldRepaint(); // try this
     //loadJnet(fullGraph); // generates entire graph again but not centered
     //centerGraph(); // if using above loadJnet need to center graph
     

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetPanel.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -1,5 +1,6 @@
 package org.nbrowse.views;
 
+import org.nbrowse.NBrowseApplet;
 import org.nbrowse.api.AbstractView;
 
 import java.awt.*;
@@ -58,7 +59,9 @@
 
     /** used to reset listener in jpanel to new viewer */
     public void loadViewer(Viewer newViewer) 
-    {
+    {          
+      //JnetAdapter adapter = new SmarterJnetAdapter(); // try      
+      //viewer = Viewer.allocateViewer(this, adapter, null, null, null, "", null); // try this      
       newViewer = Viewer.reallocateViewer(newViewer, viewer); // copy from      
       viewer = newViewer;
       JnetManager.inst().setJnetViewer(viewer); //resetViewer

Modified: nbrowse/trunk/src/org/nbrowse/views/StepManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/StepManager.java	2010-02-01 19:34:57 UTC (rev 22644)
+++ nbrowse/trunk/src/org/nbrowse/views/StepManager.java	2010-02-01 20:04:52 UTC (rev 22645)
@@ -118,9 +118,10 @@
   }
   
   /** used to set only display step for now along with depth - must be careful */
-  public void setDisplayStepDepth(short step) {
+  public void setDisplayStepDepth(short step, short depth) {
 	  displayStep = step;
-	  stepQueryDepth = step;
+	  //stepQueryDepth = step;
+	  stepQueryDepth = depth;
   }
   
   /** tabs are 0 based, display steps are 1 based */


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Revision: 22653
          http://gmod.svn.sourceforge.net/gmod/?rev=22653&view=rev
Author:   montys9
Date:     2010-02-02 21:15:30 +0000 (Tue, 02 Feb 2010)

Log Message:
-----------
Various changes - colorManager view still has issues in deserializing.  leaving out for now.  however filtering of edges seem to work now.  added edge table view singleton at one point as well in case need to use.  various fixes here.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/views/ColorManager.java
    nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-02 20:32:32 UTC (rev 22652)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-02 21:15:30 UTC (rev 22653)
@@ -445,6 +445,7 @@
     //newViewer.eval.setViewer(newViewer);
     //newViewer.g3d = oldViewer.g3d;
     //newViewer.colorManager.setGraphics3D(newViewer.g3d);
+    //newViewer.colorManager.setColorObservers(oldViewer.colorManager); // different color manager
     newViewer.g3d.setPlatform(newViewer.display);
     //newViewer.mouseManager.resetMouseManager(); // resets values
     // mouse manager copying properties not helping

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-02 20:32:32 UTC (rev 22652)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-02 21:15:30 UTC (rev 22653)
@@ -36,6 +36,8 @@
 import org.nbrowse.dataset.MetaDataManager;
 import org.nbrowse.layouts.spring.vrmlgraph.GraphData;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.ColorManager;
+import org.nbrowse.views.EdgeTableView;
 import org.nbrowse.views.GraphViewManager;
 import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.JnetPanel;
@@ -63,7 +65,10 @@
       dataLoader = dl;
       if (isSave) // added to just load save dialog info if saving
         return;
-      dlg = new JDialog(dl.getParentFrame(),"Open Nbrowse Tab File"); // should have frame/applet as owner, modal?
+      if (isSession)
+        dlg = new JDialog(dl.getParentFrame(),"Open Nbrowse Session File"); // should have frame/applet as owner, modal?
+      else
+        dlg = new JDialog(dl.getParentFrame(),"Open Nbrowse Tab File"); // should have frame/applet as owner, modal?
       //dlg.setLocation(500,1000);
       dlg.setSize(360,120);
       dlg.setLayout(new GridBagLayout());
@@ -252,7 +257,6 @@
     }
     */
     
-    
     Object stepMan = obj_in.readObject();
     if (stepMan instanceof StepManager)
     {
@@ -264,7 +268,19 @@
       int dispDepth = stepper.getStepQueryDepth();
       StepManager.inst().setDisplayStepDepth((short) dispStep, (short) dispDepth); // set only display step for now - issue     
     }
-    //graphTest = GraphData.getCurrentGraphData(); 
+    //graphTest = GraphData.getCurrentGraphData();
+    // colorManager we do want but issues right now
+    /*
+    Object colorMan = obj_in.readObject();
+    if (colorMan instanceof ColorManager)
+    {
+      //ColorManager.inst().setColorObservers((ColorManager) colorMan); // copy color observers
+      ColorManager colorManager = (ColorManager) colorMan;
+      //colorManager.setColorObservers(ColorManager.inst()); // reset observers since they are transient
+      ColorManager.inst().setColorManager((ColorManager) colorManager);
+      ColorManager.inst().resetColorObservers(); // reset color observers
+      EdgeTableView.inst().setColorObserver(); // try this
+    }*/    
     
     }
     catch(Exception ex)
@@ -475,7 +491,7 @@
       
       if (useSerialBinary && isSession) // save as .ser extension too
       {
-        
+        file.delete(); // delete existing first
     	  GraphEltSet currGraph = GraphEltSet.getCurrentGraph();
         //GraphEltSet currGraph = GraphEltSet.getCurrentGraph().getFilteredGraph(); // save filtered?
     	  GraphData graphData = GraphData.getCurrentGraphData();    	  
@@ -485,6 +501,7 @@
     	  NBSelectionManager nbselection = NBSelectionManager.inst();
         Viewer viewer = JnetManager.inst().getJnetViewer();
         EdgeFilterState edgeFilterState = EdgeFilterState.inst();
+        ColorManager cmanager = ColorManager.inst();
     	// Write to disk with FileOutputStream
     	  try{
     	  FileOutputStream f_out = new 
@@ -508,7 +525,11 @@
         
         //obj_out.writeObject(nbselection);
         
+        //obj_out.writeObject(cmanager);
         obj_out.writeObject(stepMan);
+        // cmanager is being serialized but we are still having issues deserializing it.
+        // leave out for now until it is working
+        //obj_out.writeObject(cmanager);
         
     	  obj_out.flush();
     	  }

Modified: nbrowse/trunk/src/org/nbrowse/views/ColorManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/ColorManager.java	2010-02-02 20:32:32 UTC (rev 22652)
+++ nbrowse/trunk/src/org/nbrowse/views/ColorManager.java	2010-02-02 21:15:30 UTC (rev 22653)
@@ -6,6 +6,7 @@
 package org.nbrowse.views;
 
 import java.awt.Color;
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -23,8 +24,9 @@
  *
  * @author mgibson
  */
-public class ColorManager {
-
+public class ColorManager implements Serializable {
+  static final long serialVersionUID = 1L;  
+  
   private static ColorManager singleton = new ColorManager();
   private static short DEFAULT_JNET_COLIX = 0;
 
@@ -37,7 +39,8 @@
 
 
   private HashMap<String, Color> typeToColor = new HashMap<String,Color>();
-  private List<ColorObserver> colorObservers = new ArrayList<ColorObserver>(3);
+  private transient List<ColorObserver> colorObservers = new ArrayList<ColorObserver>(3);
+  //private List<ColorObserver> colorObservers = new ArrayList<ColorObserver>(3);
   
   private ColorManager() {
     // this needs to be before EdgeFilter in observer list - explicit?
@@ -49,10 +52,30 @@
   public static void init() { inst(); }
   
   public static ColorManager inst() { return singleton; }
+  
+  /** 
+   * sets to instance of color manager
+   * @param instance
+   */
+  public void setColorManager(ColorManager instance)
+  {
+    this.singleton = instance;    
+  }
+  
+  /**
+   * resets the color observers when deserializing.
+   */
+  public void resetColorObservers()
+  {
+    colorObservers = new ArrayList<ColorObserver>(3);
+  }
+    
 //  private class MetaListener implements MetaDataChangeObserver {
 //   public void metaDataChanged(){initColors(DataManager.inst().getMetaData());}}
   /** Listens for meta data changes, redoes colors on change */
-  private class StatLis implements StatusListener {
+  private class StatLis implements StatusListener, Serializable {
+    static final long serialVersionUID = 1L;  
+    
     public void statusChanged(StatusEvent e) {
       if (!e.isMetaLoaded()) return;
       synchWithMetaData();

Modified: nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java	2010-02-02 20:32:32 UTC (rev 22652)
+++ nbrowse/trunk/src/org/nbrowse/views/EdgeTableView.java	2010-02-02 21:15:30 UTC (rev 22653)
@@ -21,8 +21,8 @@
 import org.nbrowse.io.StatusManager;
 import org.nbrowse.models.EdgeTableModel;
 
-public final class EdgeTableView extends AbstractView {
-    
+public final class EdgeTableView extends AbstractView  {
+  static final long serialVersionUID = 1L; 
   private final Dimension currentSize = new Dimension();
   private final Rectangle rectClip = new Rectangle();
   private JScrollPane scrollPane;
@@ -30,6 +30,20 @@
   public final static String TITLE = "Edge Table";
   public EdgeTableView() { init(); }
 
+  // try this-MS
+  // added code here to try to get current - where is instance?
+  //private static EdgeTableView singleton = new EdgeTableView();  
+  //public static EdgeTableView inst() { return singleton; }  
+  // end try
+  
+  /**
+   * sets the color observer
+   */
+  public void setColorObserver()
+  {
+    ColorManager.inst().addColorObserver(new InfoColorObserver());
+  }
+  
   @Override protected String getViewDisplayName() { return TITLE; }
 
   @Override protected void init() {
@@ -44,7 +58,6 @@
     ColorManager.inst().addColorObserver(new InfoColorObserver());
     StatusManager.inst().addStatusListener(new StatLis());
 }
-   
     
     private void configureTable(JXTable jxTable) {
       // just for rendering color column i think (Color.class)
@@ -79,11 +92,16 @@
     public void stepChanged() { redoTable(); }
   }
  
+  // make this public instead of private
   private class InfoColorObserver implements ColorObserver {
+    static final long serialVersionUID = 1L; 
+    
     public void colorsChanged() { redoTable(); }
   }
 
-  private class StatLis implements StatusListener {
+  private class StatLis implements StatusListener, Serializable {
+    static final long serialVersionUID = 1L; 
+    
     public void statusChanged(StatusEvent e) {
       //if (e.doneLoading()) redoTable();
       // if done loading or done loading from serial file need to redo table
@@ -122,7 +140,9 @@
 //        valCol.setHorizontalAlignment(SwingConstants.LEFT);
     }
 
-  private class LeftAlignRenderer extends DefaultTableCellRenderer {
+  private class LeftAlignRenderer extends DefaultTableCellRenderer implements Serializable {
+    static final long serialVersionUID = 1L; 
+    
     public Component getTableCellRendererComponent(JTable t,Object o,boolean sel,
       boolean foc,int r,int col) {
       Component c=super.getTableCellRendererComponent(t, o, sel, foc,r,col);

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-02 20:32:32 UTC (rev 22652)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-02 21:15:30 UTC (rev 22653)
@@ -696,6 +696,7 @@
   private NbrowseJnetAdapter nbJnetAdap() { return NbrowseJnetAdapter.inst(); }
 
   private void loadSerialData() {	
+    
 	EdgeFilterState.inst().addFilterObserver(new EdgeChangeLis());   // re-add edge change listener to deserialized EdgeFilterState
 	//StatusManager.inst().addStatusListener(new StatLis());
 	
@@ -711,7 +712,9 @@
 	
     GraphViewI fullGraph = GraphViewManager.current();
     //GraphData graphTest = GraphData.getCurrentGraphData();
-    for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
+    // try not using defaults
+   // use this until deserialized view color manager is working
+   for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
 	
 	
     redrawJnet();
@@ -726,6 +729,8 @@
     //centerGraph();
     
     int expandedStep = graphModel().getStepDepth();
+    if (expandedStep == 0)
+      expandedStep = 1; // if model is 0 depth is really 1
     System.out.println("step depth = " + expandedStep);
     GraphViewI filteredGraph = null;
     
@@ -777,7 +782,7 @@
     }
     StepManager.inst().setDisplayStep((short) displayStep); // displays last step viewed
     
-    
+    //StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode - TRY again-ensure
     //int step = 2; // need to utilize number of steps last expanded to re-add steps.
     
 
@@ -889,7 +894,9 @@
 //  }
 
   // refactor this, dont need to reload jnet do we?
-  private class JnetColorObserver implements ColorObserver {
+  private class JnetColorObserver implements ColorObserver, Serializable {
+    static final long serialVersionUID = 1L;
+    
     public void colorsChanged() {
       //loadJnetFiltered(); that aint right as it will make filter outs permanent
       // for now just redo all edge colors - may wanna do just type in future?


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22661
          http://gmod.svn.sourceforge.net/gmod/?rev=22661&view=rev
Author:   montys9
Date:     2010-02-04 15:17:03 +0000 (Thu, 04 Feb 2010)

Log Message:
-----------
in viewer commented out wasted loop doing nothing, added comment to commandline and exception dialog box for error handling in saving/loading sessions if errors (except stack overflow) for now. added comments to file dialog regarding different status manager classes.  need to look at nbrowse.io statusmanager and not other.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/CommandLine.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-04 01:40:31 UTC (rev 22660)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-04 15:17:03 UTC (rev 22661)
@@ -243,7 +243,7 @@
   public void setDimensionMode(int mode){ 
       dimension_mode = mode;
   }
-
+  
   public int getDimensionMode(){
       return dimension_mode;
   }
@@ -476,7 +476,8 @@
     
     // if navaigation is set to different viewer - can't click or move nodes around
     //Navigation.inst().setViewer(newViewer); // needs to make sure point to correct viewer
-    
+  
+    /*
     for (int i = 0; i < JnetConstants.SHAPE_MAX; i++)
     {
     	Shape shape = newViewer.modelSet.getShape(i);
@@ -487,7 +488,8 @@
     	}
 
     }
-   
+   */
+    
     //newViewer.modelSet = oldViewer.modelSet; // try this
     //newViewer.modelSet = null; // try nulling to hopefully set
     return newViewer;

Modified: nbrowse/trunk/src/org/nbrowse/CommandLine.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/CommandLine.java	2010-02-04 01:40:31 UTC (rev 22660)
+++ nbrowse/trunk/src/org/nbrowse/CommandLine.java	2010-02-04 15:17:03 UTC (rev 22661)
@@ -6,7 +6,8 @@
  * -c config file 
  * -d database space delim list 
  * -s label for search/query box 
- * -l label for locate node/gene box */
+ * -l label for locate node/gene box 
+ * -g true for enabling goose */
 final class CommandLine {
 	private static CommandLine singleton;
 	private String query;

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-04 01:40:31 UTC (rev 22660)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-04 15:17:03 UTC (rev 22661)
@@ -239,9 +239,16 @@
     Object edgeFilterState = obj_in.readObject();
     if (edgeFilterState instanceof EdgeFilterState)
     {
+        //EdgeFilterState filter = EdgeFilterState.inst();
         EdgeFilterState.inst().setEdgeFilterState((EdgeFilterState) edgeFilterState); // use for edge filtering
         GraphEltSet.setFilter(EdgeFilterState.inst()); // reset correct edge filter-this is used when generating graph with filtering.        
     }
+    
+    // check io status manager - not one in viewer
+    //StatusManager smgr = StatusManager.inst();
+    //Viewer nviewer = (Viewer) viewer;
+    //StatusManager.inst().setStatusManager(nviewer.getStatusManager()); 
+    
     //graphTest = GraphData.getCurrentGraphData(); 
     /*
     Object navigation = obj_in.readObject();
@@ -290,6 +297,10 @@
     catch(Exception ex)
     {
       ex.printStackTrace();
+      dlg.dispose();
+      ErrorUtil.urgent(this, "Failed Loading Session File", ex);
+      //ErrorUtil.urgent(this, "Failed Loading Session File");
+      return;
     }
     dlg.dispose(); // remove dialog first
     StatusManager.inst().newSerialDataDoneLoading(); // use with saving   
@@ -543,6 +554,7 @@
     	catch(Exception ex)
     	{
           ex.printStackTrace();
+          ErrorUtil.urgent(this, "Failed Saving Session File", ex);
     	}
     	
     	// tell user session is saved


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Revision: 22669
          http://gmod.svn.sourceforge.net/gmod/?rev=22669&view=rev
Author:   montys9
Date:     2010-02-05 21:17:48 +0000 (Fri, 05 Feb 2010)

Log Message:
-----------
Added work in GraphData and JnetManager in trying to address edge filter deserialization bug, made bspt code implement serialization in case it is ever invoked (normally no, but where I forced removal of all edgeview objects in experiment - objects in the package are then serialized).  Updated fileDialog to not show save complete if save fail dialog occurs.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/bspt/Bspf.java
    nbrowse/trunk/src/org/jnet/bspt/Bspt.java
    nbrowse/trunk/src/org/jnet/bspt/CubeIterator.java
    nbrowse/trunk/src/org/jnet/bspt/Element.java
    nbrowse/trunk/src/org/jnet/bspt/Leaf.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/bspt/Bspf.java
===================================================================
--- nbrowse/trunk/src/org/jnet/bspt/Bspf.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/jnet/bspt/Bspf.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -22,6 +22,7 @@
  */
 package org.jnet.bspt;
 
+import java.io.Serializable;
 import java.util.BitSet;
 
 import javax.vecmath.Point3f;
@@ -35,8 +36,8 @@
  * @author Miguel, miguel@...
 */
 
-public final class Bspf {
-
+public final class Bspf implements Serializable {
+	static final long serialVersionUID = 1L;
   int dimMax;
   Bspt bspts[];
   //SphereIterator[] sphereIterators;

Modified: nbrowse/trunk/src/org/jnet/bspt/Bspt.java
===================================================================
--- nbrowse/trunk/src/org/jnet/bspt/Bspt.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/jnet/bspt/Bspt.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -22,6 +22,8 @@
  */
 package org.jnet.bspt;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 
 //import org.jnet.util.Logger;
@@ -69,8 +71,9 @@
  * @author Miguel, miguel@...
  */
 
-public final class Bspt {
-
+public final class Bspt implements Serializable {
+	static final long serialVersionUID = 1L;
+	
   final static int leafCountMax = 2;
   // this corresponds to the max height of the tree
   final static int MAX_TREE_DEPTH = 100;

Modified: nbrowse/trunk/src/org/jnet/bspt/CubeIterator.java
===================================================================
--- nbrowse/trunk/src/org/jnet/bspt/CubeIterator.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/jnet/bspt/CubeIterator.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -22,6 +22,8 @@
  */
 package org.jnet.bspt;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 
 /**
@@ -35,7 +37,8 @@
  *
  * @author Miguel, miguel@...
  */
-public class CubeIterator {
+public class CubeIterator implements Serializable {
+  static final long serialVersionUID = 1L;	
   Bspt bspt;
 
   Element[] stack;

Modified: nbrowse/trunk/src/org/jnet/bspt/Element.java
===================================================================
--- nbrowse/trunk/src/org/jnet/bspt/Element.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/jnet/bspt/Element.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -22,6 +22,8 @@
  */
 package org.jnet.bspt;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 
 /**
@@ -29,7 +31,8 @@
  *
  * @author Miguel, miguel@...
  */
-abstract class Element {
+abstract class Element implements Serializable {
+  static final long serialVersionUID = 1L;
   Bspt bspt;
   int count;
   abstract Element addTuple(int level, Point3f tuple);

Modified: nbrowse/trunk/src/org/jnet/bspt/Leaf.java
===================================================================
--- nbrowse/trunk/src/org/jnet/bspt/Leaf.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/jnet/bspt/Leaf.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -22,6 +22,8 @@
  */
 package org.jnet.bspt;
 
+import java.io.Serializable;
+
 import javax.vecmath.Point3f;
 
 /**
@@ -29,7 +31,8 @@
  *
  * @author Miguel, miguel@...
  */
-class Leaf extends Element {
+class Leaf extends Element implements Serializable {
+	static final long serialVersionUID = 1L;	
   Point3f[] tuples;
     
   Leaf(Bspt bspt) {

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -393,6 +393,9 @@
       
       if (useSerialBinary && isSession) // save as .ser extension too
       {
+    	// the following commented out code would be used for refreshing data for a save, where edge filtering was used - not ready yet.
+    	//JnetManager.inst().refreshData();
+    	  
     	// indicate saving session        
         file.delete(); // delete existing first
     	GraphEltSet currGraph = GraphEltSet.getCurrentGraph();
@@ -441,6 +444,7 @@
     	{
           ex.printStackTrace();
           ErrorUtil.urgent(this, "Failed Saving Session File", ex);
+          return;
     	}
     	
     	// tell user session is saved

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -352,6 +352,57 @@
     addExpandedNodesFromModel(step,is3D); // iter on GraphEltSet NBNodes
     addExpandedEdgesFromModel(step);
   }
+  
+  /* 
+   * This will be used prior to saving session as to refresh data in use with edge filter.
+   */
+  public void doRefresh()
+  {
+	boolean is3d = JnetManager.inst().is3D();
+	int depth = GraphEltSet.getCurrentGraph().getStepDepth(); // used query depth for current step since just refresh
+    expandEdgePrep(depth); // clear out all jnet edges
+    expandNodePrep(depth);
+    addExpandedNodesFromModel(depth,is3d);
+    //expandNodePrepRefresh(depth);	  
+  }
+  
+  /*
+   * this is work in progress - don't know if its work doing since
+   */
+  private void expandEdgePrepClone(int step) {
+	    // could just iterate on all edges now
+	    //delEdgesIterator(getEdgeList().iterator(),step);
+	    //delEdgesIterator(cycleEdges.iterator(),step); // remove stale edge cycles
+	    Iterator<EdgeViewI> edgeIt = getEdgeList().iterator();
+	    while (edgeIt.hasNext()) {
+	      EdgeViewI edge = edgeIt.next();
+	      if (edge.getStep() >= step) edgeIt.remove(); // efficient!
+	      else { 
+	    	  
+	    	  edge.setJnetEdge(null); // null out stale jnet(in future not stale?)
+	      }
+	    }
+	  }
+  
+  /**
+   * This will be used prior to saving session and is invoked by doRefresh()
+   * @param step
+   */
+  private void expandNodePrepRefresh(int step) {
+	    //queryNodes.clear(); // ??
+	    Iterator<NodeViewI> nodeIt = getNodeIterator();
+	    while (nodeIt.hasNext()) { // do with iterator so can remove
+	      NodeViewI node = nodeIt.next();
+	      if (node.getStep() >= step) nodeIt.remove();
+	      // this isnt used anymore but may be revived?
+	      //node.setDoLayout(false); // tells layout to not move/layout this node
+	      node.synchAndClearJnetNode();//here we are saving coords when we remove jnet node
+	      //node.setJnetNode(null);//remove stale jnet(change if jnet becomes additive)
+	      // if node model is data loader query node, then set view query node
+	      //if (node.isQueryNode()) queryNodes.add(node); //= node;
+	    }
+	  }
+  
   private void expandEdgePrep(int step) {
     // could just iterate on all edges now
     //delEdgesIterator(getEdgeList().iterator(),step);
@@ -363,6 +414,7 @@
       else edge.setJnetEdge(null); // null out stale jnet(in future not stale?)
     }
   }
+    
  // private void delEdgesIterator(Iterator<EdgeViewI> edgeIt, int step) {
  // }
   /** deletes nodes of step and above, all others get layoutCalc set to false so 
@@ -383,6 +435,20 @@
       if (node.isQueryNode()) queryNodes.add(node); //= node;
     }
   }
+  
+  /** model has expanded, add expanded nodes & edges from model - here I am trying to copy nodeviews - need to figure out how */
+  private void copyExpandedNodesFromModel(int expandedStep,boolean is3D) {
+    nodeModToVw = new HashMap<NBNode,NodeViewI>(); // permanent?
+    // model.getNodesStepAndUp(expandedStep) ? - 2 iterations though unless special structure
+    for (NBNode nodeModel : modelGraph().getAllNodes()) {
+      if (nodeModel.getStep() < expandedStep) continue; // not from expansion, ignore
+      //copyNodeView(nodeModel,is3D);
+        makeNodeView(nodeModel, is3D); // needs to be replaced with copying of nodeview information
+      //addNode(nodeView);
+      //nodeModToVw.put(nodeModel,nodeView);
+    }
+  }  
+  
   /** model has expanded, add expanded nodes & edges from model */
   private void addExpandedNodesFromModel(int expandedStep,boolean is3D) {
     nodeModToVw = new HashMap<NBNode,NodeViewI>(); // permanent?
@@ -421,6 +487,28 @@
     return nodeView;
   }
   
+  /** constructs NodeViewI with copies coordinates (move coords to jnet)
+   * adds node to node list, adds node to modToVw cache for edge iterating
+   * used by expansion and new load
+   * @param nodev
+   * @param is3D
+   */
+  private NodeViewI copyNodeView(NodeViewI nodev, NBNode nodeModel,boolean is3D) {
+    //float x = random();
+    //float y = random();
+    //float z = is3D ? random() : 0;
+	float x = nodev.getX();
+	float y = nodev.getY();
+	float z = nodev.getZ();
+    NodeViewI nodeView =  new NodeView(nodeModel,x,y,z);
+    // for initial query but doesnt work for expanded, as already made
+    if (nodeView.isQueryNode()) queryNodes.add(nodeView); //=nodeView;
+    addNode(nodeView);
+    if (nodeModToVw==null) nodeModToVw = new HashMap<NBNode,NodeViewI>();
+    nodeModToVw.put(nodeModel,nodeView);
+    return nodeView;
+  }
+  
   /** constructs NodeViewI with random coords (move coords to jnet)
    * adds node to node list, adds node to modToVw cache for edge iterating
    * used by expansion and new load

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-05 14:21:26 UTC (rev 22668)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-05 21:17:48 UTC (rev 22669)
@@ -696,6 +696,16 @@
 
   private NbrowseJnetAdapter nbJnetAdap() { return NbrowseJnetAdapter.inst(); }
 
+  /**
+   * used to refresh data from for purpose of saving sessions. this is a work in progress.  need to correlate edge filters to this
+   */
+  public void refreshData() {
+	  GraphData fullGraph = (GraphData) GraphViewManager.current();
+	  fullGraph.doRefresh();
+	  int expandedStep = graphModel().getStepDepth();
+	  loadJnetFiltered(expandedStep);
+  }
+  
   private void loadSerialData() {	
     
 	EdgeFilterState.inst().addFilterObserver(new EdgeChangeLis());   // re-add edge change listener to deserialized EdgeFilterState


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22689
          http://gmod.svn.sourceforge.net/gmod/?rev=22689&view=rev
Author:   montys9
Date:     2010-02-09 21:46:29 +0000 (Tue, 09 Feb 2010)

Log Message:
-----------
updates for new edge filter fix to behave like expansion but on load where jnet edges and nodes are removed before graph generation.  However, there is an issue where a edge filtered graph saved twice in the same app won't load unless the app is restarted - expansion still works better in this respect - still working on it.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/TransformManager.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java

Modified: nbrowse/trunk/src/org/jnet/viewer/TransformManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/TransformManager.java	2010-02-09 21:04:25 UTC (rev 22688)
+++ nbrowse/trunk/src/org/jnet/viewer/TransformManager.java	2010-02-09 21:46:29 UTC (rev 22689)
@@ -628,10 +628,33 @@
     zoomPercentSetting += deltaPercent;
   }
 
+  
+  // these are added to direct get/set - test
   float getZoomPercentFloat() {
     return zoomPercent;
   }
 
+  float getZoomPercentSettingFloat() {
+    return zoomPercentSetting;
+  }
+  
+  float getZoomRatioFloat() {
+    return zoomRatio;
+  }
+  
+  void setZoomPercentFloat(float zoomPercentFloat) {
+    zoomPercent = zoomPercentFloat;
+  }
+  
+  void setZoomPercentSettingFloat(float zoomPercentSettingFloat) {
+    zoomPercentSetting = zoomPercentSettingFloat;    
+  }
+  
+  void setZoomRatioFloat(float zoomRatioFloat) {
+    zoomRatio = zoomRatioFloat;
+  }
+  // end of new get/set
+  
   void zoomToPercent(float percentZoom) {
     zoomPercentSetting = percentZoom;
     zoomRatio = 0;

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-09 21:04:25 UTC (rev 22688)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-02-09 21:46:29 UTC (rev 22689)
@@ -999,13 +999,22 @@
     moveUpdate(timeSeconds);
   }
 
-  void zoomBy(int pixels) {
+   
+  public void zoomBy(int pixels) {
     //MouseManager.mouseSinglePressDrag
     transformManager.zoomBy(pixels);
     refresh(2, statusManager.syncingMouse ? "Mouse: zoomBy " + pixels : "");
     fireZoomChange();
   }
 
+  public void zoomToPercent(float percentZoom)
+  {
+    transformManager.zoomByFactor(percentZoom);
+    refresh(2, statusManager.syncingMouse ? "Mouse: zoomToPercent " + percentZoom
+        : "");
+    fireZoomChange();    
+  }
+  
   public void zoomByFactor(float factor) {
     //MouseManager.mouseWheel
     transformManager.zoomByFactor(factor);
@@ -1130,7 +1139,29 @@
     //note -- this value is only after rendering.
     return transformManager.getZoomPercentFloat();
   }
+//ms
+  public float getZoomPercentSettingFloat() {
+    return transformManager.getZoomPercentSettingFloat();  
+  }
+  
+  public float getZoomRatioFloat() {
+    return transformManager.getZoomRatioFloat(); 
+  }
+  
+  public void setZoomPercentFloat(float zoomPercent) {
+    transformManager.setZoomPercentFloat(zoomPercent);
+  }
 
+  public void setZoomPercentSettingFloat(float zoomPercentSetting) {
+    transformManager.setZoomPercentSettingFloat(zoomPercentSetting);
+  }  
+
+  public void setZoomRatioFloat(float zoomRatio) {
+    transformManager.setZoomRatioFloat(zoomRatio);
+  }  
+  
+//end new
+  
   float getMaxZoomPercent() {
     return TransformManager.MAXIMUM_ZOOM_PERCENTAGE;
   }

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-09 21:04:25 UTC (rev 22688)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-02-09 21:46:29 UTC (rev 22689)
@@ -5,6 +5,7 @@
 
 package org.nbrowse.io;
 
