Author: sfederow
Date: 2010-10-25 11:40:25 -0700 (Mon, 25 Oct 2010)
New Revision: 22363
Modified:
csplugins/trunk/soc/sfederow/CyAnimator/.classpath
csplugins/trunk/soc/sfederow/CyAnimator/build.xml
csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java
csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimatorDialog.java
csplugins/trunk/soc/sfederow/CyAnimator/src/CyFrame.java
Log:
Modified: csplugins/trunk/soc/sfederow/CyAnimator/.classpath
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/.classpath 2010-10-25 18:22:26 UTC
(rev 22362)
+++ csplugins/trunk/soc/sfederow/CyAnimator/.classpath 2010-10-25 18:40:25 UTC
(rev 22363)
@@ -97,5 +97,14 @@
<classpathentry kind="lib"
path="/home/stephen/cytoscape/extra-jars/coltginy.jar"/>
<classpathentry kind="lib"
path="/home/stephen/cytoscape/extra-jars/jfreechart-0.9.20.jar"/>
<classpathentry kind="lib"
path="/home/stephen/cytoscape/extra-jars/jfreechart-common-0.9.5.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/equations.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/jsr173_api.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/lucene-core-3.0.1.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/mimepull.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/phoebe.dnd.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/swing-layout-1.0.3.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/swingx-1.0.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/swingx-beaninfo-1.0.jar"/>
+ <classpathentry kind="lib"
path="/home/stephen/cytoscape/lib/woodstox.jar"/>
<classpathentry kind="output" path=""/>
</classpath>
Modified: csplugins/trunk/soc/sfederow/CyAnimator/build.xml
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/build.xml 2010-10-25 18:22:26 UTC
(rev 22362)
+++ csplugins/trunk/soc/sfederow/CyAnimator/build.xml 2010-10-25 18:40:25 UTC
(rev 22363)
@@ -11,12 +11,12 @@
<property name="src.dir" value="src"/>
<!-- The directory containing library jar files -->
- <property name="cytoroot.dir" value="../cytoscape"/>
+ <property name="cytoroot.dir" value="../Cytoscape_v2.7.0"/>
<property name="images.dir" value="img"/>
- <property name="release.dir" value="../cytoscape"/>
+ <property name="release.dir" value="../Cytoscape_v2.7.0"/>
- <property name="lib.dir" value = "../cytoscape/lib"/>
+ <property name="lib.dir" value = "../Cytoscape_v2.7.0/lib"/>
<!-- Temporary build directories -->
@@ -74,7 +74,7 @@
<!-- Target to create Cytoscape Jar File -->
<target name="build_cytoscape">
- <ant antfile="${cytoroot.dir}/cytoscape/build.xml"
inheritAll="false" target="jar"/>
+ <ant antfile="${cytoroot.dir}/Cytoscape_v2.7.0/build.xml"
inheritAll="false" target="jar"/>
</target>
<!-- Target to create the javadoc information -->
@@ -102,13 +102,19 @@
<fileset dir="${pluginlib.dir}"/>
</unjar>
+ <copy file="plugin.props" todir="${build.classes}" />
<jar destfile="${build.dir}/${plugin.name}.jar">
<fileset dir="${build.classes}"/>
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
+ value="CyAnimator" />
+ </manifest>
+
</jar>
<echo message="${plugin.name}.jar is now complete. It is
located in build/ directory"/>
- <copy file="${build.dir}/${plugin.name}.jar"
todir="../cytoscape/plugins/core/"/>
+ <copy file="${build.dir}/${plugin.name}.jar"
todir="../Cytoscape_v2.7.0/plugins/"/>
</target>
</project>
Modified: csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java 2010-10-25
18:22:26 UTC (rev 22362)
+++ csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimator.java 2010-10-25
18:40:25 UTC (rev 22363)
@@ -1,23 +1,49 @@
package CyAnimator;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
+import java.util.*;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import javax.swing.*;
-
+import cytoscape.plugin.CytoscapePlugin;
+import cytoscape.util.CytoscapeAction;
import cytoscape.Cytoscape;
-import cytoscape.plugin.CytoscapePlugin;
+
+
+
public class CyAnimator extends CytoscapePlugin {
+
/**
* @param args
*/
public CyAnimator() {
+ CyAnimatorAction action = new CyAnimatorAction();
+ action.setPreferredMenu("Plugins");
+ Cytoscape.getDesktop().getCyMenus().addAction(action);
+
+ }
+
+ class CyAnimatorAction extends CytoscapeAction {
+
+
+ public CyAnimatorAction() {super("CyAnimatorrr"); }
+
+ public void actionPerformed(ActionEvent e) {
+ System.out.println("WWDDDWWWWWWWWW");
+ CyAnimatorDialog animationDialog = new
CyAnimatorDialog();
+ // Pop it up
