Author: mes
Date: 2010-02-11 17:24:45 -0800 (Thu, 11 Feb 2010)
New Revision: 19309

Modified:
   
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/GraphRenderer.java
   corelibs/trunk/render.stateful/src/cytoscape/render/stateful/NodeDetails.java
Log:
fixed bug 1827, cleaned up some deprecated code, and fixed a couple of warnings

Modified: 
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/GraphRenderer.java
===================================================================
--- 
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/GraphRenderer.java 
    2010-02-12 00:58:38 UTC (rev 19308)
+++ 
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/GraphRenderer.java 
    2010-02-12 01:24:45 UTC (rev 19309)
@@ -860,9 +860,9 @@
                final float srcOffset;
 
                if (srcArrow == GraphGraphics.ARROW_DISC)
-                       srcOffset = (float) (0.5d * srcArrowSize);
+                       srcOffset = 0.5f * srcArrowSize;
                else if (srcArrow == GraphGraphics.ARROW_TEE)
-                       srcOffset = (float) srcArrowSize;
+                       srcOffset = srcArrowSize;
                else
                        srcOffset = 0.0f;
 
@@ -921,9 +921,9 @@
                final float trgOffset;
 
                if (trgArrow == GraphGraphics.ARROW_DISC)
-                       trgOffset = (float) (0.5d * trgArrowSize);
+                       trgOffset = 0.5f * trgArrowSize;
                else if (trgArrow == GraphGraphics.ARROW_TEE)
-                       trgOffset = (float) trgArrowSize;
+                       trgOffset = trgArrowSize;
                else
                        trgOffset = 0.0f;
 
@@ -1158,6 +1158,8 @@
 
                // Take care of custom graphic rendering.
                if ((lodBits & LOD_CUSTOM_GRAPHICS) != 0) {
+
+                       // draw any nested networks first
                        final TexturePaint nestedNetworkPaint = 
nodeDetails.getNestedNetworkTexturePaint(node);
                        if (nestedNetworkPaint != null) {
                                doubleBuff1[0] = floatBuff1[0];
@@ -1168,18 +1170,19 @@
                                
grafx.drawCustomGraphicFull(nestedNetworkPaint.getAnchorRect(),  
(float)doubleBuff2[0],  (float)doubleBuff2[1], nestedNetworkPaint); 
                        }
 
+                       // draw custom graphics on top of nested networks 
                        // don't allow our custom graphics to mutate while we 
iterate over them:
                        synchronized (nodeDetails.customGraphicsLock(node)) {
                                // This iterator will return CustomGraphics in 
rendering order:
-                               Iterator<CustomGraphic> dNodeIt = 
nodeDetails.customGraphics (node);
+                               Iterator<CustomGraphic> dNodeIt = 
nodeDetails.customGraphics(node);
                                CustomGraphic cg = null;
                                // The graphic index used to retrieve non 
custom graphic info corresponds to the zero-based
                                // index of the CustomGraphic returned by the 
iterator:
                                int graphicInx = 0;
                                while (dNodeIt.hasNext()) {
                                        cg = dNodeIt.next();
-                                       final float offsetVectorX = 
nodeDetails.labelOffsetVectorX(node, graphicInx);
-                                       final float offsetVectorY = 
nodeDetails.labelOffsetVectorY(node, graphicInx);
+                                       final float offsetVectorX = 
nodeDetails.graphicOffsetVectorX(node, graphicInx);
+                                       final float offsetVectorY = 
nodeDetails.graphicOffsetVectorY(node, graphicInx);
                                        doubleBuff1[0] = floatBuff1[0];
                                        doubleBuff1[1] = floatBuff1[1];
                                        doubleBuff1[2] = floatBuff1[2];

Modified: 
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/NodeDetails.java
===================================================================
--- 
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/NodeDetails.java   
    2010-02-12 00:58:38 UTC (rev 19308)
+++ 
corelibs/trunk/render.stateful/src/cytoscape/render/stateful/NodeDetails.java   
    2010-02-12 01:24:45 UTC (rev 19309)
@@ -365,80 +365,6 @@
        }
 