+import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Frame;
 import java.awt.GridBagConstraints;
@@ -40,6 +41,7 @@
 import org.nbrowse.utils.NBrowseConstants;
 import org.nbrowse.views.ColorManager;
 import org.nbrowse.views.EdgeTableView;
+import org.nbrowse.views.GraphViewI;
 import org.nbrowse.views.GraphViewManager;
 import org.nbrowse.views.Jnet;
 import org.nbrowse.views.JnetManager;
@@ -169,6 +171,7 @@
   private void loadSessionFile() {
     
     if (useSerialBinary){
+          
     File sFile;
     try { sFile = getFile(); } catch (NoFile n) { return; }
     try
@@ -311,8 +314,15 @@
       return;
     }
     dlg.dispose(); // remove dialog first
+    
+    int expandedStep = StepManager.inst().getStepQueryDepth(); // do this
+    GraphViewI fullGraph = GraphViewManager.current();
+    ((GraphData)fullGraph).doRefresh(expandedStep); // try this  
+    
     StatusManager.inst().newSerialDataDoneLoading(); // use with saving   
     StatusManager.inst().newSerialDataDoneLoadingOver(); // use with loading other views
+    //JnetPanel.viewer.evalString("restore " + sFile.getAbsolutePath() + ";");      
+    //Navigation.viewer.evalString("restore " + sFile.getAbsolutePath() + ";");
     //dlg.dispose();
         return;    
     } // end if useSerialBinary
@@ -401,6 +411,10 @@
         file.delete(); // delete existing first
     	GraphEltSet currGraph = GraphEltSet.getCurrentGraph();
         //GraphEltSet currGraph = GraphEltSet.getCurrentGraph().getFilteredGraph(); // save filtered?
+    	// try this first
+      //JnetPanel.viewer.evalString("save " + file.getAbsolutePath() + ";");      
+      //Navigation.viewer.evalString("save " + file.getAbsolutePath() + ";");
+    	
     	GraphData graphData = GraphData.getCurrentGraphData();    	  
     	StepManager stepMan = StepManager.inst();
     	ModelSet modelset = JnetManager.inst().getJnetViewer().getModelSet();

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-02-09 21:04:25 UTC (rev 22688)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-02-09 21:46:29 UTC (rev 22689)
@@ -362,10 +362,21 @@
   {
 	boolean is3d = JnetManager.inst().is3D();
 		
+  //expandEdgePrep(depth);
+  //expandNodePrep(depth); // iterate on GraphData NodeViews
+  //addExpandedNodesFromModel(depth,is3d); // iter on GraphEltSet NBNodes
+  //addExpandedEdgesFromModel(depth);
+	
+	
 	//int depth = GraphEltSet.getCurrentGraph().getStepDepth(); // used query depth for current step since just refresh
-    expandEdgePrep(depth);
+  
+  // comment out this for now - problem with edge filter
+    expandEdgePrepRefresh(depth);
+    expandNodePrepRefresh(depth);
+    
+    
     //expandEdgePrepRefresh(depth); // clear out all jnet edges
-    expandNodePrepRefresh(depth);
+    
    // addExpandedNodesFromModel(depth,is3d);
     
     
@@ -386,14 +397,17 @@
 	    //queryNodes.clear(); // ??
 	    Iterator<NodeViewI> nodeIt = getNodeIterator();
 	    while (nodeIt.hasNext()) { // do with iterator so can remove
-	      NodeViewI node = nodeIt.next();
-	      
+	      NodeViewI node = nodeIt.next();	      
 	      // don't remove yet need to copy first
 	      //if (node.getStep() >= step) nodeIt.remove();
-	      
+	      //nodeIt.remove(); // force removal
 	      // this isnt used anymore but may be revived?
 	      node.setDoLayout(false); // tells layout to not move/layout this node
 	      node.synchAndClearJnetNode();//here we are saving coords when we remove jnet node
+	      //Node currNode = node.getJnetNode();
+	      //currNode.
+	      
+	      
 	      //node.setJnetNode(null);//remove stale jnet(change if jnet becomes additive)
 	      // if node model is data loader query node, then set view query node
 	      //if (node.isQueryNode()) queryNodes.add(node); //= node;
@@ -407,7 +421,12 @@
     Iterator<EdgeViewI> edgeIt = getEdgeList().iterator();
     while (edgeIt.hasNext()) {
       EdgeViewI edge = edgeIt.next();
+      
       edge.setJnetEdge(null); // try imitating same expansion
+      //edgeIt.remove(); // remove edge and re-add
+      //Edge currEdge = edge.getJmolEdge();
+     
+      //currEdge.getShapeVisibilityFlags()
       //if (edge.getStep() >= step) edgeIt.remove(); // efficient!
       //else edge.setJnetEdge(null); // null out stale jnet(in future not stale?)
     }

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-09 21:04:25 UTC (rev 22688)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-02-09 21:46:29 UTC (rev 22689)
@@ -15,6 +15,7 @@
 import javax.swing.JToolBar;
 import javax.vecmath.Point3f;
 
+import org.jnet.util.Escape;
 import org.jnet.viewer.Viewer;
 import org.jnet.modelset.Edge;
 import org.jnet.modelset.Node;
@@ -238,7 +239,12 @@
 	  jnetScript.clearEvals();
 	  //StepManager.inst().clearSteps();
 	  StepManager.inst().showInitialQueryDisplay();
+	 // GraphData.getCurrentGraphData().clear();
+	  GraphData.setCurrentGraphData(GraphData.getNewGraphData()); // new instance
+	  GraphEltSet.setCurrentGraph(new GraphEltSet());
+	  //EdgeFilterState.inst().clearState();
 	  //getJnetViewer().releaseScreenImage(); // will this release
+	  getJnetViewer().homePosition(); // try this
   }
   
   /** clear out jnet & navigator */
@@ -706,13 +712,16 @@
   public void refreshData() {
 	  GraphData fullGraph = (GraphData) GraphViewManager.current();
 	  int depth = StepManager.inst().getStepQueryDepth();
-	  fullGraph.doRefresh(depth);
+	  fullGraph.doRefresh(depth+1);
 	  int expandedStep = graphModel().getStepDepth();
 	  loadJnetFiltered(expandedStep);
   }
   
   private void loadSerialData() {	
   
+    float zoomPercent = this.getJnetViewer().getZoomPercentFloat();
+    float zoomPercentSetting = this.getJnetViewer().getZoomPercentSettingFloat();
+    float zoomRatio = this.getJnetViewer().getZoomRatioFloat();
   // try readding datasets to NBEdge objects
   /*
   GraphEltSet graphEltSet = GraphEltSet.getCurrentGraph();
@@ -736,7 +745,7 @@
     e.setDatasets(refreshDatasets); // replace datasets    
   } // for each nbedge - try this
   */
-    
+   
 	EdgeFilterState.inst().addFilterObserver(new EdgeChangeLis());   // re-add edge change listener to deserialized EdgeFilterState
 	EdgeTableView.inst().setEdgeLisObserver(); // adds edge lis observer from latest edge filter state 
 	//StatusManager.inst().addStatusListener(new StatLis());
@@ -750,8 +759,10 @@
     jnet.getStepButtonBar().setBackground(Color.WHITE);
     Navigation.viewer.evalString("background white;");
     //toggle = 1;
-	
+    
+    int expandedStep = StepManager.inst().getStepQueryDepth(); // do this
     GraphViewI fullGraph = GraphViewManager.current();
+    //((GraphData)fullGraph).doRefresh(expandedStep); // try this   
     
     // try doing refresh for node/edges here
     //GraphData graphTest = GraphData.getCurrentGraphData();
@@ -769,9 +780,9 @@
     System.out.println("display step = " + getDisplayStep());
     int displayStep = getDisplayStep();
    // loadJnetFiltered(); // this will load current step used in stepmanager    
-    //centerGraph();
+    centerGraph(); // before refresh
     
-    int expandedStep = graphModel().getStepDepth();
+   // int expandedStep = graphModel().getStepDepth();
     if (expandedStep == 0)
       expandedStep = 1; // if model is 0 depth is really 1
     System.out.println("step depth = " + expandedStep);
@@ -779,9 +790,12 @@
     
     // turn this on to test for edge filter fix
     //((GraphData)fullGraph).doRefresh(expandedStep); // try this   
+    //filteredGraph = fullGraph.getSubgraph(EdgeFilterState.inst(), expandedStep); // try doing this first
+    //loadJnet(filteredGraph);
     
     List<NodeViewI> nodes = fullGraph.getQueryNodes();
-    centerGraph();
+    //centerGraph(); // used to center graph - needed
+    
     // first we clear step manager for regenerating graph     
     for (int step = 1; step <= expandedStep; step++)
     {          	
@@ -795,14 +809,22 @@
     	  //centerGraph();
     	  //StepManager.inst().addStep(GraphEltSet.getCurrentGraph().getQueryNodeNames()); 
     	  String queryNode = null;    	  
-    	  queryNode = (nodes.get(step - 1)).toString();
+    	  try
+    	  {
+    	    queryNode = (nodes.get(step - 1)).toString();
+    	  }
+    	  catch(Exception ex)
+    	  {
+    	    ErrorUtil.error(this, "queryNode not found at step: " + step);
+    	  }
     	  if (queryNode != null)
-    	    StepManager.inst().addStep(queryNode);
+    	    StepManager.inst().addStep(queryNode);    	      	  
     	  else
     	    StepManager.inst().addStep(GraphEltSet.getCurrentGraph().getQueryNodeNames());
+    	
     	  // does not seem to work here - more is needed for this to work
     	  //createJnetLineBarStepButton(step);
-    	}
+    	} // if step = 1
     	else // keep separate in case change
     	{
     	  StepManager.inst().setDisplayStepDepth((short) (step), (short) (step));
@@ -813,8 +835,16 @@
     		//centerGraph();
     		
     		//StepManager.inst().addStep(GraphEltSet.getCurrentGraph().getQueryNodeNames());
-        String queryNode = null;        
-        queryNode = (nodes.get(step - 1)).toString();
+    		String queryNode = null;
+    		
+        try
+        {
+          queryNode = (nodes.get(step - 1)).toString();
+        }
+        catch(Exception ex)
+        {
+          ErrorUtil.error(this, "queryNode not found at step: " + step);          
+        }
         if (queryNode != null)
           StepManager.inst().addStep(queryNode);
         else
@@ -828,6 +858,36 @@
     }
     StepManager.inst().setDisplayStep((short) displayStep); // displays last step viewed
     
+    //refreshData(); // try after loading?
+    //JnetPanel.viewer.evalString("zoom ON " + ";");      
+    //Navigation.viewer.evalString("zoom ON " + ";");
+    
+    //String script = "zoomTo 0; zoomTo 0";
+    //getJnetViewer().script(script);
+    //Navigation.viewer.script(script);
+    //float setting = getJnetViewer().getZoomSetting();
+    //getJnetViewer().zoomToPercent(100);
+    //String script = "zoomTo 1 ({0:4}) 0;";
+    
+    //getJnetViewer().script(script);
+    //Navigation.viewer.script(script);
+    
+    //getJnetViewer().zoomBy(0);
+    
+    
+    getJnetViewer().setZoomPercentFloat(zoomPercent);
+    getJnetViewer().setZoomPercentSettingFloat(zoomPercentSetting);
+    getJnetViewer().setZoomRatioFloat(zoomRatio);
+    //getJnetViewer().zoomToPercent(zoomPercentSetting); // try this
+    
+    //getJnetViewer().fitToScreen(); shrinks graph but allows resave
+    //centerGraph();
+    
+    //getJnetViewer().refresh(2, "zoom refresh");
+    redrawJnet(); // try level 3 refresh
+    StatusManager.inst().normal();
+    
+    
     //StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode - TRY again-ensure
     //int step = 2; // need to utilize number of steps last expanded to re-add steps.
     

Modified: nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-02-09 21:04:25 UTC (rev 22688)
+++ nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-02-09 21:46:29 UTC (rev 22689)
@@ -104,9 +104,11 @@
     }
   }
 
-  private void clearState() {
+  // method is not currently used - added filterListeners clear for testing only
+  public void clearState() {
     this.showMultiEdgesOnly = false;
     filters.clear();
+    filterListeners.clear(); // added this
   }
 
   /** This is an update rather than a wipeout and reload, if filter in new & old


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22801
          http://gmod.svn.sourceforge.net/gmod/?rev=22801&view=rev
Author:   montys9
Date:     2010-03-12 20:00:56 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Made updates to keep node size the same when changing the edge filter.  Also added checks unallocated nodes if changing/zooming/edge filter changing all at same time.  Added flags for using default Node size when increasing/decreasing nodes.  The flags are checked when new nodes are created, and set accordingly.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
    nbrowse/trunk/src/org/jnet/modelset/Node.java
    nbrowse/trunk/src/org/jnet/shape/Balls.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-03-12 15:15:44 UTC (rev 22800)
+++ nbrowse/trunk/src/org/jnet/modelset/ModelLoader.java	2010-03-12 20:00:56 UTC (rev 22801)
@@ -541,7 +541,13 @@
     // node is created, but not all methods are safe, because it
     // has no group -- this is only an issue for debugging
     // Mad i think is milli angstrom diameter??
+	  	
     int size = viewer.getDefaultMadNode();
+    
+    // using getDefaultNodeSize when used - ie edge filtering-MS
+    if (viewer.useDefaultNodeSize())
+      size = viewer.getDefaultNodeSize();
+    
     // it calls a bunch of methods on the NodeIterator
     for (JnetAdapter.NodeIterator iterNode = adapter
         .getNodeIterator(clientFile); iterNode.hasNext();) {

Modified: nbrowse/trunk/src/org/jnet/modelset/Node.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-03-12 15:15:44 UTC (rev 22800)
+++ nbrowse/trunk/src/org/jnet/modelset/Node.java	2010-03-12 20:00:56 UTC (rev 22801)
@@ -300,9 +300,8 @@
   public void setMadNode(Viewer viewer, int size) {
 	// doing the conversion prevents decreasing at a certain point (not small enough).
     //madNode = convertEncodedMad(viewer, size);
-	// if size == (-2000 - global.percentVdwNode)  
-	  if (size == -2008)
-	    madNode = 275;
+	  if (size == Viewer.DEFAULT_MAD_NODE_VALUE) // same as -2000-global.percentVdwNode
+	    madNode = Viewer.DEFAULT_NODE_SIZE_BALL;
 	  else
 	  {
 	    if (size < Short.MIN_VALUE) // ensure size at least fits

Modified: nbrowse/trunk/src/org/jnet/shape/Balls.java
===================================================================
--- nbrowse/trunk/src/org/jnet/shape/Balls.java	2010-03-12 15:15:44 UTC (rev 22800)
+++ nbrowse/trunk/src/org/jnet/shape/Balls.java	2010-03-12 20:00:56 UTC (rev 22801)
@@ -33,6 +33,8 @@
 import org.jnet.modelset.Node;
 import org.jnet.viewer.JnetConstants;
 import org.jnet.viewer.MouseManager; //Victor Chest
+import org.jnet.viewer.Viewer;
+
 import java.util.Hashtable;
 
 public class Balls extends NodeShape implements Serializable {
@@ -71,13 +73,18 @@
   /** @param increase if true increate, false decrease, by NODE_SIZE_INCREMENT
    defined in BallsRenders which should correspond to a few pixels of diameter */
   public void changeSize(boolean increase) {
-    for (Node n : nodes) {
+	short lastSize = Viewer.DEFAULT_NODE_SIZE_BALL;  // allocate last size used as default size for all nodes-MS
+    for (Node n : nodes) {    	
+      if (n == null) continue; // if nodes are being swapped while this happens this seems to work
       int size = n.getMadNode();
       if (increase) size += BallsRenderer.NODE_SIZE_INCREMENT;
       else size -= BallsRenderer.NODE_SIZE_INCREMENT;
       //if (size<0) return; // negative makes setMadNode freak
       n.setMadNode(viewer,size);
+     lastSize = (short) size; // we store last size used here-
     }
+    // need to set size for all nodes in this case
+    viewer.setDefaultNodeSize(lastSize);  // we now save last size used
   }
 
   public void setProperty(String propertyName, Object value, BitSet bs) {

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-03-12 15:15:44 UTC (rev 22800)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-03-12 20:00:56 UTC (rev 22801)
@@ -184,7 +184,62 @@
   private int dimension_mode = JnetConstants.MODE_2D; 
   private float stretchFactor = 1.0f; 
   private boolean isStretch = true;
+  
+  // put defaultNodeSize in here for now - debated using StateManager global settings but that seems to over-complicated and we
+  // need to get away from that.
+  public static final short DEFAULT_NODE_SIZE_BALL = 275;
+  public static final int DEFAULT_MAD_NODE_VALUE = -2008; // same as 2000 - global.percentVdwNode via setMadNode in Node object
+  private short defaultNodeSize = DEFAULT_NODE_SIZE_BALL; // 2000 - global.percentVdwNod - ie setMadNode in Node object; // 
 
+  private transient boolean useDefaultNodeSize=false; // currently only used in edge filtering - is set and then turned off
+  
+  /**
+   * This is used for setting to use the defaultNodeSize attribute - used specifically in edge filtering 
+   *
+   * @param useNodeSize
+   */
+  public void setUseDefaultNodeSize(boolean useNodeSize)
+  {
+	  useDefaultNodeSize = useNodeSize;
+  }
+  
+  /**
+   * This is used as a check for using the defaultNodeSize attribute - used specifically when checking which node size to use - default mad value or latest general node size.
+   * This is useful especially for new nodes generated from using the edge filter.
+   * @return
+   */
+  public boolean useDefaultNodeSize()
+  {
+	  return useDefaultNodeSize;	  
+  }
+  
+  /**
+   * Returns the current default node size - used creating new nodes.
+   * @return
+   */
+  public short getDefaultNodeSize()
+  {
+	  return defaultNodeSize;
+	  
+  }
+
+  /**
+   * This resets the default node size value.
+   */
+  public void resetDefaultNodeSize()
+  {
+	  defaultNodeSize = DEFAULT_NODE_SIZE_BALL;	  
+  }
+  
+  /**
+   * This is used to set the actual default node size - used when increasing/decreasing node sizes.
+   * @param size
+   */
+  public void setDefaultNodeSize(short size)
+  {
+	  defaultNodeSize = size;
+  }
+  
   public void setStretchFactor(float value){ 
       stretchFactor = value;
   }
@@ -2327,7 +2382,10 @@
   /** no coords given, random coords assigned */
   public Node addJnetNode(String id, String name,
     short step,short colix,boolean isTransluc,boolean is3D) {
-    int size = getDefaultMadNode();
+	// disable use of getDefaultMadNode using defaultNodeSize instead
+	int size = getDefaultMadNode();
+    if (useDefaultNodeSize())
+	  size = getDefaultNodeSize();
     return modelSet.addNode(id,name,step,colix,isTransluc,size,is3D);
   }
 
@@ -2340,7 +2398,10 @@
     // nodeSetIndex 0, sym, nodeSite/number(1-based),
     int nodeSite = getNodeCount()+1; // ?? 1 based node numbering
     short elem = JnetConstants.getJnetDefaultElementNumber();
+    // disable use of getDefaultMadNode using defaultNodeSize instead
     int size = getDefaultMadNode(); // ??
+    if (useDefaultNodeSize())
+  	  size = getDefaultNodeSize();
     int i = Integer.MIN_VALUE;
     float f = Float.NaN;
     int occ = 100; // occupancy ??
@@ -6632,6 +6693,7 @@
       return;
     }
     stateManager.setJnetDefaults();
+    // this is still using the default mad node value rather than use getDefaultNodeSize since this is the true default value that does not change
     setShapeSize(JnetConstants.SHAPE_BALLS, getDefaultMadNode(),
         getModelNodeBitSet(-1, true));
   }

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-03-12 15:15:44 UTC (rev 22800)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-03-12 20:00:56 UTC (rev 22801)
@@ -500,18 +500,28 @@
     private synchronized void edgeFilterChanged(EdgeChangeEvent e) {
       // anchor existing graph, if new nodes are filt in below for 1st time they will set
       // node.doLayout to true and get laid out
-      graphView().setDoLayout(false);
-      // seems could do all 3 in same iter, gNFE,fN,cJEIN
-      List<EdgeViewI> filtEdges = getNewlyFiltEdges(e);
-      // should we do filter as we find nodes for efficiency?
-      // this actually creates jnet nodes if not created yet
-      filterNodes(e,filtEdges); // hides node (ball&halo w NODE_IN_MODEL)
-      // if there are edges with no jnet nodes, create jnet nodes. have to do
-      // after creating nodes as edges requires nodes
-      createJnetEdgesIfNeeded(filtEdges);
-      redrawJnet(); // redraw with changed node states- thread?
-      // with added nodes need todo layout, possibly with subtracted too
-      doLayout(false); // false - no fitToScreen, only lays out new nodes, doLayout=true
+      try // added this to set nodes as same size if newly created-MS
+      {
+        graphView().setDoLayout(false);
+        // seems could do all 3 in same iter, gNFE,fN,cJEIN
+        List<EdgeViewI> filtEdges = getNewlyFiltEdges(e);
+        // should we do filter as we find nodes for efficiency?
+        // this actually creates jnet nodes if not created yet
+      
+        // need to set to use defaultNodeSize nodes here-MS
+        getJnetViewer().setUseDefaultNodeSize(true);
+        filterNodes(e,filtEdges); // hides node (ball&halo w NODE_IN_MODEL)
+        // if there are edges with no jnet nodes, create jnet nodes. have to do
+        // after creating nodes as edges requires nodes
+        createJnetEdgesIfNeeded(filtEdges);
+        redrawJnet(); // redraw with changed node states- thread?
+        // with added nodes need todo layout, possibly with subtracted too
+        doLayout(false); // false - no fitToScreen, only lays out new nodes, doLayout=true
+      }
+      finally
+      {
+        getJnetViewer().setUseDefaultNodeSize(false); // always set back when done-MS
+      }
     }
 
 //    /** MG - after filtering need to tell jnet to layout new nodes or sparser


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22808
          http://gmod.svn.sourceforge.net/gmod/?rev=22808&view=rev
Author:   montys9
Date:     2010-03-15 20:01:07 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Mouse Manager updated to include support for more right-click functionality.  Now invokes DataLoader just like expansion - for now.  Perhaps this should be done via StatusManager event (but in this case, we need to pass parameter).  Still leaving tryNewMenu flag off until everything is working as expected.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/io/DataLoader.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-15 19:08:58 UTC (rev 22807)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-15 20:01:07 UTC (rev 22808)
@@ -822,7 +822,18 @@
             case ALT_LEFT: // new get neighbors instead of right click
             	selectNodeNeighborhood(nearestNodeIndex);            	
             	return;
-              
+            
+            case SHIFT_RIGHT:
+            	hideNode(nearestNodeIndex);
+            	return;
+            case CTRL_RIGHT:
+            	anchorNode(nearestNodeIndex);
+            	return;
+            case ALT_RIGHT:
+            	unanchorNode(nearestNodeIndex);
+            	return;
+            case CTRL_SHIFT_RIGHT: 
+            	DataLoader.inst().unhideAllNodes();
             // viewer.nodePicked?? not sure what this is or if used by nbrowse??
 //            case ALT_SHIFT_LEFT:
 //              if (!drawMode)
@@ -938,6 +949,25 @@
   this.mousePopupMenu.show(awtComponent, x, y);  
 }
 
+private void anchorNode(int nearestNodeIndex)
+{
+  if (nearestNodeIndex == -1)
+    return;
+  Node node = viewer.getModelSet().getNodeAt(currentNearestNodeIndex);  	    
+  String name = node.getNodeName(); // get systematic id 
+  DataLoader.inst().anchorNode(name);  
+}
+
+private void unanchorNode(int nearestNodeIndex)
+{
+  if (nearestNodeIndex == -1)
+    return;
+  Node node = viewer.getModelSet().getNodeAt(currentNearestNodeIndex);  	    
+  String name = node.getNodeName(); // get systematic id 
+  DataLoader.inst().unanchorNode(name);    
+}
+
+
 /**
  * unhideAtNode will show all nodes connected to current node .
  */
@@ -996,6 +1026,12 @@
   viewer.repaintView(); // refresh - not optimal 
   */  
   Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);
+  String name = node.getNodeName(); // get systematic id
+
+  DataLoader.inst().hideNode(name); 
+  return;
+  
+  /*
   GraphEltSet graph = GraphEltSet.getCurrentGraph();
   NBNode gnode = graph.findNodeByName(node.getNodeName());
   GraphViewI graphData = GraphViewManager.current();
@@ -1009,45 +1045,11 @@
     edge.setVisible(false);
     
   }
-  // need to iterate over nodes and not show nodes that have all hidden edges - will try next
-  
-  /* code to iterate over edges and check connected nodes - seems to be an issue in showing of nodes will debug.
-  it = edges.iterator(); // reset iterator - new check
-  while (it.hasNext())
-  {
-    EdgeViewI edge = (EdgeViewI) it.next();    
-    NodeViewI nodeFrom = edge.getFrom(); // test this
-    NodeViewI nodeTo = edge.getTo();
-    NodeViewI checkNode = null;
-    if (!nodeFrom.getID().equals(nodeView.getID()))
-    {
-      checkNode = nodeFrom;
-    }
-    else if (!nodeTo.getID().equals(nodeView.getID()))
-    {
-      checkNode = nodeTo;
-    }
-    Iterable<EdgeViewI> checkEdges = checkNode.getEdges();
-    boolean isNodeVisible = false;
-    while (it.hasNext())
-    {
-      EdgeViewI checkEdge = (EdgeViewI) it.next();
-      if (checkEdge.isVisible())
-      {
-        // if visible save node
-        isNodeVisible = true;
-      }
-    }
-    if (isNodeVisible) 
-    {
-      checkNode.setDoLayout(true); // try this force
-      checkNode.setJnetShow(true); // is this enough?
-      
-    }
-  }
   */
   
+  // need to iterate over nodes and not show nodes that have all hidden edges - will try next
   
+  /*  
   graphData.setDoLayout(false);  // anchor to not do layout for new nodes
  
   nodeView.setDoLayout(false);  // don't layout node
@@ -1058,7 +1060,7 @@
   
   viewer.refresh(3, "Hide Node"); // refresh - not optimal   
   JnetManager.inst().doLayout(false);
-   
+  */ 
 }
 /**
  * expand node finds new neighbors, re-showing hidden ones.  Invoked by menu or left double-click.
@@ -1098,9 +1100,34 @@
   };	
   ActionListener unhideAction = new ActionListener() {  
     public void actionPerformed(ActionEvent e) {        
-    unhideNode(currentNearestNodeIndex); // parent class
+    //unhideNode(currentNearestNodeIndex); // parent class
+    DataLoader.inst().unhideAllNodes();
     }
   };    
+  ActionListener anchorAllAction = new ActionListener() {  
+	    public void actionPerformed(ActionEvent e) {        
+	    //unhideNode(currentNearestNodeIndex); // parent class
+	    DataLoader.inst().anchorAllNodes();
+	    }
+	  };      
+  ActionListener unanchorAllAction = new ActionListener() {  
+		public void actionPerformed(ActionEvent e) {        
+		//unhideNode(currentNearestNodeIndex); // parent class
+		DataLoader.inst().unanchorAllNodes();
+		}
+      };  
+  ActionListener anchorAction = new ActionListener() {  
+  	    public void actionPerformed(ActionEvent e) {        
+  	    //unhideNode(currentNearestNodeIndex); // parent class
+        anchorNode(currentNearestNodeIndex);
+  	    }
+  	  };        
+ActionListener unanchorAction = new ActionListener() {  
+        public void actionPerformed(ActionEvent e) {        
+    	//unhideNode(currentNearestNodeIndex); // parent class
+        unanchorNode(currentNearestNodeIndex);
+    	}
+      };     	  
   ActionListener expandAction = new ActionListener() {	
     public void actionPerformed(ActionEvent e) {				
 	  expandNode(currentNearestNodeIndex); // parent class
@@ -1111,12 +1138,28 @@
 	  selectNodeNeighborhood(currentNearestNodeIndex); // parent class
 	}
   };
-  
+  ActionListener selectAllAction = new ActionListener() {	
+	    public void actionPerformed(ActionEvent e) {				
+		  viewer.selectAll();		  
+		}
+	  };
+  ActionListener unselectAllAction = new ActionListener() {	
+		public void actionPerformed(ActionEvent e) {				
+		  viewer.clearSelection();
+	    }
+	  };
+		  
   mousePopupMenu =  new MousePopupMenu();
   mousePopupMenu.addPopupMenuItem("Hide Node", hideAction);
   mousePopupMenu.addPopupMenuItem("Unhide Nodes", unhideAction);
+  mousePopupMenu.addPopupMenuItem("Anchor All Nodes", anchorAllAction);
+  mousePopupMenu.addPopupMenuItem("Unanchor All Nodes", unanchorAllAction);
+  mousePopupMenu.addPopupMenuItem("Anchor Node", anchorAction);
+  mousePopupMenu.addPopupMenuItem("Unanchor Node", unanchorAction);
   mousePopupMenu.addPopupMenuItem("Expand Node", expandAction);
   mousePopupMenu.addPopupMenuItem("Select Node Neighborhood", selectNodeNeighborhoodAction);
+  mousePopupMenu.addPopupMenuItem("Select All Nodes", selectAllAction);
+  mousePopupMenu.addPopupMenuItem("Unselect All Nodes", unselectAllAction);
    
   if (!viewer.isJvm12orGreater() || forceAwt)
     mousePopupMenu.addPopupMenuToAWT();	      

Modified: nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-15 19:08:58 UTC (rev 22807)
+++ nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-15 20:01:07 UTC (rev 22808)
@@ -2,6 +2,8 @@
 
 import java.awt.Frame;
 import java.io.IOException;
+import java.util.Iterator;
+
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.MetaData;
 import org.nbrowse.dataset.MetaDataManager;
@@ -10,6 +12,12 @@
 import org.nbrowse.io.database.DatabaseManager;
 import org.nbrowse.io.database.NbrowseDatabase;
 import org.nbrowse.utils.ErrorUtil;
+import org.nbrowse.views.EdgeViewI;
+import org.nbrowse.views.GraphViewI;
+import org.nbrowse.views.GraphViewManager;
+import org.nbrowse.views.JnetManager;
+import org.nbrowse.views.NodeViewI;
+import org.nbrowse.views.edgecontrol.EdgeFilterState;
 
 /**
  * Loads data & metadata
@@ -142,7 +150,120 @@
     status().newDataDoneLoading();
   }
 
+  public void anchorAllNodes()
+  {	
+    GraphViewI graphData = GraphViewManager.current();
+    graphData.setDoLayout(false);    
+  }
+  
+  public void unanchorAllNodes()
+  {
+	GraphViewI graphData = GraphViewManager.current();
+	graphData.setDoLayout(true); 	  
+  }
+  
+  public void anchorNode(String nodeName)
+  {
+    GraphViewI graphData = GraphViewManager.current();
+	for (NodeViewI n : graphData.getNodeViews()) 
+	{
+      if (n.getLabel().equals(nodeName)) // using labels
+	    n.setDoLayout(false);
+	}
+ 
+  }
 
