Author: scooter
Date: 2011-05-25 17:34:49 -0700 (Wed, 25 May 2011)
New Revision: 25544
Added:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-jchempaint-19.jar
Removed:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.3.6.jar
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-templates.jar
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/CreatePopupTask.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundPopup.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/renderers/CompoundRenderer.java
Log:
Move to cdk-jchempaint-19 and clean up handling of images a little.
Modified: csplugins/trunk/ucsf/scooter/chemViz/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/build.xml 2011-05-26 00:30:23 UTC
(rev 25543)
+++ csplugins/trunk/ucsf/scooter/chemViz/build.xml 2011-05-26 00:34:49 UTC
(rev 25544)
@@ -69,14 +69,14 @@
<target name="compile" depends="compile-core" description="Compile with
Cytoscape under development" />
<target name="compile-core" depends="init">
- <javac source="1.5" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}"
srcdir="${src.dir}" destdir="${build.dir}/classes">
+ <javac source="1.6" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}"
srcdir="${src.dir}" destdir="${build.dir}/classes">
<classpath refid="compile.classpath" />
</javac>
</target>
<target name="compile-test" depends="compile">
<mkdir dir="${build.dir}/classes/test" />
- <javac source="1.5" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}"
srcdir="${src.dir}/test" destdir="${build.dir}/classes/test">
+ <javac source="1.6" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}"
srcdir="${src.dir}/test" destdir="${build.dir}/classes/test">
<classpath refid="test.classpath" />
</javac>
</target>
Deleted: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-1.3.6.jar
===================================================================
(Binary files differ)
Added: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-jchempaint-19.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-jchempaint-19.jar
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Deleted: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk-templates.jar
===================================================================
(Binary files differ)
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2011-05-26 00:30:23 UTC (rev 25543)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2011-05-26 00:34:49 UTC (rev 25544)
@@ -37,9 +37,11 @@
import java.awt.Color;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.Graphics2D;
import java.awt.Image;
import java.awt.Rectangle;
+import java.awt.RenderingHints;
import java.awt.geom.AffineTransform;
import java.awt.geom.Rectangle2D;
import java.awt.image.AffineTransformOp;
@@ -78,6 +80,7 @@
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.fingerprint.Fingerprinter;
import org.openscience.cdk.geometry.GeometryTools;
+import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.inchi.InChIGenerator;
import org.openscience.cdk.inchi.InChIGeneratorFactory;
import org.openscience.cdk.inchi.InChIToStructure;
@@ -414,52 +417,62 @@
this.iMolecule = null;
this.iMolecule3D = null;
this.fingerPrint = null;
+ this.smilesStr = null;
+
+ List<Compound> mapList = null;
+ if (Compound.compoundMap == null)
+ Compound.compoundMap = new HashMap();
+
+ if (Compound.compoundMap.containsKey(source)) {
+ mapList = Compound.compoundMap.get(source);
+ } else {
+ mapList = new ArrayList();
+ }
+ mapList.add(this);
+ Compound.compoundMap.put(source, mapList);
+
if (attrType == AttriType.inchi) {
// Convert to smiles
this.smilesStr = convertInchiToSmiles(moleculeString);
} else {
- this.smilesStr = mstring;
- // Create the CDK Molecule object
- SmilesParser sp = new
SmilesParser(DefaultChemObjectBuilder
- .getInstance());
- try {
- iMolecule = sp.parseSmiles(this.smilesStr);
- } catch (InvalidSmilesException e) {
- iMolecule = null;
- logger.error("Unable to parse SMILES:
"+smilesStr+": "+e.getMessage());
+ if (mstring != null && mstring.length() > 0) {
+ // Strip any blanks in the string
+ this.smilesStr = mstring.replaceAll(" ", "");
}
}
+ if (smilesStr == null)
+ return;
+
+ logger.debug("smiles string = "+smilesStr);
+
+ // Create the CDK Molecule object
+ SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder
+ .getInstance());
+ try {
+ iMolecule = sp.parseSmiles(this.smilesStr);
+ } catch (InvalidSmilesException e) {
+ iMolecule = null;
+ logger.warning("Unable to parse SMILES: "+smilesStr+"
for "+source.getIdentifier()+": "+e.getMessage());
+ return;
+ }
+
// At this point, we should have an IMolecule
try {
- if (iMolecule != null) {
+
CDKHueckelAromaticityDetector.detectAromaticity(iMolecule);
-
CDKHueckelAromaticityDetector.detectAromaticity(iMolecule);
+ // Make sure we update our implicit hydrogens
+ CDKHydrogenAdder adder =
CDKHydrogenAdder.getInstance(iMolecule.getBuilder());
+ adder.addImplicitHydrogens(iMolecule);
- // Make sure we update our implicit hydrogens
- CDKHydrogenAdder adder =
CDKHydrogenAdder.getInstance(iMolecule.getBuilder());
- adder.addImplicitHydrogens(iMolecule);
-
- // Get our fingerprint
- Fingerprinter fp = new Fingerprinter();
- // Do we need to do the addh here?
