Author: scooter
Date: 2010-10-31 20:43:06 -0700 (Sun, 31 Oct 2010)
New Revision: 22672
Modified:
csplugins/trunk/ucsf/scooter/chemViz/build.xml
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateNodeGraphicsTask.java
Log:
Some bug fixes based on work preparing chemViz poster
Modified: csplugins/trunk/ucsf/scooter/chemViz/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/build.xml 2010-10-31 06:30:43 UTC
(rev 22671)
+++ csplugins/trunk/ucsf/scooter/chemViz/build.xml 2010-11-01 03:43:06 UTC
(rev 22672)
@@ -28,6 +28,9 @@
<path id="compile.classpath">
<pathelement path="${build.dir}/classes" />
<fileset dir="${cytoscape.dir}">
+ <include name="*.jar" />
+ </fileset>
+ <fileset dir="${cytoscape.dir}">
<include name="cytoscape.jar" />
</fileset>
<fileset dir="${lib.dir}">
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2010-10-31 06:30:43 UTC (rev 22671)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2010-11-01 03:43:06 UTC (rev 22672)
@@ -715,6 +715,10 @@
public Image depictWithCDK(int width, int height, Color background) {
BufferedImage bufferedImage = null;
+ if (iMolecule == null) {
+ return null;
+ }
+
try {
if (!laidOut) {
StructureDiagramGenerator sdg = new
StructureDiagramGenerator();
@@ -746,9 +750,9 @@
model.setBondWidth(model.getBondWidth()*2);
int renderWidth = width;
- // if (renderWidth < 150) renderWidth = 150;
+ if (renderWidth < 150) renderWidth = 200;
int renderHeight = height;
- // if (renderHeight < 150) renderHeight = 150;
+ if (renderHeight < 150) renderHeight = 200;
Rectangle2D bbox = new
Rectangle2D.Double(0,0,renderWidth,renderHeight);
bufferedImage = new BufferedImage(renderWidth,
renderHeight, BufferedImage.TYPE_INT_ARGB);
@@ -761,14 +765,12 @@
renderer.paintMolecule(iMolecule, new
AWTDrawVisitor(graphics), bbox, true);
- /*
if (renderWidth != width || renderHeight != height) {
if (width < height)
return
bufferedImage.getScaledInstance(width, width, java.awt.Image.SCALE_SMOOTH);
else
return
bufferedImage.getScaledInstance(height, height, java.awt.Image.SCALE_SMOOTH);
}
- */
} catch (Exception e) {
logger.warning("Unable to depict molecule with CDK
depiction: "+e.getMessage(), e);
}
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateNodeGraphicsTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateNodeGraphicsTask.java
2010-10-31 06:30:43 UTC (rev 22671)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreateNodeGraphicsTask.java
2010-11-01 03:43:06 UTC (rev 22672)
@@ -197,7 +197,8 @@
CyNetworkView view = Cytoscape.getCurrentNetworkView();
if (removeCustomGraphics) {
- for (NodeView nv: graphMap.keySet()) {
+ ArrayList<NodeView> removeList = new
ArrayList<NodeView>(graphMap.keySet());
+ for (NodeView nv: removeList) {
if (nodeSelection == null ||
nodeSelection.contains(nv.getNode())) {
// System.out.println("Removing cg for
"+nv.getNode().getIdentifier());
CustomGraphic cg = graphMap.get(nv);
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