+  public void unanchorNode(String nodeName)
+  {
+	    GraphViewI graphData = GraphViewManager.current();
+		for (NodeViewI n : graphData.getNodeViews()) 
+		{
+	      if (n.getLabel().equals(nodeName)) // using labels
+		    n.setDoLayout(true);
+		}
+  }
+  
+  public void unhideAllNodes()
+  {
+	  GraphViewI graphData = GraphViewManager.current();
+	  EdgeFilterState edgeFilter = EdgeFilterState.inst();
+	  for (NodeViewI n : graphData.getNodeViews()) 
+	  {
+	    Iterable<EdgeViewI> edges = n.getEdges();
+		Iterator it = edges.iterator();
+		while (it.hasNext())
+		{
+		  EdgeViewI edge = (EdgeViewI) it.next(); 
+		  if (edgeFilter.hasEdge(edge)) 
+		  {		    
+		    edge.setVisible(true); // edge is being shown (doesnt create jnet)		    		    
+		  }			  
+		  //n.setJnetShow(true); // don't show node		    
+		  
+		} // while
+	    it = edges.iterator(); // reset
+		boolean nodeIsVisible = false;
+		while (it.hasNext())
+		{
+			EdgeViewI ev = (EdgeViewI) it.next();
+			if (ev.isVisible())
+			{
+				nodeIsVisible = true;
+				break;
+			}
+		}
+		if (nodeIsVisible)
+		  n.setJnetShow(true);
+	  }
+	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Nodes");	  
+  }
+  
+ /**
+  * Hides node based on nodename
+  * @param nodeName
+  */
+ public void hideNode(String nodeName)
+ {
+	  GraphEltSet graph = GraphEltSet.getCurrentGraph();
+	  EdgeFilterState edgeFilter = EdgeFilterState.inst();	  
+	  NBNode gnode = graph.findNodeByName(nodeName);
+	  GraphViewI graphData = GraphViewManager.current();
+	  NodeViewI nodeView = graphData.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
+	  // edges first
+	  Iterable<EdgeViewI> edges = nodeView.getEdges();
+	  Iterator it = edges.iterator();
+	  while (it.hasNext())
+	  {
+	    EdgeViewI edge = (EdgeViewI) it.next(); 
+	    if (edgeFilter.hasEdge(edge))
+	      edge.setVisible(false);
+	    
+	  }
+	  
+	  for (NodeViewI n : graphData.getNodeViews()) 
+	  {
+		  	  
+		Iterable<EdgeViewI> nedges = n.getEdges();  
+	    it = nedges.iterator(); // reset
+        boolean nodeIsVisible = false;
+        while (it.hasNext())
+	    {
+	      EdgeViewI ev = (EdgeViewI) it.next();
+		  if (ev.isVisible())
+		  {
+		    nodeIsVisible = true;
+		    break;
+	      }
+		  
+        }	  
+	  
+        if (!nodeIsVisible)
+	      n.setJnetShow(false); // don't show node
+	  } // for
+	  //viewer.refresh(3, "Hide Node"); // refresh - not optimal   
+      JnetManager.inst().getJnetViewer().refresh(3, "Hide Node");	 
+ }
+
   private StatusManager status() { return StatusManager.inst(); }
 
   /** name of the node is passed in not id, as jnet only knows names


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22814
          http://gmod.svn.sourceforge.net/gmod/?rev=22814&view=rev
Author:   montys9
Date:     2010-03-16 19:18:55 +0000 (Tue, 16 Mar 2010)

Log Message:
-----------
Made use of test flag to use right menu option.  Added more work for anchoring /unanchoring while moving.  Still issues with slow moving layout while dragging nodes.  Mouse dragged on a node now generates slow layout.  All of the new functionality is used by test flag.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-16 13:20:04 UTC (rev 22813)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-16 19:18:55 UTC (rev 22814)
@@ -30,6 +30,7 @@
 
 import java.util.List;
 
+import org.nbrowse.CommandLine;
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.NBEdge;
 import org.nbrowse.dataset.NBNode;
@@ -51,7 +52,7 @@
   // overlap debug code switch - this code is set to true for new overlap methodology.
   final boolean tryOverlapCode = true;
   // using new key/mouse mappings
-  final boolean tryNewMenu = false ; // use when ready to use new mouse/keyboard mappings
+  //final boolean tryNewMenu = true ; // use when ready to use new mouse/keyboard mappings
   final boolean forceAwt = false; // switch used to force awt menus instead of swing for legacy
   
   /**
@@ -186,7 +187,8 @@
     if (display != null)
       display.addKeyListener(this);
     
-    if (tryNewMenu) // add popup menu if needed
+    //if (tryNewMenu) // add popup menu if needed
+    if (CommandLine.inst().useTestCode())
         addPopupMenu(); // add popup menu to this	    
   }
 
@@ -205,7 +207,8 @@
 	    if (display != null)
 	      display.addKeyListener(this);
 		    
-	    if (tryNewMenu) // add popup menu if needed
+	    //if (tryNewMenu) // add popup menu if needed
+	    if (CommandLine.inst().useTestCode())	    
 	        addPopupMenu(); // add popup menu to this
 	    //clear();
   }
@@ -437,6 +440,7 @@
     timeCurrent = mouseMovedTime = time;
     mouseMovedX = xCurrent = x;
     mouseMovedY = yCurrent = y;
+        
     //doNodeMouseOver(x,y)''
     // measurementPending always null, hoverActive always false for NB
 //    if (measurementPending != null || hoverActive)
@@ -565,6 +569,7 @@
       case LEFT:
         leftMousePressed(x, y);
      } // end of switch/case
+ 
     return; //
     //}
   }
@@ -781,8 +786,9 @@
 
     // SINGLE CLICK
     case 1:
-      setMouseMode();
-      if (tryNewMenu) // new menu mappings
+      setMouseMode();            
+      //if (tryNewMenu) // new menu mappings
+      if (CommandLine.inst().useTestCode())    	  
       {
           switch (modifiers & BUTTON_MODIFIER_MASK) {
 
@@ -841,7 +847,7 @@
 //              break;
           }    	  
       } // if tryMenu
-      else // original mapping
+      else // original mapping - comment out the else when ready to release
       {
       switch (modifiers & BUTTON_MODIFIER_MASK) {
 
@@ -1450,6 +1456,7 @@
         // DRAG SELECTED NODES
         if(nodeDraggingEnabled){  // set to true in mousePressed if click on sel, false in release
             if(!viewer.getFreezing()){ // freezing is for disabling drag (nav)
+            	            	
               // this is where the dragging happens vw->ms.cOD->Balls.cOD
               // Balls checks modifiers and grabs vw.selSet - hmmm
                viewer.checkObjectDragged(previousDragX, 
@@ -1466,6 +1473,11 @@
                calcRectNavigatorBand();
                Navigation.viewer.setNavigatorBand(rectNavigator);
                Navigation.viewer.refresh(3, "mouseMoving");
+               
+               // try doing layout here for non-anchored nodes
+               //if (tryNewMenu)
+               if (CommandLine.inst().useTestCode())               
+                 DataLoader.inst().doSlowLayout(); // try this here
             } 
         }
         // LEFT CLICK DRAG - NOT ON NODE - MOVE SCREEN/GRAPH

Modified: nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-16 13:20:04 UTC (rev 22813)
+++ nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-16 19:18:55 UTC (rev 22814)
@@ -150,29 +150,71 @@
     status().newDataDoneLoading();
   }
 
+  /**
+   * Used to anchor all nodes in graph.
+   */
   public void anchorAllNodes()
   {	
     GraphViewI graphData = GraphViewManager.current();
+    status().layoutDone();
     graphData.setDoLayout(false);    
   }
   
+  /**
+   * Used to unanchor all nodes in graph.  It then does a regular layout.
+   */
   public void unanchorAllNodes()
   {
 	GraphViewI graphData = GraphViewManager.current();
-	graphData.setDoLayout(true); 	  
+	status().layoutDone();
+	graphData.setDoLayout(true);
+	JnetManager.inst().doLayout(false); // if unanchoring all nodes - does a regular layout.
   }
   
+  /**
+   * Used to perform a slow layout while dragging nodes.
+   */
+  public void doSlowLayout()
+  {
+	boolean doLayout = false;
+	GraphViewI graphData = GraphViewManager.current();	
+	for (NodeViewI n : graphData.getNodeViews())
+	{
+		if (n.doLayout())
+	      doLayout = true;
+	}
+	if (!doLayout)
+		return;
+    
+	status().layoutDone();
+	JnetManager.inst().doLayout(false, true);	
+  }
+  
+  /**
+   * Used to anchor a node.
+   * @param nodeName
+   */
   public void anchorNode(String nodeName)
   {
     GraphViewI graphData = GraphViewManager.current();
+    boolean doLayout = false;
 	for (NodeViewI n : graphData.getNodeViews()) 
 	{
       if (n.getLabel().equals(nodeName)) // using labels
 	    n.setDoLayout(false);
+      if (n.doLayout())
+        doLayout = true;
 	}
+	status().layoutDone();
+	if (doLayout)
+	  JnetManager.inst().doLayout(false);
  
   }
 
+  /**
+   * Unanchors a node and does a regular layout.
+   * @param nodeName
+   */
   public void unanchorNode(String nodeName)
   {
 	    GraphViewI graphData = GraphViewManager.current();
@@ -180,9 +222,15 @@
 		{
 	      if (n.getLabel().equals(nodeName)) // using labels
 		    n.setDoLayout(true);
-		}
+		}		
+		status().layoutDone();
+		JnetManager.inst().doLayout(false);
+		
   }
   
+  /**
+   * Unhides all nodes in graph.
+   */
   public void unhideAllNodes()
   {
 	  GraphViewI graphData = GraphViewManager.current();
@@ -218,6 +266,7 @@
 	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Nodes");	  
   }
   
+  
  /**
   * Hides node based on nodename
   * @param nodeName

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java	2010-03-16 13:20:04 UTC (rev 22813)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeMover.java	2010-03-16 19:18:55 UTC (rev 22814)
@@ -6,6 +6,7 @@
 import org.nbrowse.CommandLine;
 import org.nbrowse.dataset.EdgeDataset;
 import org.nbrowse.io.StatusEvent;
+import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.NodeViewI;
 import org.jnet.viewer.JnetConstants;
 import org.nbrowse.io.StatusListener;
@@ -46,6 +47,7 @@
   private boolean is3D; // is2D
   private GraphViewI _graph;
   private boolean cancelLayout=false;
+  private boolean goSlow=false;
 
   public NodeMover() {
     StatusManager.inst().addStatusListener(new Stat());
@@ -107,6 +109,15 @@
     	return stat_weightedEdgeAddition;
     }
     
+    /**
+     * Used for setting to go slow
+     * @param slow
+     */
+    public void setSlow(boolean slow)
+    {
+    	goSlow = slow;
+    }
+    
     public void setGraph(GraphViewI graph) {
       _graph = graph;
       cancelLayout = false;
@@ -311,21 +322,35 @@
           if (is3D) nodeA.setFZ(nodeA.getFZ() + attractiveForce*deltaZ/distance);
         }
       }
-      //System.out.println("vis edges laid out "+edgeVisCount);
+      //System.out.println("vis edges laid out "+edgeVisCount);      
       // move each node by the appropriate amount.
       // And then reset the forces on the node for the next main loop.
+      float c4value = C4; // default is current c4-MS
+      if (goSlow) // if slow down we reduce C4 to slow down for node dragging
+        c4value = 0.00005f; // slow down
+      //c4value = 0.00005f;
+      
       Iterator nodeIt = _graph.getNodeIterator();
       while (nodeIt.hasNext()) {
         NodeView node = (NodeView) nodeIt.next();
         if (!node.doLayout()) continue;
-        node.setX(node.getX() + C4 * node.getFX());
-        node.setY(node.getY() + C4 * node.getFY());
-        if(is3D) node.setZ(node.getZ() + C4*node.getFZ());
+       // node.setX(node.getX() + C4 * node.getFX());
+       // node.setY(node.getY() + C4 * node.getFY());
+       // if(is3D) node.setZ(node.getZ() + C4*node.getFZ());
+        node.setX(node.getX() + c4value * node.getFX());
+        node.setY(node.getY() + c4value * node.getFY());
+        if(is3D) node.setZ(node.getZ() + c4value*node.getFZ());        
         else node.setZ(0);
         node.setFX(0);
         node.setFY(0);
         node.setFZ(0);
       }
+      // the following does not help with smoothness of animation
+      //if (goSlow) // refresh animation?
+      //{
+    //	JnetManager.inst().getJnetViewer().refresh(3, "filter change");
+     //   //JnetManager.inst().getNavigationViewer().refresh(3, "filter change");
+     // }
     } // end of main iterations loop, number of layout iterations to run passed in
   }
 

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-03-16 13:20:04 UTC (rev 22813)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-03-16 19:18:55 UTC (rev 22814)
@@ -1159,6 +1159,7 @@
    * 1000 is a little high/jumpy - 100 isnt bad, 1 is probably needlessly low */
   private final static int MINIMUM_GRAPH_ITERS = 18;
   // this should get lowered for larger graphs somehow
+  private final static int SLOW_ITERATIONS_PER_ANIMATION = 1;//50;//1000;//100;//2;//1;
   private final static int ITERATIONS_PER_ANIMATION = 5;//50;//1000;//100;//2;//1;
   /** how many animations iterations */
   //private final static int ANIMATION_ITERATIONS = LAYOUT_NODE_ITERATIONS/ITERATIONS_PER_ANIMATION;
@@ -1183,16 +1184,28 @@
     doLayout(fitToScreen);
   }
   
+  /**
+   * Used for creating regular Layout Thread.
+   * @param fitToScreen
+   */
   public void doLayout(boolean fitToScreen) { new LayoutThread(fitToScreen).start(); }
+  
+  /**
+   * Used to for slowing down/speeding up Layout and creating Layout thread.
+   * @param fitToScreen
+   * @param goSlow
+   */
+  public void doLayout(boolean fitToScreen, boolean goSlow) { new LayoutThread(fitToScreen, goSlow).start(); }
 
-
   /** Layout thread does layout and is a status listener and will shut down its thread/layout
    * on load and layout and layoutDone */
   private class LayoutThread extends Thread {
     private boolean fitToScreen=true;
     private boolean stopLayout = false;
+    private boolean goSlow = false; // used to slow down layout for node dragging
     private Stat statLis = new Stat();
     private LayoutThread(boolean fit) { fitToScreen = fit; }
+    private LayoutThread(boolean fit, boolean slow) { fitToScreen = fit; goSlow = slow; }
     public void run() {    
       // fire layout status then add listener so dont kill oneself (or put src in?)
       status().layout(); // kills previous layout(s)
@@ -1216,25 +1229,34 @@
     /** This is used by both expansion and new data - phase out for jnet layout
     actually bring this back - layout should happen here for both nav & jnet*/
     private synchronized void doNbrowseLayout() {
-      //status().layout();         	
-      centerGraph(); // fit to screen? no!
+      //status().layout();  
+      if (!goSlow) // if we go slow, don't center -since we are moving nodes	
+        centerGraph(); // fit to screen? no!
       // graphView has vis & nonVis, getVis returns subgraph with just vis node&edges
       GraphViewI filtGraph = graphView().getVisibleSubgraph();
       if (filtGraph.isEmpty()) { status().normal(); return; }
-            
+      
+      int iterations_anim = ITERATIONS_PER_ANIMATION; // normal iterations per animation
+      if (goSlow)
+      {
+        nodeMover().setSlow(goSlow); // slow down node mover in strength
+        iterations_anim = SLOW_ITERATIONS_PER_ANIMATION;
+      }
       nodeMover().setGraph(filtGraph);
       nodeMover().setDimension(layoutDimension); // could also be set w change
 
       //nodeMover().resetNodes(); // hopefully this will reset better
       
-      int graphIterations = calcNumLayoutIters(filtGraph);
-      int animationIterations = graphIterations / ITERATIONS_PER_ANIMATION;
+      int graphIterations = calcNumLayoutIters(filtGraph);      
+      //int animationIterations = graphIterations / ITERATIONS_PER_ANIMATION;
+      int animationIterations = graphIterations / iterations_anim;
 
       // load gui disabled til we hit status.normal() so ok to assume no new interrupt for now
       //stopLayout = false;
       //long t = new Date().getTime(),t2=t,t3=t;
       for (int i = 0; i < animationIterations; i++) {
-        nodeMover().move(ITERATIONS_PER_ANIMATION);
+        //nodeMover().move(ITERATIONS_PER_ANIMATION);
+        nodeMover().move(iterations_anim);        
         redrawJnet();
         if (stopLayout) { //stopLayout=false;//break;
           nodeMover().resetNodes(); // clear nodes fx,fy,fz if stopped


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 22823
          http://gmod.svn.sourceforge.net/gmod/?rev=22823&view=rev
Author:   montys9
Date:     2010-03-17 12:34:51 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
Migrated old unhide function in mousemanager to dataloader for now.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/io/DataLoader.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-17 00:23:54 UTC (rev 22822)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-17 12:34:51 UTC (rev 22823)
@@ -969,47 +969,22 @@
   if (nearestNodeIndex == -1)
     return;
   Node node = viewer.getModelSet().getNodeAt(currentNearestNodeIndex);  	    
-  String name = node.getNodeName(); // get systematic id 
+  String name = node.getNodeName(); // get primary node name
   DataLoader.inst().unanchorNode(name);    
 }
 
 
 /**
- * unhideAtNode will show all nodes connected to current node .
+ * unhideAtNode will show all nodes connected to current node .  This is currently not used yet.
  */
 private void unhideNode(int nearestNodeIndex)
 {
   if (nearestNodeIndex == -1)
     return;
+  
   Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);
-  GraphEltSet graph = GraphEltSet.getCurrentGraph();
-  NBNode gnode = graph.findNodeByName(node.getNodeName());
-  GraphViewI graphData = GraphViewManager.current();
-  NodeViewI nodeView = graphData.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
-  //if (!nodeView.isVisible())
-  //  nodeView.setJnetShow(true); // try this 
-  // edges first
-  Iterable<EdgeViewI> edges = nodeView.getEdges();
-  Iterator it = edges.iterator();
-  while (it.hasNext()) // checks nodes attached to edges to see if nodes are set to show and make them show 
-  {
-    EdgeViewI edge = (EdgeViewI) it.next();
-    if (edge.isVisible() == false)
-    {
-      NodeViewI from = edge.getFrom();
-      if (!from.isVisible())
-         from.setJnetShow(true);
-      NodeViewI to = edge.getTo();
-      if (!to.isVisible());
-         to.setJnetShow(true);
-    } // node check
-    edge.setVisible(true);      
-  }  
-  graphData.setDoLayout(false);  // anchor to not do layout for new nodes  
-  nodeView.setDoLayout(false);  // don't layout node
-  nodeView.setJnetShow(false); // don't show node  
-  viewer.refresh(3, "Unhide Nodes"); // refresh - not optimal   
-  JnetManager.inst().doLayout(false);  
+  String name = node.getNodeName(); // get primary node name
+  DataLoader.inst().unhideNode(name);
 }
 
 /**

Modified: nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-17 00:23:54 UTC (rev 22822)
+++ nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-17 12:34:51 UTC (rev 22823)
@@ -229,6 +229,43 @@
   }
   
   /**
+   * Unhide node - this is an old version not using the edge filter and is not used.  Will eventually be removed.
+   *
+   */
+  public void unhideNode(String name)
+  {
+	  GraphEltSet graph = GraphEltSet.getCurrentGraph();
+	  NBNode gnode = graph.findNodeByName(name);
+	  GraphViewI graphData = GraphViewManager.current();
+	  NodeViewI nodeView = graphData.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
+	  //if (!nodeView.isVisible())
+	  //  nodeView.setJnetShow(true); // try this 
+	  // edges first
+	  Iterable<EdgeViewI> edges = nodeView.getEdges();
+	  Iterator it = edges.iterator();
+	  while (it.hasNext()) // checks nodes attached to edges to see if nodes are set to show and make them show 
+	  {
+	    EdgeViewI edge = (EdgeViewI) it.next();
+	    if (edge.isVisible() == false)
+	    {
+	      NodeViewI from = edge.getFrom();
+	      if (!from.isVisible())
+	         from.setJnetShow(true);
+	      NodeViewI to = edge.getTo();
+	      if (!to.isVisible());
+	         to.setJnetShow(true);
+	    } // node check
+	    edge.setVisible(true);      
+	  }
+	  
+	  //graphData.setDoLayout(false);  // anchor to not do layout for new nodes  
+	  //nodeView.setDoLayout(false);  // don't layout node
+	  nodeView.setJnetShow(false); // don't show node  
+	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Nodes");	 
+	  JnetManager.inst().doLayout(false);  	  
+  }
+  
+  /**
    * Unhides all nodes in graph.
    */
   public void unhideAllNodes()
@@ -306,8 +343,8 @@
 		  
         }	  
 	  
-        if (!nodeIsVisible)
-	      n.setJnetShow(false); // don't show node
+        if (!nodeIsVisible)        	
+          n.setJnetShow(false); // don't show node
 	  } // for
 	  //viewer.refresh(3, "Hide Node"); // refresh - not optimal   
       JnetManager.inst().getJnetViewer().refresh(3, "Hide Node");	 


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Revision: 22826
          http://gmod.svn.sourceforge.net/gmod/?rev=22826&view=rev
Author:   montys9
Date:     2010-03-17 16:34:41 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
More changes made for unanchored nodes and their dragging of objects.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/io/DataLoader.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-17 16:21:56 UTC (rev 22825)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-17 16:34:41 UTC (rev 22826)
@@ -55,6 +55,7 @@
   //final boolean tryNewMenu = true ; // use when ready to use new mouse/keyboard mappings
   final boolean forceAwt = false; // switch used to force awt menus instead of swing for legacy
   
+  
   /**
    * This Private Mouse Popup Menu class is used with mouse to select/execute many commands. 
    * @author monty
@@ -432,6 +433,8 @@
   boolean nodeDraggingEnabled = false;
   int mouseMovedX, mouseMovedY;
   long mouseMovedTime;
+  
+  private transient String targetNodeName = null; // don't store this either
 
   void mouseMoved(long time, int x, int y, int modifiers) {
     hoverOff(); // ??
@@ -588,7 +591,12 @@
       if (overlap != null) // if overlap is found
       {
         if (overlap.isNode())      
-          nearestNodeIndex = (overlap.getNode()).getNodeIndex();      
+        {
+          nearestNodeIndex = (overlap.getNode()).getNodeIndex();
+          targetNodeName = (overlap.getNode()).getNodeName(); // we store this for mouse dragging regarding layout
+          DataLoader.inst().saveAnchorState(targetNodeName);
+          //System.out.println("target node selected: " + targetNodeName);
+        }
       }      
     }
     else
@@ -618,6 +626,8 @@
 //          if (set.get(i)) {
 //            if (i == nearestNodeIndex)
     nodeDraggingEnabled = true; // enable dragging
+    
+
 //          }
 //        }
       //}
@@ -647,6 +657,11 @@
     viewer.setInMotion(false);
    
     nodeDraggingEnabled = false;
+    
+    // if released from doing slow layout - turn off flag - even it still doing it - another node will initiate layout
+    DataLoader.inst().restoreAnchorState(targetNodeName);
+    
+    
     if(viewer.getSelectionSet() != null){ 
       viewer.addFinalSelection(viewer.getSelectionSet());
       if (Navigation.viewer != null)
@@ -1451,10 +1466,17 @@
                
                // try doing layout here for non-anchored nodes
                //if (tryNewMenu)
-               if (CommandLine.inst().useTestCode())               
-                 DataLoader.inst().doSlowLayout(); // try this here
-            } 
-        }
+               if (CommandLine.inst().useTestCode())       
+               {
+                 // use name found at mouse click for drag
+                 if (targetNodeName != null)
+                 {	
+                   DataLoader.inst().doSlowLayout(targetNodeName);
+                   //DataLoader.inst().doSlowLayout(); // try this here                         	  
+                 }
+               }
+            } // freezing        
+        } // node dragging enabled
         // LEFT CLICK DRAG - NOT ON NODE - MOVE SCREEN/GRAPH
         else {
           // JNET

Modified: nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-17 16:21:56 UTC (rev 22825)
+++ nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-17 16:34:41 UTC (rev 22826)
@@ -38,6 +38,10 @@
   private boolean loadingMeta=false;
   private boolean loadingDatabase=false;
 
+  // store last anchoring node state for dragging
+  private boolean tempAnchorState=false;
+  private boolean useSlowLayout = false; // temporary
+  
   private static DataLoader singleton=new DataLoader();
   private DataLoader() {StatusManager.inst().addStatusListener(new StatLis());}
   public static DataLoader inst() { return singleton; }
@@ -171,22 +175,56 @@
 	JnetManager.inst().doLayout(false); // if unanchoring all nodes - does a regular layout.
   }
   
+  public void saveAnchorState(String nodeName)
+  {
+    GraphViewI graphData = GraphViewManager.current(); 		
+	for (NodeViewI n : graphData.getNodeViews())
+    {
+	  if (n.getLabel().equals(nodeName)) // using labels	  
+	    tempAnchorState = n.doLayout();	    
+    }
+  }
+  
+  public void restoreAnchorState(String nodeName)
+  {
+	GraphViewI graphData = GraphViewManager.current(); 
+	status().layoutDone(); // end current layout
+    for (NodeViewI n : graphData.getNodeViews())
+	{
+	  if (n.getLabel().equals(nodeName)) // using labels
+	    n.setDoLayout(tempAnchorState);  // reset back anchor state
+	}
+    // restart layout again
+    if (useSlowLayout) // just finished slow layout, do one more
+      JnetManager.inst().doLayout(false, true);
+    useSlowLayout=false; // for next one
+  }
+  
   /**
    * Used to perform a slow layout while dragging nodes.
    */
-  public void doSlowLayout()
-  {
-	boolean doLayout = false;
-	GraphViewI graphData = GraphViewManager.current();	
-	for (NodeViewI n : graphData.getNodeViews())
+  public void doSlowLayout(String nodeName)
+  {	
+    boolean doLayout = false;
+	status().layoutDone(); // stop current before next layout
+	GraphViewI graphData = GraphViewManager.current();
+	if (!useSlowLayout)
 	{
+	  for (NodeViewI n : graphData.getNodeViews())
+  	  {
 		if (n.doLayout())
 	      doLayout = true;
+		// we are now temporarily anchoring node
+	    if (n.getLabel().equals(nodeName)) // using labels	   
+	  	  n.setDoLayout(false); // turn on anchoring	    
+	  }
+	  if (!doLayout)
+		return;
 	}
-	if (!doLayout)
-		return;
     
-	status().layoutDone();
+	useSlowLayout=true;
+	//status().layoutDone();
+	
 	JnetManager.inst().doLayout(false, true);	
   }
   


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Revision: 22843
          http://gmod.svn.sourceforge.net/gmod/?rev=22843&view=rev
Author:   montys9
Date:     2010-03-19 16:25:18 +0000 (Fri, 19 Mar 2010)

Log Message:
-----------
Updated NBNode data check for synonyms to check for null object in case sql connnection went away temporarily.
Mouse Manager has early beginnings for colorNode - issues are color is numeric via JMOL vs standard Java color.  Another issue is JMOL uses JMOL bit selection for choosing which node to color.  Do we keep in synch with this notion?

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-19 15:49:05 UTC (rev 22842)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-19 16:25:18 UTC (rev 22843)
@@ -1,5 +1,6 @@
 package org.jnet.viewer;
 
+import java.awt.Color;
 import java.awt.MenuItem;
 import java.awt.PopupMenu;
 import java.awt.Rectangle;
@@ -20,6 +21,7 @@
 import java.util.ArrayList;
 import java.util.Iterator;
 
+import javax.swing.JColorChooser;
 import javax.swing.JMenuItem;
 import javax.swing.JPopupMenu;
 import javax.vecmath.Point3f;
@@ -970,6 +972,20 @@
   this.mousePopupMenu.show(awtComponent, x, y);  
 }
 
+private void colorNode(int nearestNodeIndex)
+{
+  if (nearestNodeIndex == -1)
+    return;
+  Node node = viewer.getModelSet().getNodeAt(currentNearestNodeIndex);  	    
+  //String name = node.getNodeName(); // get systematic id 
+  //DataLoader.inst().anchorNode(name); 
+  //Color oldColor = node.get
+  //Color c = JColorChooser.showDialog(
+  //        ((Component) e.getSource()).getParent(),
+  //        "Pick me !", oldColor);
+  //if (c == null) c = oldColor;  
+}
+
 private void anchorNode(int nearestNodeIndex)
 {
   if (nearestNodeIndex == -1)

Modified: nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java	2010-03-19 15:49:05 UTC (rev 22842)
+++ nbrowse/trunk/src/org/nbrowse/dataset/NBNode.java	2010-03-19 16:25:18 UTC (rev 22843)
@@ -110,6 +110,8 @@
     if (!haveInfoRetriever()) return;
     if (synsAndLinksRetrieved) return;
     SynsAndLinks sl = infoRetriever().retrieveSynsAndLinks(getInternalDbId());
+    if (sl == null)
+      return;
     synonyms = sl.getSynonyms();
     links = sl.getLinks();
     synsAndLinksRetrieved = true;


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Revision: 22869
          http://gmod.svn.sourceforge.net/gmod/?rev=22869&view=rev
Author:   montys9
Date:     2010-03-23 15:27:08 +0000 (Tue, 23 Mar 2010)

Log Message:
-----------
Migrated graph manipulation functionality via mouse manager to graph data.  Expansion is left in data loader since it is indeed doing data loading with expansion thread.  Fixed bug in unhideAllNodes where we dont' want to set visibility to true if edge filter is set to off (only affect user defined hidden field in this case).