- fingerPrint =
fp.getFingerprint(addh(iMolecule));
- }
+ // Get our fingerprint
+ Fingerprinter fp = new Fingerprinter();
+ // Do we need to do the addh here?
+ fingerPrint = fp.getFingerprint(addh(iMolecule));
} catch (CDKException e1) {
fingerPrint = null;
}
- List<Compound> mapList = null;
- if (Compound.compoundMap == null)
- Compound.compoundMap = new HashMap();
-
- if (Compound.compoundMap.containsKey(source)) {
- mapList = Compound.compoundMap.get(source);
- } else {
- mapList = new ArrayList();
- }
- mapList.add(this);
- Compound.compoundMap.put(source, mapList);
}
/**
@@ -730,11 +743,22 @@
// System.out.println("depictWithCDK("+width+","+height+")");
if (iMolecule == null || width == 0 || height == 0) {
- return null;
+ return blankImage(iMolecule, width, height);
}
try {
if (!laidOut) {
+ // Is the structure connected?
+ if
(!ConnectivityChecker.isConnected(iMolecule)) {
+ // No, for now, find the largest
component and use that exclusively
+ IMoleculeSet molSet =
ConnectivityChecker.partitionIntoMolecules(iMolecule);
+ IMolecule largest =
molSet.getMolecule(0);
+ for (int i = 0; i <
molSet.getMoleculeCount(); i++) {
+ if
(molSet.getMolecule(i).getAtomCount() > largest.getAtomCount())
+ largest =
molSet.getMolecule(i);
+ }
+ iMolecule = largest;
+ }
StructureDiagramGenerator sdg = new
StructureDiagramGenerator();
sdg.setUseTemplates(false);
sdg.setMolecule(iMolecule);
@@ -777,6 +801,7 @@
graphics.setColor(background);
graphics.setBackground(background);
graphics.fillRect(0,0,renderWidth,renderHeight);
+
graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
renderer.paint(iMolecule, new AWTDrawVisitor(graphics),
bbox, true);
@@ -794,7 +819,7 @@
bufferedImage = op.filter(bufferedImage, null);
}
} catch (Exception e) {
- logger.warning("Unable to depict molecule with CDK
depiction: "+e.getMessage(), e);
+ logger.warning("Unable to depict molecule for
"+source.getIdentifier()+" with CDK depiction: "+e.getMessage(), e);
}
return bufferedImage;
@@ -826,6 +851,11 @@
try {
// Get the factory
InChIGeneratorFactory factory =
InChIGeneratorFactory.getInstance();
+ if (!inchi.startsWith("InChI="))
+ inchi = "InChI="+inchi;
+
+ logger.debug("Getting structure for: "+inchi);
+
InChIToStructure intostruct =
factory.getInChIToStructure(inchi, DefaultChemObjectBuilder.getInstance());
// Get the structure
@@ -833,7 +863,7 @@
if (ret == INCHI_RET.WARNING) {
logger.warning("InChI warning: " +
intostruct.getMessage());
} else if (ret != INCHI_RET.OKAY) {
- logger.error("Structure generation failed
failed: " + ret.toString()
+ logger.warning("Structure generation failed: "
+ ret.toString()
+ " [" + intostruct.getMessage() + "]");
return null;
}
@@ -843,10 +873,45 @@
SmilesGenerator sg = new SmilesGenerator();
return sg.createSMILES(iMolecule);
} catch (Exception e) {
- logger.error("Structure generation failed failed: " +
e.getMessage());
+ logger.warning("Structure generation failed: " +
e.getMessage(), e);
return null;
}
}
+ private Image blankImage(IMolecule mol, int width, int height) {
+ final String noImage = "Image Unavailable";
+
+ if (width == 0 || height == 0)
+ return null;
+
+ BufferedImage bufferedImage = new BufferedImage(width, height,
BufferedImage.TYPE_INT_ARGB);
+ Graphics2D graphics = bufferedImage.createGraphics();
+ graphics.setBackground(Color.WHITE);
+
+ graphics.setColor(Color.WHITE);
+ graphics.fillRect(0,0,width,height);
+ graphics.setColor(Color.BLACK);
+
+ // Create our font
+ Font font = new Font("SansSerif", Font.PLAIN, 18);
+ graphics.setFont(font);
+ FontMetrics metrics = graphics.getFontMetrics();
+
+ int length = metrics.stringWidth(noImage);
+ while (length+6 >= width) {
+ font = font.deriveFont((float)(font.getSize2D() *
0.9)); // Scale our font
+ graphics.setFont(font);
+ metrics = graphics.getFontMetrics();
+ length = metrics.stringWidth(noImage);
+ }
+