        /**
-        * Returns the number of custom graphics that this node has.  By 
default this
-        * method returns zero.  A custom graphic extends the concept of node 
label
-        * to include any arbitrary filled shape.
-        * @deprecated Switch to using the CustomGraphics way of manipulating 
custom graphics.
-        *             For details, see deprecation note under 
-        *             {...@link CustomGraphic#CustomGraphic CustomGraphic}.
-        *             Once switched, then
-        *             use {...@link #customGraphicCount(int) 
customGraphicCount()}.
-
-        */
-        @Deprecated public int graphicCount(final int node) {
-               return 0;
-       }
-
-       /**
-        * Returns a custom graphic's shape.  This shape will be filled by the
-        * rendering engine.  By default this method always returns null.  This
-        * method is only called by the rendering engine if graphicCount(node)
-        * returns a value greater than zero.  It is an error to return null if
-        * this method is called by the rendering engine.
-        * @param graphicInx a value in the range [0, graphicCount(node)-1]
-        *   indicating which node graphic in question.
-        * @deprecated Switch to using the CustomGraphics way of manipulating 
custom graphics.
-        *             For details, see deprecation note under 
-        *             {...@link CustomGraphic#CustomGraphic CustomGraphic}.
-        *             Once switched, then
-        *             use {...@link 
cytoscape.render.stateful.CustomGraphic#getShape() CustomGraphic.getShape()}.
-        */
-        @Deprecated public Shape graphicShape(final int node, final int 
graphicInx) {
-               return null;
-       }
-
-       /**
-        * Returns the fill paint of a custom graphic.  By default this
-        * method always returns null.  This method is only called by the 
rendering
-        * engine if graphicCount(node) returns a value greater than zero.  It 
is
-        * an error to return null if this method is called by the rendering 
engine.
-        * @param graphicInx a value in the range [0, graphicCount(node)-1]
-        *   indicating which node graphic in question.
-        * @deprecated Switch to using the CustomGraphics way of manipulating 
custom graphics.
-        *             For details, see deprecation note under 
-        *             {...@link CustomGraphic#CustomGraphic CustomGraphic}.
-        *             Once switched, then
-        *             use {...@link 
cytoscape.render.stateful.CustomGraphic#getPaint() CustomGraphic.getPaint()}.
-        */
-        @Deprecated public Paint graphicPaint(final int node, final int 
graphicInx) {
-               return null;
-       }
-
-       /**
-        * By returning one of the ANCHOR_* constants, specifies
-        * where on the node's extents rectangle the graphic anchor point lies.
-        * The filled shape is rendered at a location which is equal to this
-        * anchor point plus the offset vector.<p>
-        * By default this method always returns ANCHOR_CENTER.
-        * This method is only called by the rendering engine if 
graphicCount(node)
-        * returns a value greater than zero.
-        * @param graphicInx a value in the range [0, graphicCount(node)-1]
-        *   indicating which node graphic in question.
-        * @see #ANCHOR_CENTER
-        * @see #graphicOffsetVectorX(int, int)
-        * @see #graphicOffsetVectorY(int, int)
-        * @deprecated Switch to using the CustomGraphics way of manipulating 
custom graphics.
-        *             For details, see deprecation note under 
-        *             {...@link CustomGraphic#CustomGraphic CustomGraphic}.
-        *             Once switched, then
-        *             use {...@link 
cytoscape.render.stateful.CustomGraphic#getAnchor() CustomGraphic.getAnchor()}.
-        */
-        @Deprecated 
-       public byte graphicNodeAnchor(final int node, final int graphicInx) {
-               return ANCHOR_CENTER;
-       }
-
-       /**
         * Specifies the X component of the vector that separates the location 
of
         * a rendered graphic from the node's anchor point for that graphic.
         * By default this method always returns zero.  This method is only 
called

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