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-23 14:11:19 UTC (rev 22868)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-03-23 15:27:08 UTC (rev 22869)
@@ -40,6 +40,7 @@
 import org.nbrowse.dataset.NBNode;
 import org.nbrowse.io.DataAdapterManager;
 import org.nbrowse.io.DataLoader;
+import org.nbrowse.layouts.spring.vrmlgraph.GraphData;
 import org.nbrowse.utils.ErrorUtil;
 import org.nbrowse.views.EdgeViewI;
 import org.nbrowse.views.GraphViewI;
@@ -602,7 +603,10 @@
         {
           nearestNodeIndex = (overlap.getNode()).getNodeIndex();
           targetNodeName = (overlap.getNode()).getNodeName(); // we store this for mouse dragging regarding layout
-          DataLoader.inst().saveAnchorState(targetNodeName);
+          GraphViewI graphData = GraphViewManager.current(); 
+          if (graphData instanceof GraphData)
+            ((GraphData) graphData).saveAnchorState(targetNodeName);
+          //DataLoader.inst().saveAnchorState(targetNodeName);
           //System.out.println("target node selected: " + targetNodeName);
         }
       }      
@@ -666,8 +670,11 @@
    
     nodeDraggingEnabled = false;
     
-    // if released from doing slow layout - turn off flag - even it still doing it - another node will initiate layout
-    DataLoader.inst().restoreAnchorState(targetNodeName);
+    // if released from doing slow layout - turn off flag - even it still doing it - another node will initiate layout    
+    GraphViewI graphData = GraphViewManager.current(); 
+    if (graphData instanceof GraphData)
+      ((GraphData) graphData).restoreAnchorState(targetNodeName);    
+    //DataLoader.inst().restoreAnchorState(targetNodeName);
     
     
     if(viewer.getSelectionSet() != null){ 
@@ -862,7 +869,10 @@
             	unanchorNode(nearestNodeIndex);
             	return;
             case CTRL_SHIFT_RIGHT: 
-            	DataLoader.inst().unhideAllNodes();
+                GraphViewI graphData = GraphViewManager.current(); 
+                if (graphData instanceof GraphData)
+                  ((GraphData) graphData).unhideAllNodes();
+            	//DataLoader.inst().unhideAllNodes();
             // viewer.nodePicked?? not sure what this is or if used by nbrowse??
 //            case ALT_SHIFT_LEFT:
 //              if (!drawMode)
@@ -996,15 +1006,9 @@
   if (c == null)
 	  return;  
   GraphViewI graphData = GraphViewManager.current(); 
-  for (NodeViewI n : graphData.getNodeViews())
-  {
-    if (n.getLabel().equals(name)) // then color node using view
-    {
-    	n.setColor(c);
-    	break;
-    }
-    	  
-  }
+  if (graphData instanceof GraphData)
+    ((GraphData) graphData).colorNode(name, c);
+  
   // this version is if we wanted to set color without nodeview color storage
   //short colix = Colix3D.getColix(c.getRGB());
   //node.setColixNode(colix); // setting color of node
@@ -1021,8 +1025,11 @@
   //	  System.out.println("selected nodes found");
 	  
   Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  
-  String name = node.getNodeName(); // get systematic id 
-  DataLoader.inst().anchorNode(name);  
+  String name = node.getNodeName(); // get primary node name
+  GraphViewI graphData = GraphViewManager.current(); 
+  if (graphData instanceof GraphData)
+    ((GraphData) graphData).anchorNode(name);  
+  //DataLoader.inst().anchorNode(name);  
 }
 
 private void unanchorNode(int nearestNodeIndex)
@@ -1031,7 +1038,10 @@
     return;
   Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  	    
   String name = node.getNodeName(); // get primary node name
-  DataLoader.inst().unanchorNode(name);    
+  GraphViewI graphData = GraphViewManager.current(); 
+  if (graphData instanceof GraphData)
+    ((GraphData) graphData).unanchorNode(name);  
+  //DataLoader.inst().unanchorNode(name);    
 }
 
 
@@ -1045,7 +1055,10 @@
   
   Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);
   String name = node.getNodeName(); // get primary node name
-  DataLoader.inst().unhideNode(name);
+  GraphViewI graphData = GraphViewManager.current(); 
+  if (graphData instanceof GraphData)
+    ((GraphData) graphData).unhideNode(name);  
+  //DataLoader.inst().unhideNode(name);
 }
 
 /**
@@ -1092,7 +1105,10 @@
    
   String name = node.getNodeName(); // get systematic id
 
-  DataLoader.inst().hideNode(name); 
+  GraphViewI graphData = GraphViewManager.current(); 
+  if (graphData instanceof GraphData)
+    ((GraphData) graphData).hideNode(name);  
+  //DataLoader.inst().hideNode(name); 
   return;
   
   /*
@@ -1170,19 +1186,28 @@
   ActionListener unhideAction = new ActionListener() {  
     public void actionPerformed(ActionEvent e) {        
     //unhideNode(currentNearestNodeIndex); // parent class
-    DataLoader.inst().unhideAllNodes();
+    GraphViewI graphData = GraphViewManager.current(); 
+    if (graphData instanceof GraphData)
+      ((GraphData) graphData).unhideAllNodes();    	
+    //DataLoader.inst().unhideAllNodes();
     }
   };    
   ActionListener anchorAllAction = new ActionListener() {  
 	    public void actionPerformed(ActionEvent e) {        
 	    //unhideNode(currentNearestNodeIndex); // parent class
-	    DataLoader.inst().anchorAllNodes();
+	    GraphViewI graphData = GraphViewManager.current(); 
+	    if (graphData instanceof GraphData)
+	      ((GraphData) graphData).anchorAllNodes();	    	
+	    //DataLoader.inst().anchorAllNodes();
 	    }
 	  };      
   ActionListener unanchorAllAction = new ActionListener() {  
 		public void actionPerformed(ActionEvent e) {        
 		//unhideNode(currentNearestNodeIndex); // parent class
-		DataLoader.inst().unanchorAllNodes();
+		GraphViewI graphData = GraphViewManager.current(); 
+		  if (graphData instanceof GraphData)
+		    ((GraphData) graphData).unanchorAllNodes();			
+		//DataLoader.inst().unanchorAllNodes();
 		}
       };  
   ActionListener anchorAction = new ActionListener() {  
@@ -1227,7 +1252,7 @@
   mousePopupMenu =  new MousePopupMenu();
   mousePopupMenu.addPopupMenuItem("Color Node", colorAction);  
   mousePopupMenu.addPopupMenuItem("Hide Node", hideAction);
-  mousePopupMenu.addPopupMenuItem("Unhide Nodes", unhideAction);
+  mousePopupMenu.addPopupMenuItem("Unhide All Nodes", unhideAction);
   mousePopupMenu.addPopupMenuItem("Anchor All Nodes", anchorAllAction);
   mousePopupMenu.addPopupMenuItem("Unanchor All Nodes", unanchorAllAction);
   mousePopupMenu.addPopupMenuItem("Anchor Node", anchorAction);
@@ -1578,7 +1603,10 @@
                  // use name found at mouse click for drag
                  if (targetNodeName != null)
                  {	
-                   DataLoader.inst().doSlowLayout(targetNodeName);
+                  GraphViewI graphData = GraphViewManager.current(); 
+                  if (graphData instanceof GraphData)
+                    ((GraphData) graphData).doSlowLayout(targetNodeName);
+                   //DataLoader.inst().doSlowLayout(targetNodeName);
                    //DataLoader.inst().doSlowLayout(); // try this here                         	  
                  }
                }

Modified: nbrowse/trunk/src/org/nbrowse/io/DataLoader.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-23 14:11:19 UTC (rev 22868)
+++ nbrowse/trunk/src/org/nbrowse/io/DataLoader.java	2010-03-23 15:27:08 UTC (rev 22869)
@@ -37,10 +37,6 @@
   /** true if loading meta data */
   private boolean loadingMeta=false;
   private boolean loadingDatabase=false;
-
-  // store last anchoring node state for dragging
-  private boolean tempAnchorState=false;
-  private boolean useSlowLayout = false; // temporary
   
   private static DataLoader singleton=new DataLoader();
   private DataLoader() {StatusManager.inst().addStatusListener(new StatLis());}
@@ -160,252 +156,7 @@
     status().newDataDoneLoading();
   }
 
-  /**
-   * Used to anchor all nodes in graph.
-   */
-  public void anchorAllNodes()
-  {	
-    GraphViewI graphData = GraphViewManager.current();
-    status().layoutDone();
-    //graphData.setDoLayout(false);    
-  }
-  
-  /**
-   * Used to unanchor all nodes in graph.  It then does a regular layout.
-   */
-  public void unanchorAllNodes()
-  {
-	GraphViewI graphData = GraphViewManager.current();
-	status().layoutDone();
-	graphData.setDoLayout(true);
-	JnetManager.inst().doLayout(false, true); // if unanchoring all nodes - does a regular layout.
-  }
-  
-  public void saveAnchorState(String nodeName)
-  {
-    GraphViewI graphData = GraphViewManager.current(); 		
-	for (NodeViewI n : graphData.getNodeViews())
-    {
-	  if (n.getLabel().equals(nodeName)) // using labels	  
-	    tempAnchorState = n.doLayout();	    
-    }
-  }
-  
-  public void restoreAnchorState(String nodeName)
-  {
-	GraphViewI graphData = GraphViewManager.current(); 
-	status().layoutDone(); // end current layout
-    for (NodeViewI n : graphData.getNodeViews())
-	{
-	  if (n.getLabel().equals(nodeName)) // using labels
-	    n.setDoLayout(tempAnchorState);  // reset back anchor state
-	}
-    // restart layout again
-    if (useSlowLayout) // just finished slow layout, do one more
-      JnetManager.inst().doLayout(false, true);
-    useSlowLayout=false; // for next one
-  }
-  
-  /**
-   * Used to perform a slow layout while dragging nodes.
-   */
-  public void doSlowLayout(String nodeName)
-  {	
-    boolean doLayout = false;
-	status().layoutDone(); // stop current before next layout
-	GraphViewI graphData = GraphViewManager.current();
-	if (!useSlowLayout)
-	{
-	  for (NodeViewI n : graphData.getNodeViews())
-  	  {
-		if (n.doLayout())
-	      doLayout = true;
-		// we are now temporarily anchoring node
-	    if (n.getLabel().equals(nodeName)) // using labels	   
-	  	  n.setDoLayout(false); // turn on anchoring	    
-	  }
-	  if (!doLayout)
-		return;
-	}
-    
-	useSlowLayout=true;
-	//status().layoutDone();
-	
-	JnetManager.inst().doLayout(false, true);	
-  }
-  
-  /**
-   * Used to anchor a node.
-   * @param nodeName
-   */
-  public void anchorNode(String nodeName)
-  {
-    GraphViewI graphData = GraphViewManager.current();
-    boolean doLayout = false;
-	for (NodeViewI n : graphData.getNodeViews()) 
-	{
-      if (n.getLabel().equals(nodeName)) // using labels
-	    n.setDoLayout(false);
-      if (n.doLayout())
-        doLayout = true;
-	}
-	//status().layoutDone();
-	//if (doLayout)
-	//  JnetManager.inst().doLayout(false);
- 
-  }
 
-  /**
-   * Unanchors a node and does a regular layout.
-   * @param nodeName
-   */
-  public void unanchorNode(String nodeName)
-  {
-	    GraphViewI graphData = GraphViewManager.current();
-		for (NodeViewI n : graphData.getNodeViews()) 
-		{
-	      if (n.getLabel().equals(nodeName)) // using labels
-		    n.setDoLayout(true);
-		}		
-		status().layoutDone();
-		JnetManager.inst().doLayout(false, true);
-		
-  }
-  
-  /**
-   * Unhide node - this is an old version not using the edge filter and is not used.  Will eventually be removed.
-   *
-   */
-  public void unhideNode(String name)
-  {
-	  GraphEltSet graph = GraphEltSet.getCurrentGraph();
-	  NBNode gnode = graph.findNodeByName(name);
-	  GraphViewI graphData = GraphViewManager.current();
-	  NodeViewI nodeView = graphData.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
-	  //if (!nodeView.isVisible())
-	  //  nodeView.setJnetShow(true); // try this 
-	  // edges first
-	  Iterable<EdgeViewI> edges = nodeView.getEdges();
-	  Iterator it = edges.iterator();
-	  while (it.hasNext()) // checks nodes attached to edges to see if nodes are set to show and make them show 
-	  {
-	    EdgeViewI edge = (EdgeViewI) it.next();
-	    if (edge.isVisible() == false)
-	    {
-	      NodeViewI from = edge.getFrom();
-	      if (!from.isVisible())
-	         from.setJnetShow(true);
-	      NodeViewI to = edge.getTo();
-	      if (!to.isVisible());
-	         to.setJnetShow(true);
-	    } // node check
-	    edge.setVisible(true);      
-	  }
-	  
-	  //graphData.setDoLayout(false);  // anchor to not do layout for new nodes  
-	  //nodeView.setDoLayout(false);  // don't layout node
-	  nodeView.setJnetShow(false); // don't show node  
-	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Nodes");	 
-	  JnetManager.inst().doLayout(false);  	  
-  }
-  
-  /**
-   * Unhides all nodes in graph.
-   */
-  public void unhideAllNodes()
-  {
-	  GraphViewI graphData = GraphViewManager.current();
-	  EdgeFilterState edgeFilter = EdgeFilterState.inst();
-	  for (NodeViewI n : graphData.getNodeViews()) 
-	  {
-	    Iterable<EdgeViewI> edges = n.getEdges();
-		Iterator it = edges.iterator();
-		while (it.hasNext())
-		{
-		  EdgeViewI edge = (EdgeViewI) it.next(); 
-		  if (edgeFilter.hasEdge(edge)) 
-		  {	
-		   edge.setUserHidden(false);
-		   // edge.setVisible(true); // edge is being shown (doesnt create jnet)		    		    
-		  }			  
-		  //n.setJnetShow(true); // don't show node		    
-		  
-		} // while
-	    it = edges.iterator(); // reset
-		boolean nodeIsVisible = false;
-		while (it.hasNext())
-		{
-			EdgeViewI ev = (EdgeViewI) it.next();
-			if (ev.isVisible())
-			{
-				nodeIsVisible = true;
-				break;
-			}
-		}
-		if (nodeIsVisible)
-		  n.setUserHidden(false);
-		  //n.setJnetShow(true);
-	  }
-	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Nodes");	  
-  }
-  
-  
- /**
-  * Hides node based on nodename
-  * @param nodeName
-  */
- public void hideNode(String nodeName)
- {
-	  GraphEltSet graph = GraphEltSet.getCurrentGraph();
-	  EdgeFilterState edgeFilter = EdgeFilterState.inst();	  
-	  NBNode gnode = graph.findNodeByName(nodeName);
-	  GraphViewI graphData = GraphViewManager.current();
-	  NodeViewI nodeView = graphData.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
-	  // edges first
-	  Iterable<EdgeViewI> edges = nodeView.getEdges();
-	  Iterator it = edges.iterator();
-	  while (it.hasNext())
-	  {
-	    EdgeViewI edge = (EdgeViewI) it.next(); 
-	    if (edgeFilter.hasEdge(edge))
-	      edge.setUserHidden(true);
-	      //edge.setVisible(false);
-	    
-	  }
-	  
-	  // this iteration is to find nodes that are now orphaned by hiding of selected hidden node and not display them
-	  // if we ever change default behavior for this, then we would comment out this loop and just set the user hidden below
-	  // nodeView.setUserHidden(true);
-	  for (NodeViewI n : graphData.getNodeViews()) 
-	  {
-		  	  
-		Iterable<EdgeViewI> nedges = n.getEdges();  
-	    it = nedges.iterator(); // reset
-        boolean nodeIsVisible = false;
-        while (it.hasNext())
-	    {
-	      EdgeViewI ev = (EdgeViewI) it.next();
-		  if (ev.isVisible())
-		  {
-		    nodeIsVisible = true;
-		    break;
-	      }
-		  
-        }	  
-	  
-        if (!nodeIsVisible)
-        {
-          if (n.getID().equals(nodeView.getID())) // if node we are hiding set user hidden
-             n.setUserHidden(true);
-          else
-        	 n.setJnetShow(false); // don't show node but not user-hidden
-          
-        }
-          //n.setJnetShow(false); // don't show node        
-	  } // for
-	  //viewer.refresh(3, "Hide Node"); // refresh - not optimal   
-      JnetManager.inst().getJnetViewer().refresh(3, "Hide Node");	 
- }
 
   private StatusManager status() { return StatusManager.inst(); }
 

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-03-23 14:11:19 UTC (rev 22868)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-03-23 15:27:08 UTC (rev 22869)
@@ -70,17 +70,25 @@
 //    this.edgeModel = edgeModel;
 //  }
 
+  /**
+   * returns whether edge is hidden directly by user
+   * @return value of user-directed hidden field property
+   */
   public boolean isUserHidden()
   {
 	  return userHidden;
   }
   
+  /**
+   * sets value of user-directed hidden field only - visibility is set for edges regarding filtering and jmol
+   * @param isHidden
+   */
   public void setUserHidden(boolean isHidden)
   {
 	  userHidden = isHidden;
-	  setVisible(!isHidden);	  
+	  //setVisible(!isHidden);	  
   }
- 
+   
   public NBEdge getModel() { return edgeModel; }
   
   public String getType() { return edgeModel.getType(); }

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-03-23 14:11:19 UTC (rev 22868)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-03-23 15:27:08 UTC (rev 22869)
@@ -1,5 +1,6 @@
 package org.nbrowse.layouts.spring.vrmlgraph;
 
+import java.awt.Color;
 import java.io.Serializable;
 import java.util.*;
 // not sure if this belongs here - but both are view
@@ -11,10 +12,12 @@
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.NBEdge;
 import org.nbrowse.dataset.NBNode;
+import org.nbrowse.io.StatusManager;
 import org.nbrowse.utils.ErrorUtil;
 import org.nbrowse.views.edgecontrol.EdgeFilterState;
 import org.nbrowse.views.EdgeViewI;
 import org.nbrowse.views.GraphViewI;
+import org.nbrowse.views.GraphViewManager;
 import org.nbrowse.views.JnetManager;
 import org.nbrowse.views.NodeViewI;
 import org.nbrowse.views.StepManager;
@@ -49,6 +52,11 @@
   /** keep track of node queried - maybe do in model? */
   private List<NodeViewI> queryNodes=new ArrayList<NodeViewI>(4);
   
+  // store last anchoring node state for dragging
+  private transient boolean tempAnchorState=false;
+  // store use temporary use of slow layout for dragging
+  private transient boolean useSlowLayout = false; 
+  
   /** Constructor for the GraphData object */
   private GraphData() {}
 
@@ -746,6 +754,285 @@
       if (e.getJmolEdge() == edge) return e;
     return null;
   }
+  
+  // the following methods are used in conjunction with jmol mouse manager in graph manipulation
+  private StatusManager status() { return StatusManager.inst(); }
+  
+  /**
+   * colors node specific coloring given a primary node name and color picked
+   * @param nodeName
+   * @param color
+   */
+  public void colorNode(String nodeName, Color color)
+  {
+    for (NodeViewI n : this.getNodeViews())
+	{
+	  if (n.getLabel().equals(nodeName)) // then color node using view
+	  {
+	    n.setColor(color);
+	    break;
+	  }
+	    	  
+	}	  
+  }
+  
+  /**
+   * Used to anchor all nodes in graph.
+   */
+  public void anchorAllNodes()
+  {	
+    //GraphViewI graphData = GraphViewManager.current();
+    status().layoutDone();
+    //graphData.setDoLayout(false);
+    this.setDoLayout(false);
+  }
+  
+  /**
+   * Used to unanchor all nodes in graph.  It then does a regular layout.
+   */
+  public void unanchorAllNodes()
+  {
+	//GraphViewI graphData = GraphViewManager.current();
+	status().layoutDone();
+	this.setDoLayout(true);
+	JnetManager.inst().doLayout(false, true); // if unanchoring all nodes - does a regular layout.
+  }
+  
+  public void saveAnchorState(String nodeName)
+  {
+    //GraphViewI graphData = GraphViewManager.current(); 		
+	for (NodeViewI n : this.getNodeViews())
+    {
+	  if (n.getLabel().equals(nodeName)) // using labels	  
+	    tempAnchorState = n.doLayout();	    
+    }
+  }
+  
+  public void restoreAnchorState(String nodeName)
+  {
+	//GraphViewI graphData = GraphViewManager.current(); 
+	status().layoutDone(); // end current layout
+    for (NodeViewI n : this.getNodeViews())
+	{
+	  if (n.getLabel().equals(nodeName)) // using labels
+	    n.setDoLayout(tempAnchorState);  // reset back anchor state
+	}
+    // restart layout again
+    if (useSlowLayout) // just finished slow layout, do one more
+      JnetManager.inst().doLayout(false, true);
+    useSlowLayout=false; // for next one
+  }
+  
+  /**
+   * Used to perform a slow layout while dragging nodes.
+   */
+  public void doSlowLayout(String nodeName)
+  {	
+    boolean doLayout = false;
+	status().layoutDone(); // stop current before next layout
+	//GraphViewI graphData = GraphViewManager.current();
+	if (!useSlowLayout)
+	{
+	  for (NodeViewI n : this.getNodeViews())
+  	  {
+		if (n.doLayout())
+	      doLayout = true;
+		// we are now temporarily anchoring node
+	    if (n.getLabel().equals(nodeName)) // using labels	   
+	  	  n.setDoLayout(false); // turn on anchoring	    
+	  }
+	  if (!doLayout)
+		return;
+	}
+    
+	useSlowLayout=true;
+	//status().layoutDone();
+	
+	JnetManager.inst().doLayout(false, true);	
+  }
+  
+  /**
+   * Used to anchor a node.
+   * @param nodeName
+   */
+  public void anchorNode(String nodeName)
+  {
+    //GraphViewI graphData = GraphViewManager.current();
+    boolean doLayout = false;
+	for (NodeViewI n : this.getNodeViews()) 
+	{
+      if (n.getLabel().equals(nodeName)) // using labels
+	    n.setDoLayout(false);
+      if (n.doLayout())
+        doLayout = true;
+	}
+	//status().layoutDone();
+	//if (doLayout)
+	//  JnetManager.inst().doLayout(false);
+ 
+  }
+
+  /**
+   * Unanchors a node and does a regular layout.
+   * @param nodeName
+   */
+  public void unanchorNode(String nodeName)
+  {
+	    //GraphViewI graphData = GraphViewManager.current();
+		for (NodeViewI n : this.getNodeViews()) 
+		{
+	      if (n.getLabel().equals(nodeName)) // using labels
+		    n.setDoLayout(true);
+		}		
+		status().layoutDone();
+		JnetManager.inst().doLayout(false, true);
+		
+  }
+  
+  /**
+   * Unhide node - this is an old version not using the edge filter and is not used.  Will eventually be removed.
+   *
+   */
+  public void unhideNode(String name)
+  {
+	  GraphEltSet graph = GraphEltSet.getCurrentGraph();
+	  NBNode gnode = graph.findNodeByName(name);
+	  //GraphViewI graphData = GraphViewManager.current();
+	  NodeViewI nodeView = this.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
+	  //if (!nodeView.isVisible())
+	  //  nodeView.setJnetShow(true); // try this 
+	  // edges first
+	  Iterable<EdgeViewI> edges = nodeView.getEdges();
+	  Iterator it = edges.iterator();
+	  while (it.hasNext()) // checks nodes attached to edges to see if nodes are set to show and make them show 
+	  {
+	    EdgeViewI edge = (EdgeViewI) it.next();
+	    if (edge.isVisible() == false)
+	    {
+	      NodeViewI from = edge.getFrom();
+	      if (!from.isVisible())
+	         from.setJnetShow(true);
+	      NodeViewI to = edge.getTo();
+	      if (!to.isVisible());
+	         to.setJnetShow(true);
+	    } // node check
+	    edge.setVisible(true);      
+	  }
+	  
+	  //graphData.setDoLayout(false);  // anchor to not do layout for new nodes  
+	  //nodeView.setDoLayout(false);  // don't layout node
+	  nodeView.setJnetShow(false); // don't show node  
+	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Node");	 
+	  JnetManager.inst().doLayout(false);  	  
+  }
+  
+  /**
+   * Unhides all nodes in graph.
+   */
+  public void unhideAllNodes()
+  {
+	  //GraphViewI graphData = GraphViewManager.current();
+	  EdgeFilterState edgeFilter = EdgeFilterState.inst();
+	  for (NodeViewI n : this.getNodeViews()) 
+	  {
+	    Iterable<EdgeViewI> edges = n.getEdges();
+		Iterator it = edges.iterator();
+		while (it.hasNext())
+		{
+		  EdgeViewI edge = (EdgeViewI) it.next(); 
+		  if (edgeFilter.hasEdge(edge)) 
+		  {	
+		   edge.setUserHidden(false);
+		   edge.setVisible(true); // edge is being shown (doesnt create jnet)		    		    
+		  }			
+		  else // if filter does not have edge, we at least set no longer user hidden only
+		  {
+			  edge.setUserHidden(false);  
+		  }
+		  //n.setJnetShow(true); // don't show node		    
+		  
+		} // while
+	    it = edges.iterator(); // reset
+		boolean nodeIsVisible = false;
+		while (it.hasNext())
+		{
+			EdgeViewI ev = (EdgeViewI) it.next();
+			if (ev.isVisible())
+			{
+				nodeIsVisible = true;
+				break;
+			}
+		}
+		if (nodeIsVisible)
+		{
+		  n.setUserHidden(false);
+		  n.setJnetShow(true);
+		}
+	  }
+	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide All Nodes");	  
+  }
+  
+  
+ /**
+  * Hides node based on nodename
+  * @param nodeName
+  */
+ public void hideNode(String nodeName)
+ {
+	  GraphEltSet graph = GraphEltSet.getCurrentGraph();
+	  EdgeFilterState edgeFilter = EdgeFilterState.inst();	  
+	  NBNode gnode = graph.findNodeByName(nodeName); // must use primary name for find - no systematic id in jmol object
+	  //GraphViewI graphData = GraphViewManager.current();
+	  NodeViewI nodeView = this.getByNodeId(gnode.getID()); // is node number id - is node name sufficient
+	  // edges first
+	  Iterable<EdgeViewI> edges = nodeView.getEdges();
+	  Iterator it = edges.iterator();
+	  while (it.hasNext())
+	  {
+	    EdgeViewI edge = (EdgeViewI) it.next(); 
+	    if (edgeFilter.hasEdge(edge))
+	      edge.setUserHidden(true);
+	      edge.setVisible(false);
+	    
+	  }
+	  
+	  // this iteration is to find nodes that are now orphaned by hiding of selected hidden node and not display them
+	  // if we ever change default behavior for this, then we would comment out this loop and just set the user hidden below
+	  // nodeView.setUserHidden(true);
+	  for (NodeViewI n : this.getNodeViews()) 
+	  {
+		  	  
+		Iterable<EdgeViewI> nedges = n.getEdges();  
+	    it = nedges.iterator(); // reset
+        boolean nodeIsVisible = false;
+        while (it.hasNext())
+	    {
+	      EdgeViewI ev = (EdgeViewI) it.next();
+		  if (ev.isVisible())
+		  {
+		    nodeIsVisible = true;
+		    break;
+	      }
+		  
+        }	  
+	  
+        if (!nodeIsVisible)
+        {
+          if (n.getID().equals(nodeView.getID())) // if node we are hiding set user hidden
+          {
+             n.setUserHidden(true);
+             n.setJnetShow(false);
+          }
+          else
+        	 n.setJnetShow(false); // don't show node but not user-hidden
+          
+        }
+          //n.setJnetShow(false); // don't show node        
+	  } // for
+	  //viewer.refresh(3, "Hide Node"); // refresh - not optimal   
+      JnetManager.inst().getJnetViewer().refresh(3, "Hide Node");	 
+ }  
+  
 }
 
 

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java	2010-03-23 14:11:19 UTC (rev 22868)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java	2010-03-23 15:27:08 UTC (rev 22869)
@@ -72,15 +72,23 @@
     _fz = 0;
   }
 
+  /**
+   * returns whether node is hidden directly by user
+   * @return value of user-directed hidden field property
+   */  
   public boolean isUserHidden()
   {
 	  return userHidden;
   }
-  
+
+  /**
+   * sets value of user-directed hidden field.
+   * @param isHidden
+   */  
   public void setUserHidden(boolean isHidden)
   {
 	  userHidden = isHidden;
-	  setJnetShow(!isHidden);
+	  //setJnetShow(!isHidden);
   }  
   
   public boolean matchesAttributePostfixString(String userPostfix, String attrCategory) {


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Revision: 22879
          http://gmod.svn.sourceforge.net/gmod/?rev=22879&view=rev
Author:   montys9
Date:     2010-03-24 13:49:56 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------
Added GoosePanel interface which is part of org.systemsbiology.gaggle.core to Nbrowse.  This is how we will import funcassociate and nbrowse goose panel.

Added Paths:
-----------
    nbrowse/trunk/src/org/systemsbiology/
    nbrowse/trunk/src/org/systemsbiology/gaggle/
    nbrowse/trunk/src/org/systemsbiology/gaggle/core/
    nbrowse/trunk/src/org/systemsbiology/gaggle/core/GoosePanel.java

Added: nbrowse/trunk/src/org/systemsbiology/gaggle/core/GoosePanel.java
===================================================================
--- nbrowse/trunk/src/org/systemsbiology/gaggle/core/GoosePanel.java	                        (rev 0)
+++ nbrowse/trunk/src/org/systemsbiology/gaggle/core/GoosePanel.java	2010-03-24 13:49:56 UTC (rev 22879)
@@ -0,0 +1,29 @@
+package org.systemsbiology.gaggle.core;
+
+import javax.swing.JPanel;
+
+// actually dont need to import as will be in same package!
+//import org.systemsbiology.gaggle.core.Goose;
+
+public interface GoosePanel extends Goose {
+  
+  /**
+   * @return true if Goose actually provides a (default) panel */
+  public boolean hasPanel();
+
+  /**
+   *  @return default panel of goose, null if doesnt have panel.
+   * for example for FuncAssoc goose will return default QueryPanel */
+  public JPanel getPanel();
+
+  // Future - when we want to get a hold of more than one panel, eg Query Paenel & ResultPanel
+  /** @param panelName name of panel to query if goose has  
+   * @return true if have a panel associated with name */
+  // public boolean hasPanel(String panelName);
+
+  /** @param panelName name of panel to return 
+      @return JPanel associated with name, null if no JPanel associated with name
+      for example for FuncAssoc might do getPanel("Query Panel") & getPanel("Results Panel") */
+  // public JPanel getPanel(String panelName);
+ 
+}
\ No newline at end of file


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Revision: 22972
          http://gmod.svn.sourceforge.net/gmod/?rev=22972&view=rev
Author:   montys9
Date:     2010-04-01 18:06:08 +0000 (Thu, 01 Apr 2010)

Log Message:
-----------
colors background using swatch now from toolbar. No longer just black and white.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-01 17:00:14 UTC (rev 22971)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-01 18:06:08 UTC (rev 22972)
@@ -998,6 +998,11 @@
   //Color oldColor = node.get
   
   Color oldColor =null;
+  GraphViewI graphData = GraphViewManager.current(); 
+  if (graphData instanceof GraphData)
+    oldColor = ((GraphData) graphData).getNodeColor(name);
+  else
+    return;
   
   Color c = JColorChooser.showDialog(
           viewer.getAwtComponent(),
@@ -1005,9 +1010,9 @@
  
   if (c == null)
 	  return;  
-  GraphViewI graphData = GraphViewManager.current(); 
-  if (graphData instanceof GraphData)
-    ((GraphData) graphData).colorNode(name, c);
+
+  //if (graphData instanceof GraphData)
+  ((GraphData) graphData).colorNode(name, c);
   
   // this version is if we wanted to set color without nodeview color storage
   //short colix = Colix3D.getColix(c.getRGB());

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-04-01 17:00:14 UTC (rev 22971)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-04-01 18:06:08 UTC (rev 22972)
@@ -758,6 +758,21 @@
   // the following methods are used in conjunction with jmol mouse manager in graph manipulation
   private StatusManager status() { return StatusManager.inst(); }
   
+  public Color getNodeColor(String nodeName)
+  {
+	Color currentColor = null;
+    for (NodeViewI n : this.getNodeViews())
+    {
+      if (n.getLabel().equals(nodeName)) // then color node using view
+	  {
+		 currentColor = n.getColor();
+		 break;
+	  }
+		    	  
+	}	  	  
+	return currentColor;  
+  }
+  
   /**
    * colors node specific coloring given a primary node name and color picked
    * @param nodeName

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-04-01 17:00:14 UTC (rev 22971)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-04-01 18:06:08 UTC (rev 22972)
@@ -242,12 +242,12 @@
         JButton bgButton = createButton(createIcon("images/bg.png"));        
         bgButton.addActionListener(new javax.swing.AbstractAction() {
             public void actionPerformed(java.awt.event.ActionEvent e) {
-            	//if (CommandLine.inst().useTestCode())
-            	//{
-            	//colorBackground();            	
-            	//}
-            	//else
-            	//{
+            	if (CommandLine.inst().useTestCode())
+            	{
+            	colorBackground();            	
+            	}
+            	else
+            	{
                 if(toggle == 1){
                     JnetPanel.viewer.evalString("background black;");
                     stepButtonBar.setBackground(Color.BLACK);
@@ -259,10 +259,11 @@
                     Navigation.viewer.evalString("background white;");
                     toggle = 1;
                 }
-            	//}
+            	}
             }
         });
-        bgButton.setToolTipText("toggle white/black background");
+        //bgButton.setToolTipText("toggle white/black background");
+        bgButton.setToolTipText("pick color for background");
         //if (CommandLine.inst().useTestCode()
         //  bgButton.setToolTipTExt("set background color");
         toolbar.add(bgButton);
@@ -402,6 +403,7 @@
   private void colorBackground()
   {
 	  Color oldColor =null;
+	  oldColor = stepButtonBar.getBackground();
 	  
 	  Color c = JColorChooser.showDialog(
 	          viewer().getAwtComponent(),
@@ -410,7 +412,13 @@
 	  if (c == null)
 	    return;
 	  short colix = Graphics3D.getColix(c);
-	  viewer().getGraphics3D().setBackgroundArgb(colix);	 	  
+	  int argb = viewer().getGraphics3D().getColixArgb(colix);
+	  viewer().getGraphics3D().setBackgroundArgb(argb);      
+      //viewer().colorManager.setColixBackgroundContrast(argb);	
+	  Navigation.inst().viewer.getGraphics3D().setBackgroundArgb(argb);
+	  //viewer().colorManager.setColixBackgroundContrast(argb);
+	  //displayPanel.setBackground(c);
+	  stepButtonBar.setBackground(c);
   }
 
   private class HoverBut implements ActionListener {


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Revision: 22995
          http://gmod.svn.sourceforge.net/gmod/?rev=22995&view=rev
Author:   montys9
Date:     2010-04-05 14:43:28 +0000 (Mon, 05 Apr 2010)

Log Message:
-----------
now has inclusive multi-selection for right click menu (except for expand which selects a single node for double-click).