+ int lineHeight = metrics.getHeight();
+
+ graphics.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
RenderingHints.VALUE_ANTIALIAS_ON);
+ graphics.drawString(noImage, (width-length)/2,
(height+lineHeight)/2);
+
+ return bufferedImage;
+ }
+
}
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
2011-05-26 00:30:23 UTC (rev 25543)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/CreatePopupTask.java
2011-05-26 00:34:49 UTC (rev 25544)
@@ -128,7 +128,10 @@
if (objectList.size() == 1) {
CompoundPopup popup = new CompoundPopup(cList,
objectList, null);
} else {
- CompoundPopup popup = new CompoundPopup(cList,
objectList, labelAttribute);
+ if (labelAttribute.equals("ID"))
+ new CompoundPopup(cList, objectList,
type+".ID");
+ else
+ new CompoundPopup(cList, objectList,
labelAttribute);
}
}
}
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundPopup.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundPopup.java
2011-05-26 00:30:23 UTC (rev 25543)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/CompoundPopup.java
2011-05-26 00:34:49 UTC (rev 25544)
@@ -50,6 +50,7 @@
import java.util.List;
import java.util.Map;
+import javax.swing.BorderFactory;
import javax.swing.ImageIcon;
import javax.swing.JDialog;
import javax.swing.JFrame;
@@ -115,7 +116,8 @@
// Is it in our map?
if (imageMap.containsKey(labelComponent)) {
Image img =
imageMap.get(labelComponent).getImage(width,height, Color.WHITE);
- labelComponent.setIcon(new ImageIcon(img));
+ if (img != null)
+ labelComponent.setIcon(new ImageIcon(img));
}
}
@@ -131,11 +133,13 @@
setLayout(layout);
// Get the right attributes
- if (labelAttribute != null &&
labelAttribute.startsWith("node."))
+ if (labelAttribute != null &&
labelAttribute.startsWith("node.")) {
attributes = Cytoscape.getNodeAttributes();
- else if (labelAttribute != null &&
labelAttribute.startsWith("edge."))
+ labelAttribute = labelAttribute.substring(5);
+ } else if (labelAttribute != null &&
labelAttribute.startsWith("edge.")) {
attributes = Cytoscape.getEdgeAttributes();
- else
+ labelAttribute = labelAttribute.substring(5);
+ } else
labelAttribute = null;
for (Compound compound: compoundList) {
@@ -145,12 +149,16 @@
if (labelAttribute == null) {
label = new JLabel(new ImageIcon(img));
} else {
- String textLabel =
attributes.getAttribute(compound.getSource().getIdentifier(),labelAttribute.substring(5)).toString();
- label = new JLabel(textLabel, new
ImageIcon(img), JLabel.CENTER);
+ Object textLabel =
attributes.getAttribute(compound.getSource().getIdentifier(),labelAttribute);
+ if (textLabel == null)
+ textLabel =
compound.getSource().getIdentifier();
+ label = new JLabel(textLabel.toString(), new
ImageIcon(img), JLabel.CENTER);
label.setVerticalTextPosition(JLabel.BOTTOM);
label.setHorizontalTextPosition(JLabel.CENTER);
}
label.setBackground(Color.WHITE);
+ label.setOpaque(true);
+ label.setBorder(BorderFactory.createEtchedBorder());
label.addComponentListener(this);
imageMap.put(label, compound);
add (label);
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/renderers/CompoundRenderer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/renderers/CompoundRenderer.java
2011-05-26 00:30:23 UTC (rev 25543)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/ui/renderers/CompoundRenderer.java
2011-05-26 00:34:49 UTC (rev 25544)
@@ -94,8 +94,11 @@
if (width != table.getRowHeight())
table.setRowHeight(width); // Note, this will trigger a
repaint!
Image resizedImage = c.getImage(width,width);
- if (resizedImage == null) return null;
- JLabel l = new JLabel(new ImageIcon(resizedImage));
+ JLabel l;
+ if (resizedImage != null)
+ l = new JLabel(new ImageIcon(resizedImage));
+ else
+ l = new JLabel("No Image Available", JLabel.CENTER);
if (!rowMap.containsKey(c.getSource())) {
rowMap.put(c.getSource(), new ArrayList());
}
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