+ animationDialog.actionPerformed(e);
+
+ }
+
+ }
+ /**
+ * @param args
+ */
+ /*public CyAnimator() {
+
JMenuItem item = new JMenuItem("CyAnimator");
item.addActionListener(new CyAnimatorCommandListener());
@@ -25,10 +51,10 @@
JMenu pluginMenu =
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("Plugins");
pluginMenu.add(item);
-
-
+
}
-
+ */
+ /*
class CyAnimatorCommandListener implements ActionListener {
//BooleanAlgorithm alg = null;
@@ -45,4 +71,5 @@
//}
}
}
+ */
}
Modified: csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimatorDialog.java
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimatorDialog.java
2010-10-25 18:22:26 UTC (rev 22362)
+++ csplugins/trunk/soc/sfederow/CyAnimator/src/CyAnimatorDialog.java
2010-10-25 18:40:25 UTC (rev 22363)
@@ -114,6 +114,7 @@
private JMenuItem menuItem;
private JPanel mainPanel;
private JPopupMenu thumbnailMenu;
+ private JPopupMenu metabolicOptions;
private JSlider speedSlider;
final JFileChooser fc = new JFileChooser();
@@ -234,6 +235,16 @@
this.setSize(new Dimension(500,220));
this.setLocation(900, 100);
+ metabolicOptions = new JPopupMenu();
+ menuItem = new JMenuItem("Map Metabolic");
+ menuItem.addActionListener(this);
+ menuItem.setActionCommand("Initiate Metabolic");
+ metabolicOptions.add(menuItem);
+ //mainPanel.setComponentPopupMenu(metabolicOptions);
+ MouseListener extraPopupListener = new ExtraPopupListener();
+ framePane.addMouseListener(extraPopupListener);
+
+
setContentPane(mainPanel);
@@ -363,6 +374,26 @@
frameManager.setKeyFrameList(frameList);
updateThumbnails();
}
+
+ if(command.equals("Initiate Metabolic")){
+ MetabolicModule module = null;
+ fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+ int returnVal = fc.showOpenDialog(new JPanel());
+ if (returnVal == JFileChooser.APPROVE_OPTION) {
+ File file = fc.getSelectedFile();
+ String filePath = file.getPath();
+ //System.out.println(filePath+" "+file.getName());
+ try{
+ module = new MetabolicModule(filePath);
+ }catch (Exception excp) {
+ System.out.println(excp.getMessage());
+ }
+ }
+ frameManager = module.getFrameManager();
+ updateThumbnails();
+
+ }
+
setVisible(true);
}
@@ -720,9 +751,25 @@
}
}
}
+ class ExtraPopupListener extends MouseAdapter {
+ public void mousePressed(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ public void mouseReleased(MouseEvent e) {
+ maybeShowPopup(e);
+ }
+
+ private void maybeShowPopup(MouseEvent e) {
+ if (e.isPopupTrigger()) {
+ metabolicOptions.show(e.getComponent(),
+ e.getX(), e.getY());
+ }
+ }
+ }
+
-
protected ImageIcon createImageIcon(String path, String description) {
java.net.URL imgURL = getClass().getResource(path);
if (imgURL != null) {
Modified: csplugins/trunk/soc/sfederow/CyAnimator/src/CyFrame.java
===================================================================
--- csplugins/trunk/soc/sfederow/CyAnimator/src/CyFrame.java 2010-10-25
18:22:26 UTC (rev 22362)
+++ csplugins/trunk/soc/sfederow/CyAnimator/src/CyFrame.java 2010-10-25
18:40:25 UTC (rev 22363)
@@ -37,6 +37,7 @@
import java.awt.Graphics2D;
import java.awt.Color;
import java.awt.Image;
+import java.awt.Stroke;
import java.awt.image.*;
import java.awt.Paint;
import java.io.IOException;
@@ -116,7 +117,7 @@
nodeViewList = new ArrayList();
edgeViewList = new ArrayList();
- // Initialize our node view maps
+ // Initialize our edge view maps
Iterator<EdgeView> eviter = networkView.getEdgeViewsIterator();
while(eviter.hasNext()) {
EdgeView ev = eviter.next();
@@ -124,7 +125,7 @@
edgeViewList.add(ev);
}
- // Initialize our edge view maps
+ // Initialize our node view maps
Iterator<NodeView> nviter = networkView.getNodeViewsIterator();
while(nviter.hasNext()) {
NodeView nv = nviter.next();
@@ -307,6 +308,11 @@
if (p == null || edgeView == null) continue;
Integer trans =
edgeOpacityMap.get(edge.getIdentifier());
edgeView.setUnselectedPaint(new Color(p.getRed(),
p.getGreen(), p.getBlue(), trans));
+ //Added as of 7/1/2010, must have been some kind of
internal change in the API
+ Stroke oldStroke = edgeView.getStroke();
+ Stroke newStroke =
LineStyle.extractLineStyle(oldStroke).getStroke(edgeWidthMap.get(edge.getIdentifier()));
+ edgeView.setStroke(newStroke);
+ System.out.println(edge.getIdentifier()+":
"+edgeWidthMap.get(edge.getIdentifier()));
edgeView.setStrokeWidth(edgeWidthMap.get(edge.getIdentifier()));
}
currentView.setBackgroundPaint(backgroundPaint);
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