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-05 03:52:31 UTC (rev 22994)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-05 14:43:28 UTC (rev 22995)
@@ -46,6 +46,7 @@
 import org.nbrowse.views.GraphViewI;
 import org.nbrowse.views.GraphViewManager;
 import org.nbrowse.views.JnetManager;
+import org.nbrowse.views.NBSelectionManager;
 import org.nbrowse.views.Navigation;
 import org.nbrowse.views.JnetPanel;
 import org.nbrowse.views.NodeViewI;
@@ -990,20 +991,26 @@
 
 private void colorNode(int nearestNodeIndex)
 {
-  if (nearestNodeIndex == -1)
+  if (nearestNodeIndex != -1)
+    selectNode(nearestNodeIndex);  
+  List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+  
+  if (nbNodes.isEmpty())
     return;
-  Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  	    
-  String name = node.getNodeName(); // get primary syn id 
+  //Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  
+  //String name = node.getNodeName(); // get primary syn id 
+  
   //DataLoader.inst().anchorNode(name); 
   //Color oldColor = node.get
   
   Color oldColor =null;
-  GraphViewI graphData = GraphViewManager.current(); 
-  if (graphData instanceof GraphData)
-    oldColor = ((GraphData) graphData).getNodeColor(name);
-  else
-    return;
+  GraphViewI graphData = GraphViewManager.current();
   
+  if (nbNodes.size() == 1)
+  {
+	oldColor = nbNodes.get(0).getColor();
+  }
+    
   Color c = JColorChooser.showDialog(
           viewer.getAwtComponent(),
           "Pick me !", oldColor);
@@ -1012,8 +1019,11 @@
 	  return;  
 
   //if (graphData instanceof GraphData)
-  ((GraphData) graphData).colorNode(name, c);
+  //((GraphData) graphData).colorNode(name, c);
+  if (graphData instanceof GraphData)
+    ((GraphData) graphData).colorNodes(nbNodes, c);
   
+  
   // this version is if we wanted to set color without nodeview color storage
   //short colix = Colix3D.getColix(c.getRGB());
   //node.setColixNode(colix); // setting color of node
@@ -1023,29 +1033,38 @@
 
 private void anchorNode(int nearestNodeIndex)
 {
-  if (nearestNodeIndex == -1)
+  if (nearestNodeIndex != -1)
+    selectNode(nearestNodeIndex);  
+  List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+  if (nbNodes.isEmpty())
     return;
-	
   //if (areNodesSelected())
   //	  System.out.println("selected nodes found");
 	  
-  Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  
-  String name = node.getNodeName(); // get primary node name
+  //Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  
+  //String name = node.getNodeName(); // get primary node name
   GraphViewI graphData = GraphViewManager.current(); 
   if (graphData instanceof GraphData)
-    ((GraphData) graphData).anchorNode(name);  
+    //((GraphData) graphData).anchorNode(name);  
+    ((GraphData) graphData).anchorNodes(nbNodes);    
   //DataLoader.inst().anchorNode(name);  
 }
 
 private void unanchorNode(int nearestNodeIndex)
 {
-  if (nearestNodeIndex == -1)
+  if (nearestNodeIndex != -1)
+    selectNode(nearestNodeIndex);  
+  List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+  if (nbNodes.isEmpty())
     return;
-  Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  	    
-  String name = node.getNodeName(); // get primary node name
+  
+  //Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);  	    
+  //String name = node.getNodeName(); // get primary node name
   GraphViewI graphData = GraphViewManager.current(); 
   if (graphData instanceof GraphData)
-    ((GraphData) graphData).unanchorNode(name);  
+    //((GraphData) graphData).unanchorNode(name);
+    ((GraphData) graphData).unanchorNodes(nbNodes);  
+  
   //DataLoader.inst().unanchorNode(name);    
 }
 
@@ -1055,14 +1074,18 @@
  */
 private void unhideNode(int nearestNodeIndex)
 {
-  if (nearestNodeIndex == -1)
+  if (nearestNodeIndex != -1)
+    selectNode(nearestNodeIndex);  
+  List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+  if (nbNodes.isEmpty())
     return;
   
-  Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);
-  String name = node.getNodeName(); // get primary node name
+  //Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);
+  //String name = node.getNodeName(); // get primary node name
   GraphViewI graphData = GraphViewManager.current(); 
   if (graphData instanceof GraphData)
-    ((GraphData) graphData).unhideNode(name);  
+    //((GraphData) graphData).unhideNode(name);  
+    ((GraphData) graphData).unhideNodes(nbNodes);   
   //DataLoader.inst().unhideNode(name);
 }
 
@@ -1070,8 +1093,11 @@
  * This can be used to get an array of jnet Nodes that are currently selected
  * @return
  */
-private ArrayList getSelectionList()
+private List<NodeViewI> getSelectionList()
 {
+	List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+	
+	/*
 	ArrayList list = new ArrayList(); // used to get array of nodes that are selected-MS
 	// this code can be used to find out what is selected
 	Node[] nodes = viewer.getModelSet().getNodes();
@@ -1082,7 +1108,9 @@
       if (viewer.isSelected(nodeIndex))
 		list.add(currNode);	
 	}
-	return list;		
+	return list;
+	*/
+	return nbNodes;
 }
 
 /**
@@ -1093,8 +1121,11 @@
   // get current node and hide it
   //System.out.println("hide node");
   
-  if (nearestNodeIndex == -1)
-  return;
+  if (nearestNodeIndex != -1)
+    selectNode(nearestNodeIndex);  
+  List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+  if (nbNodes.isEmpty())
+    return;
   
   /* the commented out code below hides using Model-node and edge - re-did using NodeView and EdgeView objects*/
   /*
@@ -1105,14 +1136,14 @@
     edges[i_index].setVisible(false);
   viewer.repaintView(); // refresh - not optimal 
   */  
-  Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);
-  //this.selectNode(nearestNodeIndex);
-   
-  String name = node.getNodeName(); // get systematic id
+  
+  //Node node = viewer.getModelSet().getNodeAt(nearestNodeIndex);    
+  //String name = node.getNodeName(); // get systematic id
 
   GraphViewI graphData = GraphViewManager.current(); 
   if (graphData instanceof GraphData)
-    ((GraphData) graphData).hideNode(name);  
+    //((GraphData) graphData).hideNode(name);  
+    ((GraphData) graphData).hideNodes(nbNodes);
   //DataLoader.inst().hideNode(name); 
   return;
   
@@ -1470,8 +1501,21 @@
    an exclusive selection - more common case - can add appending if need be*/
   private void selectNodeNeighborhood(int nodeIndex) {
     if (!viewer.selectionEnabled()) return; // no sel for nav
-    viewer.clearSelection(); // exclusive select
-    if (nodeIndex==-1) return; // no node selected
+
+    // select for mult-select
+    if (nodeIndex != -1)
+        selectNode(nodeIndex);  
+    List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+    if (nbNodes.isEmpty())
+      return;    
+    
+    
+    // modified version now selects node neighborhood inclusive with current selection   
+    // the following 2 lines have been commented out for multi-selection
+    //viewer.clearSelection(); // exclusive select
+    //if (nodeIndex==-1) return; // no node selected
+    
+    
 //    if (viewer.getSelectionCount() == viewer.getNodeCount()) { // this shouldnt be needed anymore?
 //      viewer.clearSelection();
 //      Navigation.viewer.clearSelection();
@@ -1479,7 +1523,12 @@
     //viewer.loadShape(JnetConstants.SHAPE_HALOS);//only needs to happen once
     //viewer.setShapeProperty(JnetConstants.SHAPE_HALOS, "selectWithNeighbours",
       //new Integer(nodeIndex));
-    viewer.selectNodeNeighbors(nodeIndex);
+    
+    // no longer do single neighbor select - now multi
+    //viewer.selectNodeNeighbors(nodeIndex);
+    viewer.selectNodeNeighbors(nbNodes);
+    
+    
     if (viewer.getSelectionSet() != null) {
       viewer.addFinalSelection(viewer.getSelectionSet());
       Navigation.viewer.addFinalSelection(viewer.getSelectionSet());

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-04-05 03:52:31 UTC (rev 22994)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-04-05 14:43:28 UTC (rev 22995)
@@ -106,7 +106,9 @@
  */
 import org.jnet.adapter.smarter.Resolver;
 import org.jnet.shape.Hover;
+import org.nbrowse.views.NBSelectionManager;
 import org.nbrowse.views.Navigation;
+import org.nbrowse.views.NodeViewI;
 
 /** Viewer and JnetViewer should maybe have their names switched? */
 public class Viewer extends JnetViewer implements NodeDataServer, Serializable {
@@ -1837,6 +1839,36 @@
 
   /** select node and all nodes attached to it, migrated from Halos.setProp
    * of all places
+   */  
+  void selectNodeNeighbors(List<NodeViewI> nodeViews)
+  {
+    for (NodeViewI n : nodeViews)  
+    {
+      Node root = n.getJnetNode();      
+      if (root == null) // if something wrong continue
+        continue;
+      int nodeIndex = root.getNodeIndex();
+	  for (int i = 0; i < root.getEdges().length; i++) 
+	  {
+	    if (root.getEdges()[i].getShapeVisibilityFlags() != 0) 
+	    {
+	      if (root.getEdges()[i].getNodeIndex1() != nodeIndex) 
+	      {
+	        if (root.getEdges()[i].getNode1().isVisible())
+	          addSelection(root.getEdges()[i].getNodeIndex1());
+	      } 
+	      else 
+	      {
+	        if (root.getEdges()[i].getNode2().isVisible())
+	          addSelection(root.getEdges()[i].getNodeIndex2());
+	      }
+	    }
+	  }
+    }
+  }
+  
+  /** select node and all nodes attached to it, migrated from Halos.setProp
+   * of all places
    * @param nodeIndex node to sel neighbors of
    */
   void selectNodeNeighbors(int nodeIndex) {

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-04-05 03:52:31 UTC (rev 22994)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-04-05 14:43:28 UTC (rev 22995)
@@ -757,7 +757,12 @@
   
   // the following methods are used in conjunction with jmol mouse manager in graph manipulation
   private StatusManager status() { return StatusManager.inst(); }
-  
+    
+  /**
+   * This is one version of getting color - unique node names in graph
+   * @param nodeName
+   * @return
+   */
   public Color getNodeColor(String nodeName)
   {
 	Color currentColor = null;
@@ -772,9 +777,23 @@
 	}	  	  
 	return currentColor;  
   }
+
+ /**
+  * Used to iterate over a list of nodes to color them
+  * @param nodeViews
+  * @param color
+  */
+ public void colorNodes(List<NodeViewI> nodeViews, Color color)
+ {
+   for (NodeViewI n : nodeViews)
+   {
+     n.setColor(color);
+   }
+ }
   
   /**
-   * colors node specific coloring given a primary node name and color picked
+   * Colors node specific coloring given a primary node name and color picked.
+   * This method assumes node names in graph are unique
    * @param nodeName
    * @param color
    */
@@ -866,8 +885,21 @@
 	JnetManager.inst().doLayout(false, true);	
   }
   
+  
   /**
-   * Used to anchor a node.
+   * Used now to anchor list of nodes
+   * @param nodeViews
+   */
+  public void anchorNodes(List<NodeViewI> nodeViews)
+  {   
+    for (NodeViewI n: nodeViews)
+    {
+      n.setDoLayout(false);
+    }
+  }
+  
+  /**
+   * Used to anchor a single node using node name 
    * @param nodeName
    */
   public void anchorNode(String nodeName)
@@ -888,6 +920,18 @@
   }
 
   /**
+   * Used now to unanchor list of nodes
+   * @param nodeViews
+   */
+  public void unanchorNodes(List<NodeViewI> nodeViews)
+  {   
+    for (NodeViewI n: nodeViews)
+    {
+      n.setDoLayout(true);
+    }
+  }
+  
+  /**
    * Unanchors a node and does a regular layout.
    * @param nodeName
    */
@@ -986,8 +1030,113 @@
 	  }
 	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide All Nodes");	  
   }
+
+  public void unhideNodes(List<NodeViewI> nodeViews)
+  {
+	  //GraphViewI graphData = GraphViewManager.current();
+	  EdgeFilterState edgeFilter = EdgeFilterState.inst();
+	  for (NodeViewI n : nodeViews) 
+	  {
+	    Iterable<EdgeViewI> edges = n.getEdges();
+		Iterator it = edges.iterator();
+		while (it.hasNext())
+		{
+		  EdgeViewI edge = (EdgeViewI) it.next(); 
+		  if (edgeFilter.hasEdge(edge)) 
+		  {	
+		   edge.setUserHidden(false);
+		   edge.setVisible(true); // edge is being shown (doesnt create jnet)		    		    
+		  }			
+		  else // if filter does not have edge, we at least set no longer user hidden only
+		  {
+			  edge.setUserHidden(false);  
+		  }
+		  //n.setJnetShow(true); // don't show node		    
+		  
+		} // while
+	    it = edges.iterator(); // reset
+		boolean nodeIsVisible = false;
+		while (it.hasNext())
+		{
+			EdgeViewI ev = (EdgeViewI) it.next();
+			if (ev.isVisible())
+			{
+				nodeIsVisible = true;
+				break;
+			}
+		}
+		if (nodeIsVisible)
+		{
+		  n.setUserHidden(false);
+		  n.setJnetShow(true);
+		}
+	  }
+	  JnetManager.inst().getJnetViewer().refresh(3, "Unhide Nodes");	  
+  }
   
+private void hideOrphanNodes(NodeViewI nodeView)
+{
+  // this iteration is to find nodes that are now orphaned by hiding of selected hidden node and not display them
+  // if we ever change default behavior for this, then we would comment out this loop and just set the user hidden below
+  // nodeView.setUserHidden(true);
+  	
+  for (NodeViewI n : this.getNodeViews()) 
+  {
+		  	  
+    Iterable<EdgeViewI> nedges = n.getEdges();  
+    Iterator it = nedges.iterator(); // reset
+    boolean nodeIsVisible = false;
+    while (it.hasNext())
+    {
+      EdgeViewI ev = (EdgeViewI) it.next();
+      if (ev.isVisible())
+  	  {
+	    nodeIsVisible = true;
+	    break;
+	  } // if
+		  
+    } // while	  
+	  
+    if (!nodeIsVisible)
+    {
+      if (n.getID().equals(nodeView.getID())) // if node we are hiding set user hidden
+      {
+        n.setUserHidden(true);
+        n.setJnetShow(false);
+      }
+      else
+        n.setJnetShow(false); // don't show node but not user-hidden
+        
+    }
+        //n.setJnetShow(false); // don't show node        
+  } // for	
+}
   
+ public void hideNodes(List<NodeViewI> nodeViews)
+ {
+   EdgeFilterState edgeFilter = EdgeFilterState.inst();
+   for (NodeViewI n: nodeViews)
+   {
+     // edges first
+	 Iterable<EdgeViewI> edges = n.getEdges();
+	 Iterator it = edges.iterator();
+     while (it.hasNext())
+	 {
+	   EdgeViewI edge = (EdgeViewI) it.next(); 
+	   if (edgeFilter.hasEdge(edge))
+	   {
+	     edge.setUserHidden(true);
+		 edge.setVisible(false);
+	   }   
+	 } // while
+     hideOrphanNodes(n);
+   } // for
+   
+	  //viewer.refresh(3, "Hide Node"); // refresh - not optimal   
+   JnetManager.inst().getJnetViewer().refresh(3, "Hide Nodes");	   
+ }
+
+ 
  /**
   * Hides node based on nodename
   * @param nodeName
@@ -1010,40 +1159,8 @@
 	      edge.setVisible(false);
 	    
 	  }
-	  
-	  // this iteration is to find nodes that are now orphaned by hiding of selected hidden node and not display them
-	  // if we ever change default behavior for this, then we would comment out this loop and just set the user hidden below
-	  // nodeView.setUserHidden(true);
-	  for (NodeViewI n : this.getNodeViews()) 
-	  {
-		  	  
-		Iterable<EdgeViewI> nedges = n.getEdges();  
-	    it = nedges.iterator(); // reset
-        boolean nodeIsVisible = false;
-        while (it.hasNext())
-	    {
-	      EdgeViewI ev = (EdgeViewI) it.next();
-		  if (ev.isVisible())
-		  {
-		    nodeIsVisible = true;
-		    break;
-	      }
-		  
-        }	  
-	  
-        if (!nodeIsVisible)
-        {
-          if (n.getID().equals(nodeView.getID())) // if node we are hiding set user hidden
-          {
-             n.setUserHidden(true);
-             n.setJnetShow(false);
-          }
-          else
-        	 n.setJnetShow(false); // don't show node but not user-hidden
-          
-        }
-          //n.setJnetShow(false); // don't show node        
-	  } // for
+	  hideOrphanNodes(nodeView);
+
 	  //viewer.refresh(3, "Hide Node"); // refresh - not optimal   
       JnetManager.inst().getJnetViewer().refresh(3, "Hide Node");	 
  }  


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 23062
          http://gmod.svn.sourceforge.net/gmod/?rev=23062&view=rev
Author:   montys9
Date:     2010-04-19 19:53:41 +0000 (Mon, 19 Apr 2010)

Log Message:
-----------
Infonode updated to return jnet/jmol view for manipulation (work in progress to ensure showing of graph after deserialization).
Added commented out code to access viewer and JnetManager after deserialization for trying to ensure showing of graph.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-04-19 16:22:09 UTC (rev 23061)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-04-19 19:53:41 UTC (rev 23062)
@@ -24,6 +24,9 @@
 package org.jnet.viewer;
 
 import java.util.logging.Level;
+
+import net.infonode.docking.DockingWindow;
+
 import org.jnet.shape.Shape;
 import org.jnet.shape.Sticks;
 import org.jnet.i18n.GT;
@@ -53,10 +56,12 @@
 import org.jnet.shape.Text;
 
 import java.awt.Cursor;
+import java.awt.Frame;
 import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Dimension;
 import java.awt.MediaTracker;
+import java.awt.Point;
 import java.awt.Rectangle;
 import java.awt.Component;
 import java.awt.Event;
@@ -67,6 +72,8 @@
 import java.util.Properties;
 import java.util.Vector;
 import java.util.Random;
+
+import javax.swing.JFrame;
 import javax.vecmath.Point3f;
 import javax.vecmath.Vector3f;
 import javax.vecmath.Point4f;
@@ -106,6 +113,10 @@
  */
 import org.jnet.adapter.smarter.Resolver;
 import org.jnet.shape.Hover;
+import org.nbrowse.NBrowseApplet;
+import org.nbrowse.io.DataLoader;
+import org.nbrowse.views.InfoNodeMan;
+import org.nbrowse.views.Jnet;
 import org.nbrowse.views.NBSelectionManager;
 import org.nbrowse.views.Navigation;
 import org.nbrowse.views.NodeViewI;
@@ -196,6 +207,85 @@
   private transient boolean useDefaultNodeSize=false; // currently only used in edge filtering - is set and then turned off
   
   /**
+   * added to update serialized view for viewability
+   */
+  public void revalidateDisplay()
+  {	
+
+	  // need to change size of window to guarantee deserialization is always displayed
+	  /*
+	  DockingWindow win = InfoNodeMan.inst().getJnetWin();
+	  win.setVisible(false);
+	  //win.undock(new Point(0,0));
+      win.makeVisible();
+      win.maximize();
+      win.setVisible(true);      
+      win.restore();
+      */
+      
+	  //win.restore();
+	  //win.dock();
+	  //InfoNodeMan.inst().getRootWindow().restore();
+	  
+	  //Jnet.jnetPanel.setVisible(false);
+	  //Jnet.jnetPanel.revalidate();
+	  //Jnet.jnetPanel.repaint();
+	  //Jnet.jnetPanel.setVisible(true);
+	  //display.getParent().setVisible(true);
+	  
+	  //InfoNodeMan.inst().getRootWindow().revalidate();
+	  //InfoNodeMan.inst().getRootWindow().repaint();
+	  
+	  //Jnet.jnetPanel.validate();
+	  //Jnet.jnetPanel.setVisible(true);
+      //display.setVisible(false);
+      //display.invalidate();
+      //display.setVisible(true);
+      
+	  //InfoNodeMan.inst().getRootWindow().getRootPane().revalidate();
+	  //InfoNodeMan.inst().getRootWindow().getRootPane().repaint();
+	  //InfoNodeMan.inst().getRootWindow().getRootPane().setVisible(true);
+      
+	  //InfoNodeMan.inst().getRootWindow().repaint();
+	  //InfoNodeMan.inst().getRootWindow().setVisible(true);
+	  //display.getParent().validate(); 
+	  //display.getParent().repaint(); 
+      //InfoNodeMan.inst().getRootWindow().validate();
+      //InfoNodeMan.inst().getRootWindow().repaint();
+	  //InfoNodeMan.inst().getRootWindow().getParent().validate();
+	  //InfoNodeMan.inst().getRootWindow().getParent().repaint();
+	  //InfoNodeMan.inst().setDefaultLayout();
+	  //NBrowseApplet.inst().invalidate();
+	  //NBrowseApplet.inst().repaint();
+	  
+	  
+	//display.getParent().invalidate();
+	//display.getParent().validate();
+	//display.getParent().repaint();
+	
+	//popHoldRepaint();
+    //Frame frame = DataLoader.inst().getParentFrame();
+    //frame.invalidate();
+    //frame.validate();
+    //frame.setVisible(true);
+	//setTainted(true);
+	//requestRepaintAndWait();
+	//homePosition(); // try
+	  
+	
+	//reset();
+	//display.invalidate();	  
+	//display.doLayout();
+	//display.invalidate();
+	//display.repaint();	 
+	//display.setSize(display.getSize()); // resize
+	//display.setVisible(true);
+
+	
+	//display.validate();  
+  }
+  
+  /**
    * This is used for setting to use the defaultNodeSize attribute - used specifically in edge filtering 
    *
    * @param useNodeSize

Modified: nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java	2010-04-19 16:22:09 UTC (rev 23061)
+++ nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java	2010-04-19 19:53:41 UTC (rev 23062)
@@ -560,6 +560,9 @@
     // don't add Navigation - Birds eye view
     //windowBar.addTab(navWin());
   }
+  
+  public DockingWindow getJnetWin() { return views.get(0); }
+  
   // original goWin was at position 6 when Navigation (birds eye view) was used
   private DockingWindow goWin() { return views.get(5); } // presumptious! 
   

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-04-19 16:22:09 UTC (rev 23061)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-04-19 19:53:41 UTC (rev 23062)
@@ -1,6 +1,7 @@
 package org.nbrowse.views;
 
 import java.awt.Color;
+import java.awt.Graphics;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.io.Serializable;
@@ -772,6 +773,9 @@
     float zoomPercent = this.getJnetViewer().getZoomPercentFloat();
     float zoomPercentSetting = this.getJnetViewer().getZoomPercentSettingFloat();
     float zoomRatio = this.getJnetViewer().getZoomRatioFloat();
+    
+
+    
   // try readding datasets to NBEdge objects
   /*
   GraphEltSet graphEltSet = GraphEltSet.getCurrentGraph();
@@ -946,6 +950,22 @@
     StatusManager.inst().normal();
     
     
+// try this for guarantee see graph without using sizing of infonodes
+    //getJnetViewer().revalidateDisplay();
+  
+    //getJnetViewer().haltScriptExecution();
+    //getJnetViewer().resumeScriptExecution();
+    //String script = "refresh;";
+    //getJnetViewer().script(script);
+    
+    //jnet.getParent().setVisible(false);
+    //jnet.getParent().invalidate();
+    //jnet.getParent().setVisible(true);
+    //jnet.invalidate();
+    //jnet.update(jnet.getGraphics());
+    //jnet.repaint();
+    //jnet.doLayout();
+    
     //StatusManager.inst().layoutDone(); // layout already done see about this in pure raw mode - TRY again-ensure
     //int step = 2; // need to utilize number of steps last expanded to re-add steps.
     


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Revision: 23070
          http://gmod.svn.sourceforge.net/gmod/?rev=23070&view=rev
Author:   montys9
Date:     2010-04-20 19:21:00 +0000 (Tue, 20 Apr 2010)

Log Message:
-----------
Updated commented out code for viewer and JnetManager in trying to prevent need for when graph doesn't display when loading serialized file to use workaround of fiddling with split pane sizer or undocking.
Updated commented out code in session converter to try to set nodeview objs that don't have jnet nodes from old serialized file to be set to hide.  However, this is not enough to fix this.
EdgeFilter State and and EdgeFilterGui are updated so that the cutoff values are displayed when loading from serialized file.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java
    nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterTypeGui.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-04-20 16:36:19 UTC (rev 23069)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-04-20 19:21:00 UTC (rev 23070)
@@ -26,6 +26,8 @@
 import java.util.logging.Level;
 
 import net.infonode.docking.DockingWindow;
+import net.infonode.docking.RootWindow;
+import net.infonode.docking.SplitWindow;
 
 import org.jnet.shape.Shape;
 import org.jnet.shape.Sticks;
@@ -211,10 +213,33 @@
    */
   public void revalidateDisplay()
   {	
-
+      
 	  // need to change size of window to guarantee deserialization is always displayed
+	  //SplitWindow sp = InfoNodeMan.inst().getSplitWindow();
+	  //sp.setDividerLocation(0);
+	  
 	  /*
 	  DockingWindow win = InfoNodeMan.inst().getJnetWin();
+	  RootWindow rwin = InfoNodeMan.inst().getRootWindow();
+	 // win.setVisible(false);
+	  win.undock(new Point(0,0));
+      rwin.revalidate();
+      rwin.repaint();
+      win.dock();
+      */
+	  
+	  //win.getToolkit().sync();
+	  //rwin.getToolkit().sync();
+	  //rwin.removeAll();
+	  
+	  //rwin.makeVisible();
+	  //InfoNodeMan.inst().createRootWindow();
+	  //InfoNodeMan.inst().setDefaultLayout();	
+	  //rwin.replaceChildWindow(win, win);
+	  //InfoNodeMan.inst().createRootWindow();
+	  //InfoNodeMan.inst().setDefaultLayout();
+	  
+	  /*
 	  win.setVisible(false);
 	  //win.undock(new Point(0,0));
       win.makeVisible();

Modified: nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java	2010-04-20 16:36:19 UTC (rev 23069)
+++ nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java	2010-04-20 19:21:00 UTC (rev 23070)
@@ -369,8 +369,7 @@
 		{
 			Iterable<NBEdge> nedges = node.getEdges();
 		    Iterator<NBEdge> nit = nedges.iterator();
-		    
-		    
+		    		    
 		    while (nit.hasNext())
 		    {
 		    	NBEdge nbedge = nit.next();
@@ -530,6 +529,14 @@
 		HashMap  nvMap = new HashMap();
 		for (NodeViewI gnode : gnodes)
 		{
+			
+		  // check nodeview for having jnet connection - if not - make hidden
+		  /* 	
+		  if (!gnode.hasJnetNodeIndex())
+			//gnode.setJnetShow(false);
+		    gnode.setNbrowseShow(false);		   
+		 */
+			
 		  Iterable<EdgeViewI> gnedges = gnode.getEdges();
 		  Iterator<EdgeViewI> gnit = gnedges.iterator();
 		  dcurrentindex = 0;

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-04-20 16:36:19 UTC (rev 23069)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-04-20 19:21:00 UTC (rev 23070)
@@ -18,6 +18,8 @@
 import javax.swing.JToolBar;
 import javax.vecmath.Point3f;
 
+import net.infonode.docking.DockingWindow;
+
 import org.jnet.util.Escape;
 import org.jnet.viewer.Viewer;
 import org.jnet.modelset.Edge;
@@ -952,7 +954,7 @@
     
 // try this for guarantee see graph without using sizing of infonodes
     //getJnetViewer().revalidateDisplay();
-  
+    
     //getJnetViewer().haltScriptExecution();
     //getJnetViewer().resumeScriptExecution();
     //String script = "refresh;";
@@ -1130,9 +1132,11 @@
         getJnetViewer().clearNodeInfoHoverShape();// clear out hover shape for realloc with new model
         getJnetStepButtonBar().removeAll(); // TRY THIS here
         //StatusManager.inst().metaDataChanged(); // try this first
-    	  loadSerialData(); // will invoke from serialized binary data  
+    	  loadSerialData(); // will invoke from serialized binary data
+
       	String msg = "Session File Is Loaded";
     	JOptionPane.showMessageDialog(JnetManager.inst().getJnetViewer().getAwtComponent(),"Session Loaded",msg,JOptionPane.INFORMATION_MESSAGE);;
+    	
       }
       else if (e.expansionLoaded()) {
         getJnetViewer().clearNodeInfoHoverShape();// clear out hover shape for realloc with new model

Modified: nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-04-20 16:36:19 UTC (rev 23069)
+++ nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterState.java	2010-04-20 19:21:00 UTC (rev 23070)
@@ -235,10 +235,21 @@
   }
 
  
-  private boolean hasFilterForMeta(EdgeDataSetMetaData datasetMeta) {
+  /**
+   * This is made available public for EdgeFilterType GUI for default value
+   * @param datasetMeta
+   * @return
+   */
+  public boolean hasFilterForMeta(EdgeDataSetMetaData datasetMeta) {
     return getFilter(datasetMeta)!=null;
   }
-  private DatasetFilter getFilter(EdgeDataSetMetaData datasetMeta) {
+  
+  /**
+   * This is made available public for EdgeFilterType GUI for default value
+   * @param datasetMeta
+   * @return
+   */  
+  public DatasetFilter getFilter(EdgeDataSetMetaData datasetMeta) {
     for (DatasetFilter df : filters)
       if (df.has(datasetMeta)) return df;
     return null; // shouldnt happen
@@ -437,7 +448,15 @@
     }
 
     private void setShow(boolean b) { show = b; }
-    private double getCutoff() { return cutoff; }
+    
+    
+    // used for edge filter type gui
+    public boolean hasCutoff() {return hasCutoff;};
+    
+    //private double getCutoff() { return cutoff; }
+    // available for edge filter type gui
+    public double getCutoff() { return cutoff; }
+    
     private void setCutoff(double d) {
       hasCutoff = true;
       cutoff = d;

Modified: nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterTypeGui.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterTypeGui.java	2010-04-20 16:36:19 UTC (rev 23069)
+++ nbrowse/trunk/src/org/nbrowse/views/edgecontrol/EdgeFilterTypeGui.java	2010-04-20 19:21:00 UTC (rev 23070)
@@ -33,6 +33,7 @@
 import org.nbrowse.dataset.EdgeDataSetMetaData;
 import org.nbrowse.io.UrlManager;
 import org.nbrowse.views.ColorManager;
+import org.nbrowse.views.edgecontrol.EdgeFilterState.DatasetFilter;
 
 /**
  * This is a tree branch in the EdgeFilter viewer, a line for each edge type
@@ -292,6 +293,19 @@
       public void actionPerformed(ActionEvent e) {
         setDatasetCutoff(datasetMeta, txtFld.getText()); } });
 
+    // place for code to set default dataset cutoff values if any for txtFld  
+    // this seems to work.
+    if (filterState().hasFilterForMeta(datasetMeta))
+    {
+      DatasetFilter filter = filterState().getFilter(datasetMeta);
+      if (filter.hasCutoff())
+      {
+    	  double val = filter.getCutoff();
+    	  txtFld.setText(String.valueOf(val));
+      }
+      
+    }
+    
     // SLIDER (scrollbar)
     // slider works with integers, so mult & div by 100 for needed decimal #s
     final int tempMin = (int) (dsaMin * 100);


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Revision: 23080
          http://gmod.svn.sourceforge.net/gmod/?rev=23080&view=rev
Author:   montys9
Date:     2010-04-22 14:55:10 +0000 (Thu, 22 Apr 2010)

Log Message:
-----------
Updated edgeview to fix hide bug where if move away from gui and come back, edges can appear without node.
Also updated to reshow nodes upon expansion.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-22 14:45:10 UTC (rev 23079)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-22 14:55:10 UTC (rev 23080)
@@ -1184,6 +1184,11 @@
 private void expandNode(int nearestNodeIndex)
 {
   if (nearestNodeIndex > -1) {
+	  
+	GraphViewI graphData = GraphViewManager.current(); 
+	if (graphData instanceof GraphData)
+	  ((GraphData) graphData).unhideAllNodes();   // unhide all nodes before expansion 	- this is needed now  
+
     // jnet only has nmes, eventually will have ids as well
     String nodeName = viewer.getNodeName(nearestNodeIndex);
     ErrorUtil.debug(this, "MouseMan get expand click for "+nodeName);

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-04-22 14:45:10 UTC (rev 23079)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-04-22 14:55:10 UTC (rev 23080)
@@ -220,15 +220,19 @@
   /** set internal isVisible state, set jnet isVisible state if jnet exists
    * @param isVisible true shoe, false hide */
   public void setVisible(boolean isVisible) {
-    this.isVisible = isVisible;
+	  
+	if (userHidden) // if user hidden - we need to really clear this flag first before anything else
+	  this.isVisible = false;
+	else
+      this.isVisible = isVisible;
     // if being shown for 1st time jnet edge may not exist
     // actually cant do here as needed nodes may not exist yet
     // see JNetManager.filterChanged
     //if (jnetEdge == null) createJnetEdge();
     if (jnetEdge!=null)
-      jnetEdge.setShapeVisConstant(JnetConstants.SHAPE_STICKS, isVisible);
+      jnetEdge.setShapeVisConstant(JnetConstants.SHAPE_STICKS, this.isVisible);
     if (jnetNavigatorEdge!=null)
-      jnetNavigatorEdge.setShapeVisConstant(JnetConstants.SHAPE_STICKS, isVisible);
+      jnetNavigatorEdge.setShapeVisConstant(JnetConstants.SHAPE_STICKS, this.isVisible);
     //else ErrorUtil.error(this, "EdgeView lacks jnet edge! "+this);
     // jnetNavigatorEdge
   }


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Revision: 23092
          http://gmod.svn.sourceforge.net/gmod/?rev=23092&view=rev
Author:   montys9
Date:     2010-04-26 16:07:39 +0000 (Mon, 26 Apr 2010)

Log Message:
-----------
Updated NodeInfoMaker and GraphData to query jnet node index via visible nodes - since invisible nodes may not have jnet nodes to query.
Updated MouseManager to use control left click to be same as right click for right-click menu.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-23 20:22:31 UTC (rev 23091)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-04-26 16:07:39 UTC (rev 23092)
@@ -829,10 +829,10 @@
               //{
               //  if (!b_isOnNode)
               //    return;
-             // }
+              // }
               //else
-             // {
-             //   if (nearestNodeIndex!=-1) return;
+              // {
+              //   if (nearestNodeIndex!=-1) return;
               //}
               if (nearestNodeIndex!=-1) return; // this is not for nodes but for edges, etc.
               //if (b_isOnNode)
@@ -844,8 +844,8 @@
             	  this.leftClick(/*nearestNodeIndex,*/ x, y, modifiers); // nearestPoint        	  
               break;
             
-            // SHIFT LEFT 
-            // whitespace -> center on selected nodes if any
+              // SHIFT LEFT 
+              // whitespace -> center on selected nodes if any
             case SHIFT_LEFT:
               shiftLeftClick(nearestNodeIndex);
               return;
@@ -856,29 +856,33 @@
               //popupMenu.show(viewer.getAwtComponent(), x, y);
               return;
 
+            case CTRL_LEFT: // same as right click menu
+              showPopup(viewer.getAwtComponent(), x, y, nearestNodeIndex); // this will use the correct version of popup based on java level
+              return;
+            	
             case ALT_LEFT: // new get neighbors instead of right click
-            	selectNodeNeighborhood(nearestNodeIndex);            	
-            	return;
+              selectNodeNeighborhood(nearestNodeIndex);            	
+              return;
             
             case SHIFT_RIGHT:
-            	hideNode(nearestNodeIndex);
-            	return;
+              hideNode(nearestNodeIndex);
+              return;
             case CTRL_RIGHT:
-            	anchorNode(nearestNodeIndex);
-            	return;
+              anchorNode(nearestNodeIndex);
+              return;
             case ALT_RIGHT:
-            	unanchorNode(nearestNodeIndex);
-            	return;
+              unanchorNode(nearestNodeIndex);
+              return;
             case CTRL_SHIFT_RIGHT: 
-                GraphViewI graphData = GraphViewManager.current(); 
-                if (graphData instanceof GraphData)
-                  ((GraphData) graphData).unhideAllNodes();
+              GraphViewI graphData = GraphViewManager.current(); 
+              if (graphData instanceof GraphData)
+                ((GraphData) graphData).unhideAllNodes();
             	//DataLoader.inst().unhideAllNodes();
-            // viewer.nodePicked?? not sure what this is or if used by nbrowse??
-//            case ALT_SHIFT_LEFT:
-//              if (!drawMode)
-//                viewer.nodePicked(nearestNodeIndex, nearestPoint, modifiers);
-//              break;
+              // viewer.nodePicked?? not sure what this is or if used by nbrowse??
+//          case ALT_SHIFT_LEFT:
+//            if (!drawMode)
+//              viewer.nodePicked(nearestNodeIndex, nearestPoint, modifiers);
+//          break;
           }    	  
       } // if tryMenu
       else // original mapping - comment out the else when ready to release

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-04-23 20:22:31 UTC (rev 23091)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-04-26 16:07:39 UTC (rev 23092)
@@ -99,6 +99,24 @@
     return _edges.listIterator();
   }
 
+/**
+ * Used for visible jnet node selection based on jnet node index
+ * @param jnetNodeIndex
+ * @return
+ * @throws Exception
+ */
+  public NodeViewI getVisibleNodeViewForJnetNodeId(int jnetNodeIndex) throws Exception {
+	    for (NodeViewI n : getNodeViews())
+	      if (n.isVisible() && n.getNodeIndex() == jnetNodeIndex) return n;
+	    throw new Exception("No node found for jnet node index "+jnetNodeIndex);
+	  }  
+
+/**
+ * Used to get NodeView based on jnet node index
+ * @param jnetNodeIndex
+ * @return
+ * @throws Exception
+ */
   public NodeViewI getNodeViewForJnetNodeId(int jnetNodeIndex) throws Exception {
     for (NodeViewI n : getNodeViews())
       if (n.getNodeIndex() == jnetNodeIndex) return n;

Modified: nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-04-23 20:22:31 UTC (rev 23091)
+++ nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-04-26 16:07:39 UTC (rev 23092)
@@ -96,7 +96,9 @@
     NodeViewI node;
     try {
       // put this in MM/JnetMsEv? cant its jmol
-      node = GraphData.getCurrentGraphData().getNodeViewForJnetNodeId(jnetNodeIndex);
+      node = GraphData.getCurrentGraphData().getVisibleNodeViewForJnetNodeId(jnetNodeIndex);
+      
+      //node = GraphData.getCurrentGraphData().getNodeViewForJnetNodeId(jnetNodeIndex);
       //if (displayNode!=null && node == displayNode) return; // dont redundantly display
       displayNode = node;
     } catch (Exception ex) { // failed to find node for jnetNodeId, shouldnt happen


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Revision: 23121
          http://gmod.svn.sourceforge.net/gmod/?rev=23121&view=rev
Author:   montys9
Date:     2010-05-03 15:37:41 +0000 (Mon, 03 May 2010)

Log Message:
-----------
added new colorswatch class that handles foreground and background colors.  Also added new color space icon

Added Paths:
-----------
    nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java
    nbrowse/trunk/src/org/nbrowse/images/ColorSpace.20.png

Added: nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java	                        (rev 0)
+++ nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java	2010-05-03 15:37:41 UTC (rev 23121)
@@ -0,0 +1,242 @@
+package org.jnet.viewer;
+
+import java.awt.*;
+
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.border.BevelBorder;
+import javax.swing.border.Border;
+import javax.swing.border.CompoundBorder;
+import javax.swing.border.EmptyBorder;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+
+public class ColorSwatch
+
+{
+
+  protected JColorChooser m_colorChooser;
+
+  protected PreviewPanel m_previewPanel;
+
+  protected JDialog m_colorDialog;
+
+  public ColorSwatch() {
+
+    //super("ColorSwatch");
+    //setSize(450, 350);
+
+    //ImageIcon icon = new ImageIcon("ColorSpace20.gif");
+
+    //setIconImage(icon.getImage());
+
+    m_colorChooser = new JColorChooser();
+
+    m_previewPanel = new PreviewPanel(m_colorChooser);
+
+    m_colorChooser.setPreviewPanel(m_previewPanel);
+
+    // Unchanged code from section 14.2
+
+  }
+
+  public void createColorDialog(Component parent, Color foregroundColor, Color backgroundColor) {
+
+    if (m_colorDialog == null)
+    {
+
+        m_colorDialog = JColorChooser.createDialog(parent, 
+        		        "Select Background and Foreground Color", 
+        		        true, 
+        		        m_colorChooser, 
+        		        m_previewPanel, 
+        		        null);
+
+        m_previewPanel.setTextForeground(foregroundColor);
+
+        m_previewPanel.setTextBackground(foregroundColor);
+
+        m_colorDialog.setVisible(true);
+
+        
+        /*
+         if (m_previewPanel.isSelected()) {
+            m_monitor.setBackground(
+            m_previewPanel.getTextBackground());
+          m_monitor.setForeground(
+            m_previewPanel.getTextForeground());
+        }
+        */
+
+      }
+    
+    /*
+    mOpt.addSeparator();
+    item =  mOpt.add(actionChooser);  
+    item.setMnemonic('c');
+    menuBar.add(mOpt);
+    // Unchanged code from section 14.2
+    */
+  
+  }
+}
+
+// Unchanged code from section 14.2
+
+class PreviewPanel extends JPanel 
+
+ implements ChangeListener, ActionListener
+
+{
+
+  protected JColorChooser m_chooser;
+
+  protected JLabel m_preview;
+
+  protected JToggleButton m_btBack;
+
+  protected JToggleButton m_btFore;
+
+  protected boolean m_isSelected = false;
+
+  public PreviewPanel(JColorChooser chooser) {
+
+    this(chooser, Color.white, Color.black);
+
+  }
+
+  public PreviewPanel(JColorChooser chooser, 
+
+   Color background, Color foreground) {
+
+    m_chooser = chooser;
+
+    chooser.getSelectionModel().addChangeListener(this);
+
+    setLayout(new BorderLayout());
+
+    JPanel p = new JPanel(new GridLayout(2, 1, 0, 0));
+
+    ButtonGroup group = new ButtonGroup();
+
+    m_btBack = new JToggleButton("Background");
+
+    m_btBack.setSelected(true);
+
+    m_btBack.addActionListener(this);
+
+    group.add(m_btBack);
+
+    p.add(m_btBack);
+
+    m_btFore = new JToggleButton("Foreground");
+
+    m_btFore.addActionListener(this);
+
+    group.add(m_btFore);
+
+    p.add(m_btFore);
+
+    add(p, BorderLayout.WEST);
+
+    p = new JPanel(new BorderLayout());
+
+    Border b1 = new EmptyBorder(5, 10, 5, 10);
+
+    Border b2 = new BevelBorder(BevelBorder.RAISED);
+
+    Border b3 = new EmptyBorder(2, 2, 2, 2);
+
+    Border cb1 = new CompoundBorder(b1, b2);
+
+    Border cb2 = new CompoundBorder(cb1, b3);
+
+    p.setBorder(cb2);
+
+    m_preview = new JLabel("Text colors preview",
+
+      JLabel.CENTER);
+
+    m_preview.setBackground(background);
+
+    m_preview.setForeground(foreground);
+
+    m_preview.setFont(new Font("Arial",Font.BOLD, 24));
+
+    m_preview.setOpaque(true);
+
+    p.add(m_preview, BorderLayout.CENTER);
+
+    add(p, BorderLayout.CENTER);
+
+    m_chooser.setColor(background);
+
+  }
+
+  protected boolean isSelected() {
+
+    return m_isSelected;
+
+  }
+
+  public void setTextBackground(Color c) {
+
+    m_preview.setBackground(c);
+
+  }
+
+  public Color getTextBackground() {
+
+    return m_preview.getBackground();
+
+  }
+
+  public void setTextForeground(Color c) {
+
+    m_preview.setForeground(c);
+
+  }
+
+  public Color getTextForeground() {
+
+    return m_preview.getForeground();
+
+  }
+
+  public void stateChanged(ChangeEvent evt) {
+
+    Color c = m_chooser.getColor();
+
+    if (c != null) {
+
+      if (m_btBack.isSelected())
+
+        m_preview.setBackground(c);
+
+      else
+
+        m_preview.setForeground(c);
+
+    }
+
+  }
+
+  public void actionPerformed(ActionEvent evt) {
+
+    if (evt.getSource() == m_btBack)
+
+      m_chooser.setColor(getTextBackground());
+
+    else if (evt.getSource() == m_btFore)
+
+      m_chooser.setColor(getTextForeground());
+
+    else
+
+      m_isSelected = true;
+
+  }
+
+}
+

Added: nbrowse/trunk/src/org/nbrowse/images/ColorSpace.20.png
===================================================================
(Binary files differ)


Property changes on: nbrowse/trunk/src/org/nbrowse/images/ColorSpace.20.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 23124
          http://gmod.svn.sourceforge.net/gmod/?rev=23124&view=rev
Author:   montys9
Date:     2010-05-03 19:43:30 +0000 (Mon, 03 May 2010)

Log Message:
-----------
Color Swatch is now updated to work.
We need to update foreground and background correctly.  Still need to get current foreground and use foreground for future expansions/searches.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java	2010-05-03 17:56:00 UTC (rev 23123)
+++ nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java	2010-05-03 19:43:30 UTC (rev 23124)
@@ -15,12 +15,14 @@
 public class ColorSwatch
 
 {
-
+ 
+  //protected boolean isForeground = false;
+  
   protected JColorChooser m_colorChooser;
 
   protected PreviewPanel m_previewPanel;
 
-  protected JDialog m_colorDialog;
+  protected JDialog m_colorDialog = null;
 
   public ColorSwatch() {
 
@@ -35,12 +37,32 @@
 
     m_previewPanel = new PreviewPanel(m_colorChooser);
 
+
+    // this is a fix for using custom preview panel - this is required to overload preview panel
+    m_previewPanel.setSize(m_previewPanel.getPreferredSize()); 
+    m_previewPanel.setBorder(BorderFactory.createEmptyBorder(0,0,1,0));    
+    
+    
     m_colorChooser.setPreviewPanel(m_previewPanel);
+ 
+  }
 
-    // Unchanged code from section 14.2
-
+  public Color getForeground()
+  {
+	Color foreground = null;
+	if (m_previewPanel != null)
+	  foreground = m_previewPanel.getTextForeground();
+	return foreground;
   }
-
+  
+  public Color getBackground()
+  {
+	Color background = null;
+	if (m_previewPanel != null)
+	  background = m_previewPanel.getTextBackground();
+	return background;
+  }
+  
   public void createColorDialog(Component parent, Color foregroundColor, Color backgroundColor) {
 
     if (m_colorDialog == null)
@@ -55,7 +77,7 @@
 
         m_previewPanel.setTextForeground(foregroundColor);
 
-        m_previewPanel.setTextBackground(foregroundColor);
+        m_previewPanel.setTextBackground(backgroundColor);             
 
         m_colorDialog.setVisible(true);
 
@@ -80,6 +102,11 @@
     */
   
   }
+  
+  public Color getColor()
+  {
+	  return m_colorChooser.getColor();
+  }
 }
 
 // Unchanged code from section 14.2
@@ -91,7 +118,7 @@
 {
 
   protected JColorChooser m_chooser;
-
+  
   protected JLabel m_preview;
 
   protected JToggleButton m_btBack;
@@ -99,10 +126,10 @@
   protected JToggleButton m_btFore;
 
   protected boolean m_isSelected = false;
-
+  
   public PreviewPanel(JColorChooser chooser) {
 
-    this(chooser, Color.white, Color.black);
+    this(chooser, Color.white, Color.black);    
 
   }
 
@@ -116,7 +143,8 @@
 
     setLayout(new BorderLayout());
 
-    JPanel p = new JPanel(new GridLayout(2, 1, 0, 0));
+    
+    JPanel p1 = new JPanel(new GridLayout(2, 1, 0, 0));
 
     ButtonGroup group = new ButtonGroup();
 
@@ -128,7 +156,7 @@
 
     group.add(m_btBack);
 
-    p.add(m_btBack);
+    p1.add(m_btBack);
 
     m_btFore = new JToggleButton("Foreground");
 
@@ -136,12 +164,14 @@
 
     group.add(m_btFore);
 
-    p.add(m_btFore);
+    p1.add(m_btFore);
 
-    add(p, BorderLayout.WEST);
+    add(p1, BorderLayout.WEST);
+   
+    
+    
+    JPanel p2 = new JPanel(new BorderLayout());
 
-    p = new JPanel(new BorderLayout());
-
     Border b1 = new EmptyBorder(5, 10, 5, 10);
 
     Border b2 = new BevelBorder(BevelBorder.RAISED);
@@ -152,12 +182,10 @@
 
     Border cb2 = new CompoundBorder(cb1, b3);
 
-    p.setBorder(cb2);
+    p2.setBorder(cb2);
+    
+    m_preview = new JLabel("Graph colors preview", JLabel.CENTER);
 
-    m_preview = new JLabel("Text colors preview",
-
-      JLabel.CENTER);
-
     m_preview.setBackground(background);
 
     m_preview.setForeground(foreground);
@@ -165,11 +193,13 @@
     m_preview.setFont(new Font("Arial",Font.BOLD, 24));
 
     m_preview.setOpaque(true);
+    
+    p2.add(m_preview, BorderLayout.CENTER);
 
-    p.add(m_preview, BorderLayout.CENTER);
+    add(p2, BorderLayout.CENTER);
+    
+    //add(new JLabel("HI"));
 
-    add(p, BorderLayout.CENTER);
-
     m_chooser.setColor(background);
 
   }
@@ -211,13 +241,14 @@
     if (c != null) {
 
       if (m_btBack.isSelected())
-
+      {
         m_preview.setBackground(c);
+      }
 
       else
-
+      {
         m_preview.setForeground(c);
-
+      }
     }
 
   }
@@ -225,13 +256,14 @@
   public void actionPerformed(ActionEvent evt) {
 
     if (evt.getSource() == m_btBack)
+    {
 
       m_chooser.setColor(getTextBackground());
-
+    }
     else if (evt.getSource() == m_btFore)
-
+    {
       m_chooser.setColor(getTextForeground());
-
+    }
     else
 
       m_isSelected = true;

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-05-03 17:56:00 UTC (rev 23123)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-05-03 19:43:30 UTC (rev 23124)
@@ -30,6 +30,7 @@
 import org.nbrowse.NBrowseApplet;
 
 import org.jnet.g3d.Graphics3D;
+import org.jnet.viewer.ColorSwatch;
 import org.jnet.viewer.Viewer;
 import org.jnet.viewer.ZoomObserver;
 import org.nbrowse.io.UrlManager;
@@ -252,7 +253,11 @@
             	if (CommandLine.inst().useTestCode())
             	{
             	*/
-            	colorBackground();
+            	
+            	colorForegroundBackground();
+            	//colorBackground();
+            	
+            	
             	/*
             	}
             	else
@@ -412,6 +417,58 @@
         return toolbar;
     }
 
+    /**
+     * To be used for setting new background color. Still work in progress.
+     */
+    private void colorForegroundBackground()
+    {
+  	  Color oldColorBk =null;
+  	  Color oldColorFg = null;
+  	  oldColorBk = stepButtonBar.getBackground();
+  	  
+  	  short oldcolix =  JnetManager.inst().getDefaultNodeColix();
+  	  // need to conver oldcolix to awt color
+  	  
+  	  ColorSwatch csw = new ColorSwatch();
+  	  csw.createColorDialog(viewer().getAwtComponent(), null, oldColorBk);
+  	  
+  	  /*
+  	  Color c = JColorChooser.showDialog(
+  	          viewer().getAwtComponent(),
+  	          "Pick me !", oldColor);
+  	 */
+  	  //if (!csw.isForeground())
+  	  
+  	  Color f = csw.getForeground();
+  	  if (f!= null)
+  	  {
+  	    short colix = Graphics3D.getColix(f);
+  	    if (colix != oldcolix)
+  	    {
+  	      // if new we update 	
+  	      JnetManager.inst().setDefaultNodeColix(colix); // first update colix for future nodes and now update for current
+  	      Iterable<NodeViewI> nodeViews = GraphViewManager.current().getNodeViews();
+  	      for (NodeViewI n : nodeViews)  	  
+  	        n.setColor(f);  	   
+  	    }
+  	  }
+  	  
+  	  Color c = csw.getBackground();  	    	  
+  	  if (c != null && c != oldColorBk)
+  	  {  
+  	    short colix = Graphics3D.getColix(c);
+  	    int argb = viewer().getGraphics3D().getColixArgb(colix);
+  	  
+  	    // check if foreground and set nodes to color
+  	    viewer().getGraphics3D().setBackgroundArgb(argb);      
+        //viewer().colorManager.setColixBackgroundContrast(argb);	
+  	    Navigation.inst().viewer.getGraphics3D().setBackgroundArgb(argb);
+  	    //viewer().colorManager.setColixBackgroundContrast(argb);
+  	    //displayPanel.setBackground(c);
+  	    stepButtonBar.setBackground(c);
+  	  } // if new background color
+    }    
+    
   /**
    * To be used for setting new background color. Still work in progress.
    */

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-05-03 17:56:00 UTC (rev 23123)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-05-03 19:43:30 UTC (rev 23124)
@@ -62,6 +62,8 @@
 
   private static JnetManager singleton; // don't save instance should always use latest
 
+  private short defaultNodeColorIndex = -1; // default color index;
+  
   /** 
    * This class uses raw screen data for use when loading directly
    * @author Monty
@@ -196,11 +198,22 @@
     redrawJnet();
   }
 
+  void setDefaultNodeColix(short colix)
+  {
+	  defaultNodeColorIndex = colix;
+  }
+  
   /** Jnet has colix which is an index for colors, get default for default element 78 Pt*/
   short getDefaultNodeColix() {
     // This serves the function of initializing colix, otherwise get arr ex
-    getNavigationViewer().getDefaultNodeColix(); // init colix array/index
-    return getJnetViewer().getDefaultNodeColix();
+	  
+	if (defaultNodeColorIndex == -1)
+	{	
+      defaultNodeColorIndex = getNavigationViewer().getDefaultNodeColix(); // init colix array/index
+      getJnetViewer().getDefaultNodeColix();
+	}
+    return defaultNodeColorIndex;
+    
   }
 
   /** increase node size by standard increment */


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 23125
          http://gmod.svn.sourceforge.net/gmod/?rev=23125&view=rev
Author:   montys9
Date:     2010-05-04 15:31:38 +0000 (Tue, 04 May 2010)

Log Message:
-----------
Updated to use new color swatch in toolbar.  Updated for color swatches to load initial correct color from nodes.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java	2010-05-03 19:43:30 UTC (rev 23124)
+++ nbrowse/trunk/src/org/jnet/viewer/ColorSwatch.java	2010-05-04 15:31:38 UTC (rev 23125)
@@ -47,6 +47,18 @@
  
   }
 
+  /**
+   * This is used to determine if ok was used for setting the colors or now.
+   * @return
+   */
+  public boolean isSelected()
+  {
+	boolean isOk = false;
+	if (m_previewPanel != null)
+	  isOk = m_previewPanel.isSelected();
+	return isOk;
+  }
+  
   public Color getForeground()
   {
 	Color foreground = null;
@@ -103,10 +115,6 @@
   
   }
   
-  public Color getColor()
-  {
-	  return m_colorChooser.getColor();
-  }
 }
 
 // Unchanged code from section 14.2
@@ -149,6 +157,7 @@
     ButtonGroup group = new ButtonGroup();
 
     m_btBack = new JToggleButton("Background");
+    m_btBack.setToolTipText("Use for graph background color selection");
 
     m_btBack.setSelected(true);
 
@@ -159,6 +168,7 @@
     p1.add(m_btBack);
 
     m_btFore = new JToggleButton("Foreground");
+    m_btFore.setToolTipText("Use for selected node(s) foreground color selection");
 
     m_btFore.addActionListener(this);
 
@@ -184,8 +194,8 @@
 
     p2.setBorder(cb2);
     
-    m_preview = new JLabel("Graph colors preview", JLabel.CENTER);
-
+    //m_preview = new JLabel("Graph colors preview", JLabel.CENTER);
+    m_preview = new JLabel("Sample Text Sample Text", JLabel.CENTER);
     m_preview.setBackground(background);
 
     m_preview.setForeground(foreground);
@@ -204,7 +214,7 @@
 
   }
 
-  protected boolean isSelected() {
+  public boolean isSelected() {
 
     return m_isSelected;
 

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-05-03 19:43:30 UTC (rev 23124)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-05-04 15:31:38 UTC (rev 23125)
@@ -1010,11 +1010,26 @@
   Color oldColor =null;
   GraphViewI graphData = GraphViewManager.current();
   
+  /*
   if (nbNodes.size() == 1)
   {
 	oldColor = nbNodes.get(0).getColor();
   }
-    
+  */
+  if (nbNodes.size() == 1)
+  {
+    //oldColor = nbNodes.get(0).getColor();
+    short oldcolix = nbNodes.get(0).getJnetColix();
+  	int oldargb = viewer.getGraphics3D().getColixArgb(oldcolix);
+    oldColor = new Color(oldargb);
+  }
+  else
+  {
+    short oldcolix = JnetManager.inst().getDefaultNodeColix();
+    int oldargb = viewer.getGraphics3D().getColixArgb(oldcolix);
+    oldColor = new Color(oldargb);  	    
+  }
+	  
   Color c = JColorChooser.showDialog(
           viewer.getAwtComponent(),
           "Pick me !", oldColor);

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-05-03 19:43:30 UTC (rev 23124)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-05-04 15:31:38 UTC (rev 23125)
@@ -9,6 +9,7 @@
 import java.awt.Toolkit;
 import java.io.Serializable;
 import java.net.URL;
+import java.util.List;
 import java.awt.Insets;
 import java.awt.Font;
 
@@ -245,7 +246,8 @@
         homeButton.setToolTipText("back to home position");
         toolbar.add(homeButton);
         
-        JButton bgButton = createButton(createIcon("images/bg.png"));        
+        //JButton bgButton = createButton(createIcon("images/bg.png"));
+        JButton bgButton = createButton(createIcon("images/ColorSpace.20.png"));
         bgButton.addActionListener(new javax.swing.AbstractAction() {
             public void actionPerformed(java.awt.event.ActionEvent e) {
             	// removed use of testcode only for color background swatch
@@ -279,6 +281,7 @@
         });
         //bgButton.setToolTipText("toggle white/black background");
         bgButton.setToolTipText("pick color for background");
+        bgButton.setToolTipText("pick colors for selected nodes and background");        
         //if (CommandLine.inst().useTestCode()
         //  bgButton.setToolTipTExt("set background color");
         toolbar.add(bgButton);
@@ -425,13 +428,29 @@
   	  Color oldColorBk =null;
   	  Color oldColorFg = null;
   	  oldColorBk = stepButtonBar.getBackground();
-  	  
-  	  short oldcolix =  JnetManager.inst().getDefaultNodeColix();
+  	  List<NodeViewI> nbNodes = NBSelectionManager.inst().getSelectedNodeViews();
+  	  if (nbNodes.size() == 1)
+  	  {
+  		//oldColorFg = nbNodes.get(0).getColor();
+  		short oldcolix = nbNodes.get(0).getJnetColix();
+  		int oldargb = viewer().getGraphics3D().getColixArgb(oldcolix);
+  		oldColorFg = new Color(oldargb);
+  	  }
+  	  else
+  	  {
+  	    short oldcolix = JnetManager.inst().getDefaultNodeColix();
+  		int oldargb = viewer().getGraphics3D().getColixArgb(oldcolix);
+  		oldColorFg = new Color(oldargb);  	    
+  	  }
+  	  //short oldcolix =  JnetManager.inst().getDefaultNodeColix();
   	  // need to conver oldcolix to awt color
+  	  //oldColorFg = new Color(oldcolix);
   	  
   	  ColorSwatch csw = new ColorSwatch();
-  	  csw.createColorDialog(viewer().getAwtComponent(), null, oldColorBk);
+  	  csw.createColorDialog(viewer().getAwtComponent(), oldColorFg, oldColorBk);
   	  
+  	  if (!csw.isSelected()) // if cancelled, return
+  	    return;
   	  /*
   	  Color c = JColorChooser.showDialog(
   	          viewer().getAwtComponent(),
@@ -442,14 +461,21 @@
   	  Color f = csw.getForeground();
   	  if (f!= null)
   	  {
-  	    short colix = Graphics3D.getColix(f);
-  	    if (colix != oldcolix)
+  	    //short colix = Graphics3D.getColix(f);
+  	    //if (colix != oldcolix)
+  		if (f != oldColorFg)
   	    {
-  	      // if new we update 	
-  	      JnetManager.inst().setDefaultNodeColix(colix); // first update colix for future nodes and now update for current
+  	      // if new we update
+  	      // this update did not work - so disabling for now
+  	      //JnetManager.inst().setDefaultNodeColix(colix); // first update colix for future nodes and now update for current
+  		  // for all nodes - if needed
+  		  /*	
   	      Iterable<NodeViewI> nodeViews = GraphViewManager.current().getNodeViews();
   	      for (NodeViewI n : nodeViews)  	  
-  	        n.setColor(f);  	   
+  	        n.setColor(f);
+  	      */
+  		  for (NodeViewI n : nbNodes)
+  		    n.setColor(f);
   	    }
   	  }
   	  

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-05-03 19:43:30 UTC (rev 23124)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-05-04 15:31:38 UTC (rev 23125)
@@ -203,17 +203,23 @@
 	  defaultNodeColorIndex = colix;
   }
   
+  // this is now public for default node color
   /** Jnet has colix which is an index for colors, get default for default element 78 Pt*/
-  short getDefaultNodeColix() {
+  public short getDefaultNodeColix() {
     // This serves the function of initializing colix, otherwise get arr ex
-	  
+	// the folowing code was a try to save color of nodes for all nodes.
+	// however, this was not enough to save for nodes in expansion or search - kept elsewhere
+	// this code for maintaining color for all nodes is abandoned for now...
+	/*  
 	if (defaultNodeColorIndex == -1)
 	{	
       defaultNodeColorIndex = getNavigationViewer().getDefaultNodeColix(); // init colix array/index
       getJnetViewer().getDefaultNodeColix();
 	}
     return defaultNodeColorIndex;
-    
+    */
+	getNavigationViewer().getDefaultNodeColix(); // init colix array/index
+	return getJnetViewer().getDefaultNodeColix();
   }
 
   /** increase node size by standard increment */


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Revision: 23179
          http://gmod.svn.sourceforge.net/gmod/?rev=23179&view=rev
Author:   montys9
Date:     2010-05-11 17:33:38 +0000 (Tue, 11 May 2010)

Log Message:
-----------
Provided setInfo methods, for edge and edgeview objects. made not final the Info String attribute.  Sessiosn convertor now updates the info cached in the edgeview and edge jmol objects.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/Edge.java
    nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
    nbrowse/trunk/src/org/nbrowse/views/EdgeViewI.java

Modified: nbrowse/trunk/src/org/jnet/modelset/Edge.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-05-10 18:49:06 UTC (rev 23178)
+++ nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-05-11 17:33:38 UTC (rev 23179)
@@ -59,7 +59,8 @@
   int index = -1;
   int shapeVisibilityFlags;
   short colix;
-  private final String info;
+  //private final String info;
+  private String info;
 
   Edge(Node node1, Node node2, short order, short mad, short colix, String info, String width, short step) {
     if (node1 == null || node2 == null)
@@ -119,6 +120,11 @@
   public String getInfo() { return info; } 
     //return /*"#"+*/node1.getNodeName()+" => "+node2.getNodeName() +"; Type: " + type + " ";
 
+  public void setInfo(String newinfo)
+  {
+	  info = new String(newinfo);
+  }
+  
   public String formatLabel(String strFormat, int[] indices) {
     if (strFormat == null || strFormat.length() == 0)
       return getIdentity();

Modified: nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java	2010-05-10 18:49:06 UTC (rev 23178)
+++ nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java	2010-05-11 17:33:38 UTC (rev 23179)
@@ -17,8 +17,10 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.StringTokenizer;
 import java.util.Vector;
 
+import org.jnet.modelset.Edge;
 import org.jnet.modelset.Node;
 import org.jnet.viewer.Viewer;
 import org.nbrowse.dataset.EdgeDataset;
@@ -172,6 +174,7 @@
 	map.put("PaTrNN_on_embryo", "Functional Connection-Embryo");
 	map.put("pp", "Protein-Protein Interaction");
 	map.put("cor", "PCC");
+	map.put("ec", "Expression-Correlation"); // latest
 	
 	list.add("pc");
 	list.add("gpc");
@@ -531,7 +534,11 @@
 			    //gedge.remove(gedt);
 			  }			  
 			}
-						
+			
+								
+			// map.containsKey(type)
+			//if (gedge.getInfo().contains("")
+			
 			dcurrentindex = dcurrentindex + 1;
 		}
 		
@@ -646,6 +653,7 @@
 
 		
 		// right now we are looking into removing nodes without jnet nodes - what to do?
+		
 		for (NodeViewI bnode : badNodes)
 		{
 			System.out.println("bad node: " + bnode.getLabel()); // gets info from nbnode objs
@@ -674,10 +682,80 @@
 			//addJnetNode
 			
 		}
-		System.out.println("remaing null jnet nodes from edges count: " + String.valueOf(nocount));
 		
+		List<EdgeViewI> iedges = graphData.getEdgeList();
+		int ieinfocount = 0;
+		for (EdgeViewI edgev : iedges)
+		{
+		  String info = edgev.getInfo();
+		  if (info != null)
+		  {
+
+			    Set mset = map.keySet();
+			    Iterator mit = mset.iterator();
+			    boolean isFound = false;
+			    String result = null;
+			    while (mit.hasNext())
+			    {
+			      String key = (String) mit.next();
+			      String typekey = "<br>" + key;
+			      String value = (String) map.get(key);
+			      String typevalue = "<br>" + value;		      
+			      result = info.replaceFirst(typekey, typevalue);
+			      if (!result.equals(info))
+			      {
+			        isFound = true;
+			        info = new String(result);
+			      }
+		      		      
+			    }
+				if (isFound) // we replace if found
+				{
+				  //System.out.println("modifying new info : " + newInfo);
+				  edgev.setInfo(info);
+				  ieinfocount = ieinfocount + 1;
+				}			  
+		  }
+			
+		}
+		
+		int infocount = 0;
+		Edge[] sedges = jviewer.getModelSet().getEdges();			  
+		for (int sindex = 0; sindex < sedges.length; sindex++)
+		{
+		    Edge sedge = sedges[sindex];
+		    String sinfo = sedge.getInfo();
+		    Set mset = map.keySet();
+		    Iterator mit = mset.iterator();
+		    boolean isFound = false;
+		    String result = null;
+		    while (mit.hasNext())
+		    {
+		      String key = (String) mit.next();
+		      String typekey = "<br>" + key;
+		      String value = (String) map.get(key);
+		      String typevalue = "<br>" + value;		      
+		      result = sinfo.replaceFirst(typekey, typevalue);
+		      if (!result.equals(sinfo))
+		      {
+		        isFound = true;
+		        sinfo = new String(result);
+		      }
+	      		      
+		    }
+			if (isFound) // we replace if found
+			{
+			  //System.out.println("modifying new info : " + newInfo);
+			  sedge.setInfo(sinfo);
+			  infocount = infocount + 1;
+			}
+		} // for		
+		
+		System.out.println("remaining null jnet nodes from edges count: " + String.valueOf(nocount));
+		System.out.println("updated edgeview info count: " + String.valueOf(ieinfocount));		
+		System.out.println("updated jnet edge info count: " + String.valueOf(infocount));
 		System.out.println("EdgeView count to remove from nodeview list: " + String.valueOf(removeCount));
-		System.out.println("Removing bad nodes: " + String.valueOf(badNodes.size()));
+		System.out.println("Nodes with no jnet nodes attached found: " + String.valueOf(badNodes.size()));
 		
 		System.out.println("Modify done");
   }

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-05-10 18:49:06 UTC (rev 23178)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-05-11 17:33:38 UTC (rev 23179)
@@ -243,6 +243,11 @@
 
   public boolean hasJnetEdge() { return jnetEdge!=null; }
 
+  public void setInfo(String newInfo)
+  {
+    info = new String(newInfo);
+  }
+  
   public String getInfo() { 
     if (info==null) {
       StringBuffer s = new StringBuffer(getFrom().getLabel());

Modified: nbrowse/trunk/src/org/nbrowse/views/EdgeViewI.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/EdgeViewI.java	2010-05-10 18:49:06 UTC (rev 23178)
+++ nbrowse/trunk/src/org/nbrowse/views/EdgeViewI.java	2010-05-11 17:33:38 UTC (rev 23179)
@@ -46,6 +46,8 @@
   public String getType();
   public String getInfo();
 
+  public void setInfo(String newInfo);
+  
   public boolean isTranslucent();
 
   public void setWidth(EdgeSize biggestSize);


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Revision: 23182
          http://gmod.svn.sourceforge.net/gmod/?rev=23182&view=rev
Author:   montys9
Date:     2010-05-12 14:21:51 +0000 (Wed, 12 May 2010)

Log Message:
-----------
Added commented out code SessionConvertor for testing of setting info for edgeview and edge objects.
The EdgeView and Edge objects are updated to handle null for setting the info for display.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/modelset/Edge.java
    nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java

Modified: nbrowse/trunk/src/org/jnet/modelset/Edge.java
===================================================================
--- nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-05-11 21:19:55 UTC (rev 23181)
+++ nbrowse/trunk/src/org/jnet/modelset/Edge.java	2010-05-12 14:21:51 UTC (rev 23182)
@@ -122,7 +122,10 @@
 
   public void setInfo(String newinfo)
   {
-	  info = new String(newinfo);
+	  if (newinfo == null)
+	    info = null;
+	  else
+	    info = new String(newinfo);
   }
   
   public String formatLabel(String strFormat, int[] indices) {

Modified: nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java	2010-05-11 21:19:55 UTC (rev 23181)
+++ nbrowse/trunk/src/org/nbrowse/io/SessionConvertor.java	2010-05-12 14:21:51 UTC (rev 23182)
@@ -688,6 +688,13 @@
 		for (EdgeViewI edgev : iedges)
 		{
 		  String info = edgev.getInfo();
+		  /*
+		  if (edgev.getType().equals("Protein-Protein Interaction") || edgev.getType().equals("Expression-Correlation"))
+		  {	  
+			  info = null;
+			  edgev.setInfo(null); // will reset itself - try			  
+		  }
+		  */
 		  if (info != null)
 		  {
 
@@ -729,6 +736,15 @@
 		    Iterator mit = mset.iterator();
 		    boolean isFound = false;
 		    String result = null;
+		    
+		    /*
+			if ((sinfo.contains("Protein-Protein Interaction") || sinfo.contains("Expression-Correlation")))
+			{	  
+				  sinfo = null;
+				  sedge.setInfo(null); // will reset itself - try			  
+			}
+		    */
+		    
 		    while (mit.hasNext())
 		    {
 		      String key = (String) mit.next();

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-05-11 21:19:55 UTC (rev 23181)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/EdgeView.java	2010-05-12 14:21:51 UTC (rev 23182)
@@ -245,7 +245,10 @@
 
   public void setInfo(String newInfo)
   {
-    info = new String(newInfo);
+	if (newInfo == null)
+	  info = null;
+	else
+      info = new String(newInfo);
   }
   
   public String getInfo() { 


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Revision: 23233
          http://gmod.svn.sourceforge.net/gmod/?rev=23233&view=rev
Author:   montys9
Date:     2010-05-18 19:25:43 +0000 (Tue, 18 May 2010)

Log Message:
-----------
more updates for handling of splitter reset.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
    nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-05-18 19:15:29 UTC (rev 23232)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-05-18 19:25:43 UTC (rev 23233)
@@ -667,6 +667,10 @@
     return newViewer;
   }
   
+  public short getBackgroundColor()
+  {
+	  return g3d.getColix();
+  }
   public void setAppletContext(String fullName, URL documentBase, URL codeBase,
                                String commandOptions) {
     this.fullName = fullName = (fullName == null ? "" : fullName);

Modified: nbrowse/trunk/src/org/nbrowse/io/FileDialog.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-05-18 19:15:29 UTC (rev 23232)
+++ nbrowse/trunk/src/org/nbrowse/io/FileDialog.java	2010-05-18 19:25:43 UTC (rev 23233)
@@ -561,7 +561,7 @@
     	  
     	// indicate saving session        
         file.delete(); // delete existing first
-        InfoNodeMan.inst().resetSplitter(); // fix for loading when saving loaded/modified graph
+        InfoNodeMan.inst().resetSplitterSave(); // fix for loading when saving loaded/modified graph
     	GraphEltSet currGraph = GraphEltSet.getCurrentGraph();
         //GraphEltSet currGraph = GraphEltSet.getCurrentGraph().getFilteredGraph(); // save filtered?
     	// try this first
@@ -614,7 +614,7 @@
           ErrorUtil.urgent(this, "Failed Saving Session File", ex);
           return;
     	}
-    	
+    	InfoNodeMan.inst().resetSplitterLoad(); // fix for loading when saving loaded/modified graph - reset back splitter
     	// tell user session is saved
     	String msg = "Session File Is Saved";
     	JOptionPane.showMessageDialog(JnetManager.inst().getJnetViewer().getAwtComponent(),"Session Saved",msg,JOptionPane.INFORMATION_MESSAGE);

Modified: nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java	2010-05-18 19:15:29 UTC (rev 23232)
+++ nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java	2010-05-18 19:25:43 UTC (rev 23233)
@@ -148,16 +148,24 @@
     return menu;
   }
 
-  public void resetSplitter()
+  public void resetSplitterLoad()
   {
     // this seems to fix a bug where infonode goes nuts and won't display graph when loading from deserialized and adding panels,etc.
 	// this will wake it up
 	float loc = mainSplitWindow.getDividerLocation();
 	  mainSplitWindow.setDividerLocation(loc-0.1f);
-	  mainSplitWindow.setDividerLocation(loc);	  
+	  //mainSplitWindow.setDividerLocation(loc);	  
   }
+
+  public void resetSplitterSave()
+  {
+    // this seems to fix a bug where infonode goes nuts and won't display graph when loading from deserialized and adding panels,etc.
+	// this will wake it up
+	float loc = mainSplitWindow.getDividerLocation();
+	  mainSplitWindow.setDividerLocation(loc+0.1f);
+	  //mainSplitWindow.setDividerLocation(loc);	  
+  }  
   
-  
   public void enableGooseMenu(String title)
   {
 	  if (title == GOOSE_TITLE)

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-05-18 19:15:29 UTC (rev 23232)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-05-18 19:25:43 UTC (rev 23233)
@@ -836,11 +836,16 @@
     
     //changeColorManager(); // for testing
     
-    // set to white background for default - otherwise it becomes black
+
+    // this will change the background color appropriately - new solution in splitter fix for using this
+    int bgcolor = getJnetViewer().getGraphics3D().bgcolor;
+    getJnetViewer().getGraphics3D().setBackgroundArgb(bgcolor);  
+    Navigation.inst().viewer.getGraphics3D().setBackgroundArgb(bgcolor);
+    jnet.getStepButtonBar().setBackground(new Color(bgcolor));   
     
-    JnetPanel.viewer.evalString("background white;");
-    jnet.getStepButtonBar().setBackground(Color.WHITE);
-    Navigation.viewer.evalString("background white;");
+    //JnetPanel.viewer.evalString("background white;");
+    //jnet.getStepButtonBar().setBackground(Color.WHITE);
+    //Navigation.viewer.evalString("background white;");
     
     //toggle = 1;
     
@@ -854,10 +859,10 @@
    // use this until deserialized view color manager is working
     
    // removing this now just uses a yellow color - we need to convert nodeview colix values before loading for regeneration
-   for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
+   //for (NodeViewI n : graphView().getNodeViews()) n.setDefaultColor();
     
     // this seems to work
-    /*
+    
     for (NodeViewI n : graphView().getNodeViews()) {
     	short defaultColix = ColorManager.getDefaultJnetColix();
  		short oldcolix = n.getJnetColix();
@@ -865,14 +870,19 @@
  		  n.setColor(null);
  		else
  		{
- 	  	  short colix = Graphics3D.getColix(n.getColor()); 	  	    		
-  		  int oldargb = getJnetViewer().getGraphics3D().getColixArgb(colix);
-  		  Color oldColorFg = new Color(oldargb);
-  		  n.setColor(oldColorFg);
+ 		  Color oldColor = n.getColor();
+ 		  short colix;
+ 		  if (oldColor != null)
+ 		  {
+ 	  	    colix = Graphics3D.getColix(n.getColor()); 	  	   	  	   	  	    		
+  		    int oldargb = getJnetViewer().getGraphics3D().getColixArgb(colix);
+  		    Color oldColorFg = new Color(oldargb);
+  		    n.setColor(oldColorFg);
+  		  }
  		  
  		}
    }
-   */
+   
   	
     redrawJnet();
     if (nodeMover != null)
@@ -943,7 +953,7 @@
     	  
     	  // if this is used then info node resize is needed to view - however - the steps buttons will show properly - re-enable when graph is visible
     	  //InfoNodeMan.inst().resetSplitter();
-    	  //createJnetLineBarStepButton(1); // try this?
+    	  createJnetLineBarStepButton(1); // try this?
     	  
           //InfoNodeMan.inst().getRootWindow().invalidate();
           //InfoNodeMan.inst().getRootWindow().validate();
@@ -989,7 +999,7 @@
         	StepManager.inst().addStep(queryNode);
           }
           // if this is used then info node resize is needed to view - however - the steps buttons will show properly - re-enable when graph is visible  
-          //createJnetLineBarStepButton(step);
+          createJnetLineBarStepButton(step);
           //InfoNodeMan.inst().resetSplitter();
           //InfoNodeMan.inst().getRootWindow().invalidate();
           //InfoNodeMan.inst().getRootWindow().validate();
@@ -1046,8 +1056,9 @@
     getJnetViewer().setZoomRatioFloat(zoomRatio);
     
     // this seems to fix a bug where infonode goes nuts and won't display graph.
-    // this will wake it up - not needed here unless old graph that didn't save with resetSplitter - legacy
-    InfoNodeMan.inst().resetSplitter();
+    // this will wake it up - not needed here unless old graph that didn't save with resetSplitter - legacy    
+    InfoNodeMan.inst().resetSplitterLoad();
+
     
     // reload go viewer -doesn't seem to help show terms anymore
     //GraphEltSet currG = GraphEltSet.getCurrentGraph();
@@ -1069,8 +1080,8 @@
     //getJnetViewer().refresh(2, "zoom refresh");
     redrawJnet(); // try level 3 refresh
     StatusManager.inst().normal();
-    
-    
+
+         
 // try this for guarantee see graph without using sizing of infonodes
     //getJnetViewer().revalidateDisplay();
     
@@ -1254,8 +1265,9 @@
     	  loadSerialData(); // will invoke from serialized binary data
 
       	String msg = "Session File Is Loaded";
+      	//InfoNodeMan.inst().resetSplitterSave();
     	JOptionPane.showMessageDialog(JnetManager.inst().getJnetViewer().getAwtComponent(),"Session Loaded",msg,JOptionPane.INFORMATION_MESSAGE);;
-    	
+    	InfoNodeMan.inst().resetSplitterSave();
       }
       else if (e.expansionLoaded()) {
         getJnetViewer().clearNodeInfoHoverShape();// clear out hover shape for realloc with new model


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Revision: 23248
          http://gmod.svn.sourceforge.net/gmod/?rev=23248&view=rev
Author:   montys9
Date:     2010-05-21 13:39:45 +0000 (Fri, 21 May 2010)

Log Message:
-----------
N-Browse now exports EPS graphic documents - similar to N-Browse 1.  However, it exports colored nodes and background colors as well.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/export/image/EPSEncoder.java
    nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java

Modified: nbrowse/trunk/src/org/jnet/export/image/EPSEncoder.java
===================================================================
--- nbrowse/trunk/src/org/jnet/export/image/EPSEncoder.java	2010-05-21 04:30:26 UTC (rev 23247)
+++ nbrowse/trunk/src/org/jnet/export/image/EPSEncoder.java	2010-05-21 13:39:45 UTC (rev 23248)
@@ -1,5 +1,6 @@
 package org.jnet.export.image;
 
+import java.awt.BasicStroke;
 import java.awt.Color;
 import java.awt.Image;
 import java.awt.geom.AffineTransform;
@@ -29,14 +30,34 @@
 		  viewer = jviewer;
 	  }
 	  
+	  /**
+	   * encodes using eps graphics package which works - ensure you are using a decent viewer to acess the eps document.
+	   * a website found to check your eps is: http://www.fixlogo.com/viewer/EPS_viewer.php
+	   * @throws IOException
+	   */
 	  public synchronized void encode() throws IOException {
 		  int width = viewer.getScreenWidth();
 		  int height = viewer.getScreenHeight();
-		  EpsGraphics ep = new EpsGraphics("NBrowse Canvas", outStream, 0, 0, width, height, ColorMode.COLOR_CMYK);				  
+		  EpsGraphics ep = new EpsGraphics("NBrowse Canvas", outStream, 0, 0, width, height, ColorMode.COLOR_CMYK);
+		  
 		  //AffineTransform transform = new AffineTransform();
 		  //transform.translate(0, 0);		 
-		  //ep.drawImage(image, 0, 0, width, height, new Color(viewer.getGraphics3D().bgcolor),null);
-		  ep.drawImage(image, 0, 0, null); 
+		  ep.drawImage(image, 0, 0, width, height, new Color(viewer.getGraphics3D().bgcolor),null);
+		 
+		  // code from package example - used for testing
+		  /*
+		  ep.setColor(Color.black);		    
+		  // Line thickness 2.
+		  ep.setStroke(new BasicStroke(2.0f));		    
+		  // Draw a line.
+		  ep.drawLine(10, 10, 50, 10);
+		  // Fill a rectangle in blue
+		  ep.setColor(Color.blue);
+		  ep.fillRect(10, 0, 20, 20);
+          */
+
+		  //ep.drawImage(image, 0, 0, null); 
+		  
 		  //ep.drawImage(image, 0, 0, null);
 		  //ep.drawImage(image, transform, null); // parameters image, AffineTransform, imageObserver
 		  ep.flush();

Modified: nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java	2010-05-21 04:30:26 UTC (rev 23247)
+++ nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java	2010-05-21 13:39:45 UTC (rev 23248)
@@ -1563,10 +1563,10 @@
 
   
     Dialog sd;
-    //final static String[] imageChoices = { "JPEG", "PNG", "GIF", "EPS"};
-    final static String[] imageChoices = { "JPEG", "PNG", "GIF"};
-    //final static String[] imageExtensions = { "jpg", "png", "gif", "eps"};
-    final static String[] imageExtensions = { "jpg", "png", "gif"};    
+    final static String[] imageChoices = { "JPEG", "PNG", "GIF", "EPS"};
+    //final static String[] imageChoices = { "JPEG", "PNG", "GIF"};
+    final static String[] imageExtensions = { "jpg", "png", "gif", "eps"};
+    //final static String[] imageExtensions = { "jpg", "png", "gif"};    
     int qualityJPG = -1;
     int qualityPNG = -1;
     String imageType;


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Revision: 23334
          http://gmod.svn.sourceforge.net/gmod/?rev=23334&view=rev
Author:   montys9
Date:     2010-06-07 18:56:49 +0000 (Mon, 07 Jun 2010)

Log Message:
-----------
Added zoom in / zoom out icons that have transparent backgrounds, and added check for modelSet before trying to change node size (prevents exception if no modelSet found).

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/images/Zoom-In-icon.png
    nbrowse/trunk/src/org/nbrowse/images/Zoom-Out-icon.png
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-06-07 18:00:27 UTC (rev 23333)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-06-07 18:56:49 UTC (rev 23334)
@@ -4754,7 +4754,8 @@
     //refresh(0, "Viewer:setShapeSize(" + shapeID + "," + size + ")");
   }
   private void changeShapeSize(int shapeID,boolean increase) {
-    modelSet.changeShapeSize(shapeID,increase);
+    if (modelSet != null)	  
+      modelSet.changeShapeSize(shapeID,increase);
   }
   
   /** increase size of all nodes (not just selected) */

Modified: nbrowse/trunk/src/org/nbrowse/images/Zoom-In-icon.png
===================================================================
(Binary files differ)

Modified: nbrowse/trunk/src/org/nbrowse/images/Zoom-Out-icon.png
===================================================================
(Binary files differ)

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-06-07 18:00:27 UTC (rev 23333)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-06-07 18:56:49 UTC (rev 23334)
@@ -60,6 +60,10 @@
     public static JToolBar stepButtonBar;
     // jnet toolbar created in createToolbar - no ref
     private static boolean continueLoop = true;
+    // used for zooming in and out
+	final static float zoomClickFractionUp = 1.15f;
+	final static float zoomClickFractionDown = 1 / zoomClickFractionUp;  
+	  
   private ZoomSliderListener zoomSliderListener = new ZoomSliderListener();
   private JButton hoveredNodeEdgeInfoButton;
 
@@ -347,7 +351,31 @@
 
       toolbar.addSeparator();
 
+      // for zooming in/out
+      JButton zoomInButton = createButton(createIcon("images/Zoom-In-icon.png"));
+      zoomInButton.addActionListener(new javax.swing.AbstractAction() {
+  	  
+    	  public void actionPerformed(java.awt.event.ActionEvent e) {
+    	      float zoomFactor = zoomClickFractionUp ;  		
+    	      JnetPanel.viewer.zoomByFactor(zoomFactor);  	          		  
+    	  }
+      });
+      zoomInButton.setToolTipText("zoom in graph");
+      toolbar.add(zoomInButton);
+
+      // for zooming in/out
+      JButton zoomOutButton = createButton(createIcon("images/Zoom-Out-icon.png"));
+      zoomOutButton.addActionListener(new javax.swing.AbstractAction() {
+    	  public void actionPerformed(java.awt.event.ActionEvent e) {
+    	    float zoomFactor = zoomClickFractionDown ;  		
+    	    JnetPanel.viewer.zoomByFactor(zoomFactor);    		      		  
+    	  }
+      });
+      zoomOutButton.setToolTipText("zoom out graph");
+      toolbar.add(zoomOutButton);
       
+      toolbar.addSeparator();
+      
       JButton springButton = createButton(createIcon("images/spring.png"));        
         springButton.addActionListener(new javax.swing.AbstractAction() {
           public void actionPerformed(java.awt.event.ActionEvent e) {


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Revision: 23520
          http://gmod.svn.sourceforge.net/gmod/?rev=23520&view=rev
Author:   montys9
Date:     2010-07-01 15:55:40 +0000 (Thu, 01 Jul 2010)

Log Message:
-----------
updated mouse manager to no longer jump out with exception if calcRect functionality in mouseMouseManager has a problem.  We can still call slow layout in test mode for unanchoring when a node is dragged.
setSize is updated to cancel layout if current layout is going on when setSize is invoked.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-06-30 20:51:05 UTC (rev 23519)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-07-01 15:55:40 UTC (rev 23520)
@@ -1678,9 +1678,16 @@
                
                Navigation.viewer.checkObjectDragged(previousDragX, 
                     previousDragY, deltaX, deltaY, modifiers);
-               calcRectNavigatorBand();
-               Navigation.viewer.setNavigatorBand(rectNavigator);
-               Navigation.viewer.refresh(3, "mouseMoving");
+               try
+               {
+                 calcRectNavigatorBand();
+                 Navigation.viewer.setNavigatorBand(rectNavigator);
+                 Navigation.viewer.refresh(3, "mouseMoving");
+               }
+               catch(Exception ex) // if exception, still try to use slow algorithm if enabled
+               {
+                 ex.printStackTrace(); // don't kill system if exception occurs in calcRectNavigatorBand
+               }
                
                // try doing layout here for non-anchored nodes
                //if (tryNewMenu)

Modified: nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java	2010-06-30 20:51:05 UTC (rev 23519)
+++ nbrowse/trunk/src/org/nbrowse/NBrowseApplet.java	2010-07-01 15:55:40 UTC (rev 23520)
@@ -620,6 +620,20 @@
   public void setSize(int width, int height) 
   { 
 	  super.setSize(width,height);
+	  
+	  StatusManager.inst().layoutCancelled(); // cancel layout if we are resetting size of screen
+	  
+	 
+	  // currently just sleep but eventually plan to have either a list or single layout Manager reference so that we can wait for layout cancel to be over 
+	  try {
+//		    thread.join();
+		    Thread.sleep(0); // 
+		    // Finished
+		} catch (InterruptedException e) {
+		    // Thread was interrupted
+		}
+      
+	  
 	  Dimension dim = new Dimension(width, height);
 	  if (JnetPanel.viewer != null)
 	  {


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Revision: 23850
          http://gmod.svn.sourceforge.net/gmod/?rev=23850&view=rev
Author:   montys9
Date:     2010-09-27 15:40:34 +0000 (Mon, 27 Sep 2010)

Log Message:
-----------
Added to loadJnetFiltered check for empty filteredGraph and non-empty full graph (edge filtering too much).
Now shows error message and to re-query after adjusting edge filter.
NodeView and Viewer now have checks for no modelSet object since we no longer load the model if no edges are initially visible.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-09-24 19:11:48 UTC (rev 23849)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-09-27 15:40:34 UTC (rev 23850)
@@ -2538,6 +2538,10 @@
 	int size = getDefaultMadNode();
     if (useDefaultNodeSize())
 	  size = getDefaultNodeSize();
+    if (modelSet==null) {
+      System.out.println("ModelSet is null in Viewer, cant add node");
+      return null;
+    }
     return modelSet.addNode(id,name,step,colix,isTransluc,size,is3D);
   }
 
@@ -2564,6 +2568,11 @@
   }
 
   public Edge addJnetEdge(Node f,Node t,short colix,String type,String width,short step) {
+	if (modelSet == null) // if not set we return
+	{
+      System.out.println("ModelSet is null in Viewer, cant add edge");
+	  return null;
+	}
     return modelSet.addEdge(f,t,colix,type,width, step);
   }
 

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java	2010-09-24 19:11:48 UTC (rev 23849)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/NodeView.java	2010-09-27 15:40:34 UTC (rev 23850)
@@ -398,6 +398,8 @@
     // this hides/shows ball/node but not node halo
     //jnetNode.setShapeVisConstant(JnetConstants.SHAPE_BALLS, s);
     //jnetNode.setShapeVisibility(JnetConstants.NODE_IN_MODEL, s);
+    if (jnetNode==null) // if still null return
+      return;
     jnetNode.setIsHidden(!s);
     // navNode...
     if (navigatorNode==null) createNavNode();

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-09-24 19:11:48 UTC (rev 23849)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-09-27 15:40:34 UTC (rev 23850)
@@ -713,17 +713,43 @@
     // sets edge widths as well - funny?
     GraphViewI filteredGraph = fullGraph.getSubgraph(EdgeFilterState.inst(), step);
     
-    // if filtered graph is empty due to edge filters turned off during initial search, there needs to be a way to be able to re-set filters without 
+    // original thought: if filtered graph is empty due to edge filters turned off during initial search, there needs to be a way to be able to re-set filters without 
     // error 
     // this code seems to work but need to update bottom label for current graph even though graph is not visible or even layout invisible nodes
     // this requires more thought on handling empty graph due to no visible edge/nodes in pre-filter
+    // current solution: if loading new new graph (since expansion means at least 1 edge found), show error.
+    if (filteredGraph.isEmpty() && !fullGraph.isEmpty())
+    {
+        String m = "There are no interactions found due to use of edge filter.  Please adjust filter and re-query!";
+        ErrorUtil.urgent(this, m);    	
+        //ErrorUtil.warning(msg)
+    	return;
+    }
     /*
     if (filteredGraph.isEmpty())
     {
+    	//loadJnet(GraphData.getNewGraphData());
     	
+    
+        // put message on bottom of window describing contents
+    	jnetScript.clearEvals();    	
+    	getJnetViewer().clear();
+        String q = graphView().getQueryString();
+        String geneStr = q!=null ? "gene(s): "+q : "";
+        // move this to JnetScript!
+        String s ="set echo bottom left;" +
+              "font echo 12 serif; echo \"step "+getDisplayStep() + "; " +
+              geneStr +
+              " (nodes " + graphModel().nodeNum() +
+              ", edges " + graphModel().edgeNum() + ");\"";
+        getJnetViewer().evalString(s);
+        if (graphView().hasQueryNodes())
+            selectJnetNodes(graphView().getQueryNodes()); // for n : queryNodes select(n) ??
+          	
     	return;
     }
-    */    
+    */
+    
     loadJnet(filteredGraph);
   }
   


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Revision: 23960
          http://gmod.svn.sourceforge.net/gmod/?rev=23960&view=rev
Author:   montys9
Date:     2010-10-13 12:07:46 +0000 (Wed, 13 Oct 2010)

Log Message:
-----------
added comments regarding anchoring/unanchoring of nodes and use of slow layout.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-13 00:30:19 UTC (rev 23959)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-13 12:07:46 UTC (rev 23960)
@@ -573,7 +573,7 @@
     // right -> select neighbors, still have ctrl_left for popup
     //case RIGHT: // with multi-button mice, this will too
       case CTRL_RIGHT:
-    	// test code is anchor  
+    	// if anchor node is enabled (test code), ctrl_right is already anchor node
     	if (!CommandLine.inst().useTestCode())
     	{        	  
           viewer.popupMenu(x, y);
@@ -871,10 +871,12 @@
               hideNode(nearestNodeIndex);
               return;
             case CTRL_RIGHT:
+              // if anchoring of node is enabled, ctrl_right is same as anchor node
               if (CommandLine.inst().useTestCode())	
                 anchorNode(nearestNodeIndex);
               return;
             case ALT_RIGHT:
+            	// if unanchoring of node is enabled, alt_right is same as unanchor node
                 if (CommandLine.inst().useTestCode())		
                   unanchorNode(nearestNodeIndex);
               return;
@@ -1690,7 +1692,8 @@
                }
                
                // try doing layout here for non-anchored nodes
-               //if (tryNewMenu)
+               // if dragging a node - slow algorithm is performed here for non-anchored nodes
+               // code is still in test code since slow algorithm behaves differently between different client desktops and graph sizes.               
                if (CommandLine.inst().useTestCode())       
                {
                  // use name found at mouse click for drag

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-13 00:30:19 UTC (rev 23959)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-13 12:07:46 UTC (rev 23960)
@@ -961,7 +961,8 @@
   }
   
   /**
-   * Used to anchor a single node using node name 
+   * Used to anchor a single node using node name.
+   * This function is currently not used.
    * @param nodeName
    */
   public void anchorNode(String nodeName)
@@ -994,7 +995,8 @@
   }
   
   /**
-   * Unanchors a node and does a regular layout.
+   * Unanchors a node and does a slow layout.
+   * This method is currently not used.
    * @param nodeName
    */
   public void unanchorNode(String nodeName)

Modified: nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java	2010-10-13 00:30:19 UTC (rev 23959)
+++ nbrowse/trunk/src/org/nbrowse/views/InfoNodeMan.java	2010-10-13 12:07:46 UTC (rev 23960)
@@ -158,6 +158,7 @@
     if (CommandLine.inst().useGoose())
     {
       loadGooseViews();
+      // under test code FuncAssociate Gaggle View is available - which needs work
       if (CommandLine.inst().useTestCode())
         loadFuncViews();
     }


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Revision: 23978
          http://gmod.svn.sourceforge.net/gmod/?rev=23978&view=rev
Author:   montys9
Date:     2010-10-14 19:29:11 +0000 (Thu, 14 Oct 2010)

Log Message:
-----------
Updated to have anchor nodes/unanchor nodes now available for production.
This includes having formulaview doing forced layout and need for new forced layout button besides current unforced layout.
NodeInfoMaker has code turned off for showing Layout Status: Anchored or Unanchored.
However, this means that check for node info already selected is then wrong.  Need to review need to Layout Status field and see if
still needed.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/FormulaView.java
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java
    nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
    nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-14 17:31:41 UTC (rev 23977)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-14 19:29:11 UTC (rev 23978)
@@ -52,6 +52,7 @@
   // using new key/mouse mappings
   //final boolean tryNewMenu = true ; // use when ready to use new mouse/keyboard mappings
   final boolean forceAwt = false; // switch used to force awt menus instead of swing for legacy
+  private static boolean ALLOW_ANCHOR = true;
   
   
   /**
@@ -564,8 +565,9 @@
     // right -> select neighbors, still have ctrl_left for popup
     //case RIGHT: // with multi-button mice, this will too
       case CTRL_RIGHT:
-    	// if anchor node is enabled (test code), ctrl_right is already anchor node
-    	if (!CommandLine.inst().useTestCode())
+    	// if anchor node is enabled (ALLOW_ANCHOR - previously test code), ctrl_right is already anchor node
+    	//if (!CommandLine.inst().useTestCode())
+    	if (!ALLOW_ANCHOR) 
     	{        	  
           viewer.popupMenu(x, y);
           return;
@@ -863,12 +865,14 @@
               return;
             case CTRL_RIGHT:
               // if anchoring of node is enabled, ctrl_right is same as anchor node
-              if (CommandLine.inst().useTestCode())	
+              //if (CommandLine.inst().useTestCode())
+              if (ALLOW_ANCHOR) 	
                 anchorNode(nearestNodeIndex);
               return;
             case ALT_RIGHT:
             	// if unanchoring of node is enabled, alt_right is same as unanchor node
-                if (CommandLine.inst().useTestCode())		
+                //if (CommandLine.inst().useTestCode())
+            	if (ALLOW_ANCHOR)
                   unanchorNode(nearestNodeIndex);
               return;
             case CTRL_SHIFT_RIGHT: 
@@ -1311,7 +1315,9 @@
   mousePopupMenu.addPopupMenuItem("Color Node", colorAction);  
   mousePopupMenu.addPopupMenuItem("Hide Node", hideAction);
   mousePopupMenu.addPopupMenuItem("Unhide All Nodes", unhideAction);
-  if (CommandLine.inst().useTestCode())	
+  // no longer test code - only slow layout is in test version and spring button won't force layouts for all nodes
+  //if (CommandLine.inst().useTestCode())
+  if (ALLOW_ANCHOR)
   {	  
     mousePopupMenu.addPopupMenuItem("Anchor All Nodes", anchorAllAction);
     mousePopupMenu.addPopupMenuItem("Unanchor All Nodes", unanchorAllAction);

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-14 17:31:41 UTC (rev 23977)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-14 19:29:11 UTC (rev 23978)
@@ -9,6 +9,7 @@
 
 import org.jnet.modelset.Edge;
 import org.jnet.modelset.Node;
+import org.nbrowse.CommandLine;
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.NBEdge;
 import org.nbrowse.dataset.NBNode;
@@ -891,7 +892,8 @@
 	//GraphViewI graphData = GraphViewManager.current();
 	status().layoutDone();
 	this.setDoLayout(true);
-	JnetManager.inst().doLayout(false, true); // if unanchoring all nodes - does a regular layout.
+	if (CommandLine.inst().useTestCode())
+	  JnetManager.inst().doLayout(false, true); // if unanchoring all nodes - does a slow layout.
   }
   
   public void saveAnchorState(String nodeName)
@@ -914,7 +916,7 @@
 	    n.setDoLayout(tempAnchorState);  // reset back anchor state
 	}
     // restart layout again
-    if (useSlowLayout) // just finished slow layout, do one more
+    if (useSlowLayout) // just finished slow layout, do one more - if no slow layout invoked - will never be called
       JnetManager.inst().doLayout(false, true);
     useSlowLayout=false; // for next one
   }
@@ -1008,7 +1010,8 @@
 		    n.setDoLayout(true);
 		}		
 		status().layoutDone();
-		JnetManager.inst().doLayout(false, true);
+		if (CommandLine.inst().useTestCode()) // if test code and unanchor - do slow layout
+		  JnetManager.inst().doLayout(false, true);
 		
   }
   

Modified: nbrowse/trunk/src/org/nbrowse/views/FormulaView.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/FormulaView.java	2010-10-14 17:31:41 UTC (rev 23977)
+++ nbrowse/trunk/src/org/nbrowse/views/FormulaView.java	2010-10-14 19:29:11 UTC (rev 23978)
@@ -317,7 +317,7 @@
 	             if (!isValid)
 	               return;
 	             JnetManager.inst().resetNodePositions();
-	             JnetManager.inst().layoutAllNodes(false); // do a layout	             
+	             JnetManager.inst().layoutAllNodes(false, true); // do a layout	on all nodes             
 	            }
 	        });
 	        

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-10-14 17:31:41 UTC (rev 23977)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-10-14 19:29:11 UTC (rev 23978)
@@ -164,13 +164,17 @@
 
   private JnetManager jnetMan() { return JnetManager.inst(); }
   private static final boolean DO_LAYOUT_IN_NBROWSE = true; // false - jnet
-  private void layoutGraph() {
-    if (DO_LAYOUT_IN_NBROWSE) nbrowseLayout();
+  private void layoutGraph(boolean layoutAll) {
+    if (DO_LAYOUT_IN_NBROWSE) nbrowseLayout(layoutAll);
     else jnetLayout();
   }
   /** layout all nodes, whole graph - override nodes that have doLayout=false
    * and DO NOT do fit to screen - per fabio request - if user is zoomed in should stay at zoom */
-  private void nbrowseLayout() { jnetMan().layoutAllNodes(false); }//doLayout(true); } // true->fitToScreen
+  private void nbrowseLayout(boolean layoutAll) 
+  { 
+	  jnetMan().layoutAllNodes(false, layoutAll); 
+  }//doLayout(true); } // true->fitToScreen
+  
   private void jnetLayout() {
     String lS = "layout;";
     JnetPanel.viewer.evalString(lS);
@@ -382,12 +386,21 @@
       JButton springButton = createButton(createIcon("images/spring.png"));        
         springButton.addActionListener(new javax.swing.AbstractAction() {
           public void actionPerformed(java.awt.event.ActionEvent e) {
-            layoutGraph();
+            layoutGraph(false); // this does not force layout on all nodes - only anchored ones
           }
       });
       springButton.setToolTipText("additional layout calculation (spring by default)");
       toolbar.add(springButton);
 
+      JButton forceSpringButton = createButton(createIcon("images/spring.png"));  // forced button      
+      forceSpringButton.addActionListener(new javax.swing.AbstractAction() {
+        public void actionPerformed(java.awt.event.ActionEvent e) {
+          layoutGraph(true); // this forces layout on all nodes - anchored or unanchored
+        }
+      });
+      forceSpringButton.setToolTipText("additional forced layout calculation (spring by default)");
+      toolbar.add(forceSpringButton);
+    
       JButton stopSpringButton = createButton(createIcon("images/stop.png"));
       stopSpringButton.addActionListener(new javax.swing.AbstractAction() {
         public void actionPerformed(java.awt.event.ActionEvent e) {

Modified: nbrowse/trunk/src/org/nbrowse/views/JnetManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-10-14 17:31:41 UTC (rev 23977)
+++ nbrowse/trunk/src/org/nbrowse/views/JnetManager.java	2010-10-14 19:29:11 UTC (rev 23978)
@@ -68,7 +68,9 @@
   public final static boolean DO_PJM = false;
 
   private static JnetManager singleton; // don't save instance should always use latest
-
+  private static boolean FORCE_LAYOUT = false; // originally true - Here spring button will not force anchored nodes to layout.
+  // if a node has been moved -it becomes anchored - so this means that you need to unanchor nodes to make them move.
+  
   private short defaultNodeColorIndex = -1; // default color index;
   
   /** 
@@ -1540,8 +1542,15 @@
 	  nodeMover().resetNodePositions();
   }
   
-  void layoutAllNodes(boolean fitToScreen) {
-    graphView().setDoLayout(true); // sets all nodes to be laid out
+  /**
+   * do a layout on nodes given fitting to screen and whether to ignore anchoring/unachoring of nodes.
+   * @param fitToScreen
+   * @param useForce
+   */
+  public void layoutAllNodes(boolean fitToScreen, boolean useForce) {
+	
+	if (useForce)	 // useForce means we force nodes to be laid out - anchored or not
+      graphView().setDoLayout(true); // sets all nodes to be laid out
     //boolean fitToScreen = true; // ??
     doLayout(fitToScreen);
   }

Modified: nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-10-14 17:31:41 UTC (rev 23977)
+++ nbrowse/trunk/src/org/nbrowse/views/NodeInfoMaker.java	2010-10-14 19:29:11 UTC (rev 23978)
@@ -35,7 +35,9 @@
   private int previousJnetNodeIndex=-1;
   private final static String PREFIX = "<html><body>";
   private final static String SUFFIX = "</body></html>";  
-
+  
+  private final static boolean showAnchorState=false; // turned off for now since isNewInfo won't show it again unless node selection change
+  
   private static NodeInfoMaker singleton;
   static NodeInfoMaker inst() {
     if (singleton==null) singleton = new NodeInfoMaker();
@@ -64,7 +66,7 @@
     public void mouseChanged(JnetMouseEvent e) {
       if (!e.isHover()) return;
       if (!e.hasNode()) return;
-      if (!isNewInfo(e.getJnetNodeIndex())) return;
+      if (!isNewInfo(e.getJnetNodeIndex())) return; // we don't show info unless mouse over has changed
       makeNodeInfo(e.getJnetNodeIndex());
     }
   }
@@ -148,6 +150,7 @@
   private final static String ID_TAG = "<b>Node systematic ID : </b> ";
   private final static String NAME_TAG = "<br><b>Node Common Synonym : </b> ";
   private final static String OTHER_NAMES_TAG = "<br><b>Other Names: </b> ";
+  private final static String ANCHOR_STATE_TAG = "<br><b>Layout State: </b> ";
   
   /**
    * this is a consolidated method for testing.
@@ -253,6 +256,15 @@
   private void printIdAndName(StringBuilder doc,NodeViewI node) {
     doc.append(ID_TAG).append(node.getID());
     doc.append(NAME_TAG).append(node.getLabel());
+    if (showAnchorState)    
+    {
+      if (node.doLayout())      
+        doc.append(ANCHOR_STATE_TAG).append("Unanchored");
+      else
+    	doc.append(ANCHOR_STATE_TAG).append("Anchored");    	  
+    }   
+        	
+    		
     //description = node.getDescription(); // get description early        
     fireNodeInfoChanged();
   }


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Revision: 24002
          http://gmod.svn.sourceforge.net/gmod/?rev=24002&view=rev
Author:   montys9
Date:     2010-10-19 18:30:50 +0000 (Tue, 19 Oct 2010)

Log Message:
-----------
MouseManager is updated for mouseDragged to invoke GraphData doLayout() - which sets anchor for selected node in production version.
doLayout() used to be doSlowLayout(), now handles slow and regular layouts.  For production version, doLayout will update node layout state and not stop and do another layout.
restoreAnchorState is updated to only update layout state. 
Test version only stops layout, restores anchor state, and does slow layout.

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-19 15:59:38 UTC (rev 24001)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-19 18:30:50 UTC (rev 24002)
@@ -1741,18 +1741,19 @@
                // try doing layout here for non-anchored nodes
                // if dragging a node - slow algorithm is performed here for non-anchored nodes
                // code is still in test code since slow algorithm behaves differently between different client desktops and graph sizes.               
-               if (CommandLine.inst().useTestCode())       
-               {
+               //if (CommandLine.inst().useTestCode())   
+               //{
                  // use name found at mouse click for drag
                  if (targetNodeName != null)
                  {	
                   GraphViewI graphData = GraphViewManager.current(); 
                   if (graphData instanceof GraphData)
-                    ((GraphData) graphData).doSlowLayout(targetNodeName);
+                    ((GraphData) graphData).doLayout(targetNodeName);
                    //DataLoader.inst().doSlowLayout(targetNodeName);
                    //DataLoader.inst().doSlowLayout(); // try this here                         	  
                  }
-               }
+               //}
+               
             } // freezing        
         } // node dragging enabled
         // LEFT CLICK DRAG - NOT ON NODE - MOVE SCREEN/GRAPH

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-19 15:59:38 UTC (rev 24001)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-19 18:30:50 UTC (rev 24002)
@@ -56,7 +56,7 @@
   // store last anchoring node state for dragging
   private transient boolean tempAnchorState=false;
   // store use temporary use of slow layout for dragging
-  private transient boolean useSlowLayout = false; 
+  private transient boolean useLayout = false; 
   
   /** Constructor for the GraphData object */
   private GraphData() {}
@@ -896,6 +896,10 @@
 	  JnetManager.inst().doLayout(false, true); // if unanchoring all nodes - does a slow layout.
   }
   
+  /**
+   * when a node is dragged, save the anchor state since we anchor node when moving.
+   * @param nodeName
+   */
   public void saveAnchorState(String nodeName)
   {
     //GraphViewI graphData = GraphViewManager.current(); 		
@@ -906,30 +910,38 @@
     }
   }
   
+  /**
+   * when node is no longer dragged, restores the original anchor state.
+   * test version will stop current slow layout and re-do another after node layout state is restored.
+   * @param nodeName
+   */
   public void restoreAnchorState(String nodeName)
   {
-	//GraphViewI graphData = GraphViewManager.current(); 
-	status().layoutDone(); // end current layout
+	//GraphViewI graphData = GraphViewManager.current();
+	if (CommandLine.inst().useTestCode()) // if test version end current layout to do another slow layout
+	  status().layoutDone(); // end current layout
     for (NodeViewI n : this.getNodeViews())
 	{
 	  if (n.getLabel().equals(nodeName)) // using labels
 	    n.setDoLayout(tempAnchorState);  // reset back anchor state
 	}
     // restart layout again
-    if (useSlowLayout) // just finished slow layout, do one more - if no slow layout invoked - will never be called
+    if (CommandLine.inst().useTestCode() && useLayout) // just finished slow layout, do one more - if no slow layout invoked - will never be called
       JnetManager.inst().doLayout(false, true);
-    useSlowLayout=false; // for next one
+    useLayout=false; // for next one
   }
   
   /**
-   * Used to perform a slow layout while dragging nodes.
+   * Used to perform a layout while dragging nodes.  test code end current layout sets node and does slow layout instead
    */
-  public void doSlowLayout(String nodeName)
+  public void doLayout(String nodeName)
   {	
     boolean doLayout = false;
-	status().layoutDone(); // stop current before next layout
+    // only end layout if test version
+    if (CommandLine.inst().useTestCode())
+	  status().layoutDone(); // stop current before next layout
 	//GraphViewI graphData = GraphViewManager.current();
-	if (!useSlowLayout)
+	if (!useLayout)
 	{
 	  for (NodeViewI n : this.getNodeViews())
   	  {
@@ -943,10 +955,10 @@
 		return;
 	}
     
-	useSlowLayout=true;
+	useLayout=true;
 	//status().layoutDone();
-	
-	JnetManager.inst().doLayout(false, true);	
+	if (CommandLine.inst().useTestCode())
+	  JnetManager.inst().doLayout(false, true);
   }
   
   


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Revision: 24007
          http://gmod.svn.sourceforge.net/gmod/?rev=24007&view=rev
Author:   montys9
Date:     2010-10-20 14:57:32 +0000 (Wed, 20 Oct 2010)

Log Message:
-----------
Added support for interactive mode.  When dragging a node in interactive mode, the initial drag will initiate a layout.
The test version now supports interactive mode as well, but does a lot more layouts (in test version, unanchor causes layout as well as mouse released-though slow layout is used instead of regular version).

Modified Paths:
--------------
    nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
    nbrowse/trunk/src/org/jnet/viewer/Viewer.java
    nbrowse/trunk/src/org/nbrowse/io/UrlManager.java
    nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
    nbrowse/trunk/src/org/nbrowse/views/Jnet.java

Added Paths:
-----------
    nbrowse/trunk/src/org/nbrowse/images/interact.png

Modified: nbrowse/trunk/src/org/jnet/viewer/MouseManager.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-20 12:42:07 UTC (rev 24006)
+++ nbrowse/trunk/src/org/jnet/viewer/MouseManager.java	2010-10-20 14:57:32 UTC (rev 24007)
@@ -602,8 +602,10 @@
           GraphViewI graphData = GraphViewManager.current(); 
           if (graphData instanceof GraphData)
             ((GraphData) graphData).saveAnchorState(targetNodeName);
+                    
           //DataLoader.inst().saveAnchorState(targetNodeName);
           //System.out.println("target node selected: " + targetNodeName);
+         
         }
       }      
     }

Modified: nbrowse/trunk/src/org/jnet/viewer/Viewer.java
===================================================================
--- nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-10-20 12:42:07 UTC (rev 24006)
+++ nbrowse/trunk/src/org/jnet/viewer/Viewer.java	2010-10-20 14:57:32 UTC (rev 24007)
@@ -130,6 +130,7 @@
   /** if false then selection is disabled -- MG*/
   private boolean selectionEnabled = true;
   private boolean hoverVisibility=false; // default false?
+  private boolean interactMode=false; // default toggle for interact mode or not (no interact by default)
 
 
   public Hashtable getCollapseHashtable(){ //vc collapsing
@@ -7911,5 +7912,8 @@
   
   public void toggleHoverEnabled() { hoverVisibility = !hoverVisibility; }
   public boolean hoverIsEnabled() { return hoverVisibility; }
+  
+  public void toggleInteractModeEnabled() { interactMode = !interactMode; }
+  public boolean interactModeIsEnabled() { return interactMode; }
 
 }

Added: nbrowse/trunk/src/org/nbrowse/images/interact.png
===================================================================
(Binary files differ)


Property changes on: nbrowse/trunk/src/org/nbrowse/images/interact.png
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Modified: nbrowse/trunk/src/org/nbrowse/io/UrlManager.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/io/UrlManager.java	2010-10-20 12:42:07 UTC (rev 24006)
+++ nbrowse/trunk/src/org/nbrowse/io/UrlManager.java	2010-10-20 14:57:32 UTC (rev 24007)
@@ -81,12 +81,14 @@
   private final static String GO =
     "http://www.ebi.ac.uk/QuickGO/GMultiTerm?format=image&id=";
  //www.ebi.ac.uk/ego/gohieracrchy?code= nematoda.bio.nyu.edu:8080/NBrowse/goGraph.jsp?go=
-  private final static String HOVER_IM = "hover.png";
+  private final static String HOVER_IM = "hover.png"; // hover png image for toolbar small vs large
+  private final static String INTERACT_IM = "interact.png"; // interact png image for toolbar small vs large
 
   //private String imagesUrl;
   private JApplet applet;
   private String externalFrame;
-  private Icon hoverInfoIcon;
+  private Icon hoverInfoIcon; // HOVER ICON used for geting large size vs small size - used by tool bar
+  private Icon interactIcon;
           
   private UrlManager() {}
   public static UrlManager inst() {
@@ -310,7 +312,11 @@
     return hoverInfoIcon;
   }
 
-
+  public Icon getInteractIcon() {
+	    if (interactIcon==null) interactIcon = createIconFromResource(INTERACT_IM);
+	    return interactIcon;
+	  }  
+  
   /** returns null if url fails - throw ex? */ 
   private ImageIcon getImageIcon(String filename) {
     String urlStr = getImagesUrlString() + filename;

Modified: nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-20 12:42:07 UTC (rev 24006)
+++ nbrowse/trunk/src/org/nbrowse/layouts/spring/vrmlgraph/GraphData.java	2010-10-20 14:57:32 UTC (rev 24007)
@@ -9,6 +9,7 @@
 
 import org.jnet.modelset.Edge;
 import org.jnet.modelset.Node;
+import org.jnet.viewer.Viewer;
 import org.nbrowse.CommandLine;
 import org.nbrowse.dataset.GraphEltSet;
 import org.nbrowse.dataset.NBEdge;
@@ -35,6 +36,7 @@
 public class GraphData implements GraphViewI, Serializable {
   static final long serialVersionUID = 1L;		
   private static GraphData currentGraphData = new GraphData();
+  
   // why linked list? more efficient?
   private LinkedList<NodeViewI> _nodes = new LinkedList<NodeViewI>();
   // linked hash set gives constant time iteration & remove/add/contains
@@ -55,8 +57,10 @@
   
   // store last anchoring node state for dragging
   private transient boolean tempAnchorState=false;
-  // store use temporary use of slow layout for dragging
+  // store use temporary use of layout for dragging
   private transient boolean useLayout = false; 
+  // store initial layout to do when do layout for production
+  private static boolean initialLayout = true;
   
   /** Constructor for the GraphData object */
   private GraphData() {}
@@ -892,7 +896,7 @@
 	//GraphViewI graphData = GraphViewManager.current();
 	status().layoutDone();
 	this.setDoLayout(true);
-	if (CommandLine.inst().useTestCode())
+	if (CommandLine.inst().useTestCode() && JnetManager.inst().getJnetViewer().interactModeIsEnabled())
 	  JnetManager.inst().doLayout(false, true); // if unanchoring all nodes - does a slow layout.
   }
   
@@ -908,6 +912,7 @@
 	  if (n.getLabel().equals(nodeName)) // using labels	  
 	    tempAnchorState = n.doLayout();	    
     }
+	initialLayout = true; // always reset to true
   }
   
   /**
@@ -926,7 +931,7 @@
 	    n.setDoLayout(tempAnchorState);  // reset back anchor state
 	}
     // restart layout again
-    if (CommandLine.inst().useTestCode() && useLayout) // just finished slow layout, do one more - if no slow layout invoked - will never be called
+    if (CommandLine.inst().useTestCode() && JnetManager.inst().getJnetViewer().interactModeIsEnabled() && useLayout) // just finished slow layout, do one more - if no slow layout invoked - will never be called
       JnetManager.inst().doLayout(false, true);
     useLayout=false; // for next one
   }
@@ -937,10 +942,12 @@
   public void doLayout(String nodeName)
   {	
     boolean doLayout = false;
-    // only end layout if test version
-    if (CommandLine.inst().useTestCode())
+
+    if ((JnetManager.inst().getJnetViewer().interactModeIsEnabled()  && initialLayout == true) ||
+        (CommandLine.inst().useTestCode() && JnetManager.inst().getJnetViewer().interactModeIsEnabled())) // stop initial layout or every time
 	  status().layoutDone(); // stop current before next layout
 	//GraphViewI graphData = GraphViewManager.current();
+    
 	if (!useLayout)
 	{
 	  for (NodeViewI n : this.getNodeViews())
@@ -957,8 +964,14 @@
     
 	useLayout=true;
 	//status().layoutDone();
-	if (CommandLine.inst().useTestCode())
+	if (CommandLine.inst().useTestCode() && JnetManager.inst().getJnetViewer().interactModeIsEnabled())
 	  JnetManager.inst().doLayout(false, true);
+	else if (JnetManager.inst().getJnetViewer().interactModeIsEnabled() && initialLayout == true)
+	   JnetManager.inst().doLayout(false, false);
+	
+    // only end layout if test version
+    if (initialLayout== true)
+    	initialLayout = false; // turn off layout    	    	
   }
   
   
@@ -1022,7 +1035,7 @@
 		    n.setDoLayout(true);
 		}		
 		status().layoutDone();
-		if (CommandLine.inst().useTestCode()) // if test code and unanchor - do slow layout
+		if (CommandLine.inst().useTestCode() && JnetManager.inst().getJnetViewer().interactModeIsEnabled()) // if test code and unanchor - do slow layout
 		  JnetManager.inst().doLayout(false, true);
 		
   }

Modified: nbrowse/trunk/src/org/nbrowse/views/Jnet.java
===================================================================
--- nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-10-20 12:42:07 UTC (rev 24006)
+++ nbrowse/trunk/src/org/nbrowse/views/Jnet.java	2010-10-20 14:57:32 UTC (rev 24007)
@@ -72,6 +72,7 @@
 	  
   private ZoomSliderListener zoomSliderListener = new ZoomSliderListener();
   private JButton hoveredNodeEdgeInfoButton;
+  private JButton interactModeButton;
 
   public Jnet() {
     //super();
@@ -416,6 +417,12 @@
        });
       stopSpringButton.setToolTipText("Stop layout calculation (spring by default)");
       toolbar.add(stopSpringButton);
+      
+      interactModeButton = createButton(getInteractIcon());
+      interactModeButton.addActionListener(new InteractBut());
+      interactModeButton.setToolTipText("Toggle on/off interactive mode for node dragging");
+      toolbar.add(interactModeButton);
+      
       if (ALLOW_ANCHOR)
       {
         JButton anchorButton = createButton(createIcon("images/anchor.gif"));
@@ -628,6 +635,24 @@
     return viewer().hoverIsEnabled() ? normalHover() : smallHover();
   }
 
+  private class InteractBut implements ActionListener {
+	    public void actionPerformed(ActionEvent e) {
+	      viewer().toggleInteractModeEnabled();
+	      //interactModeButton.setSelected(viewer().interactModeIsEnabled());
+	      interactModeButton.setIcon(getInteractIcon());
+	    // this is nutty one shouldnt be modifying a "constant"
+//	                if(hovToggle == 1){
+//	                    JnetConstants.isHoverPermission = true;
+//	                    hovToggle = 0;
+//	                } else {
+//	                    JnetConstants.isHoverPermission = false;
+//	                    hovToggle = 1;
+//	                }
+	    }
+	  }
+	  private Icon getInteractIcon() {
+	    return viewer().interactModeIsEnabled() ? normalInteract() : smallInteract();
+	  }  
         
     private Icon createIcon(String icon) {
         return new ImageIcon(createImageImpl(icon));
@@ -650,6 +675,8 @@
     reducedInitialized = true;
     smallHoverIcon = null;
     makeSmallHover();
+    smallInteractIcon = null;
+    makeSmallInteract();
   }
   private Icon smallHoverIcon;
   private Icon normalHoverIcon;
@@ -663,7 +690,21 @@
   private Icon normalHover() {
     return UrlManager.inst().getHoverIcon(); // caches
   }
+  
+  private Icon smallInteractIcon;
+  private Icon normalInteractIcon;
+  private Icon smallInteract() {
+    if (smallInteractIcon==null) makeSmallInteract();
+    return smallInteractIcon;
+  }
+  private void makeSmallInteract() { // --> url manager handle half sizing!
+    smallInteractIcon = createReducedIcon("images/interact.png");
+  }
+  private Icon normalInteract() {
+    return UrlManager.inst().getInteractIcon(); // caches
+  }  
 
+  
     private ImageIcon createImageIcon(String icon) {
         return new ImageIcon(createImageImpl(icon));
     }


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