Author: kono
Date: 2009-07-20 12:37:13 -0700 (Mon, 20 Jul 2009)
New Revision: 17489
Added:
csplugins/trunk/ucsd/kono/ShortestPath2/resources/
csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
csplugins/trunk/ucsd/kono/ShortestPath2/src/
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
Removed:
csplugins/trunk/ucsd/kono/ShortestPath2/org/
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathDialog.java
Modified:
csplugins/trunk/ucsd/kono/ShortestPath2/build.xml
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
Log:
Modified: csplugins/trunk/ucsd/kono/ShortestPath2/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/ShortestPath2/build.xml 2009-07-20 19:29:52 UTC
(rev 17488)
+++ csplugins/trunk/ucsd/kono/ShortestPath2/build.xml 2009-07-20 19:37:13 UTC
(rev 17489)
@@ -1,98 +1,81 @@
<?xml version = "1.0"?>
-<project name = "ShortestPath" default = "compile_release" basedir = ".">
-
- <property name = "src" location = "src"/>
- <property name = "build" location = "build"/>
- <property name = "build.compiler" value = "modern"/>
- <!-- path to Cytoscape under development (CVS) -->
- <property name = "lib.dev" location = "../../../../cytoscape"/>
- <!-- path to Cytoscape 2.2 official release -->
- <!-- <property name = "lib.release" location = "../../../../C2.1/source"/>
-->
- <property name = "lib.release" location = "../../../../cytoscape"/>
- <property name = "jar" location = "jar"/>
- <property name = "doc" location = "doc"/>
+<project name="shortestPathPlugin2" default="all" basedir=".">
- <property name="cytoscape.plugin.release" value="${lib.release}/plugins"/>
+ <property name="src" location="src" />
+ <property name="build" location="build" />
+ <property name="build.compiler" value="modern" />
+ <!-- path to Cytoscape under development (CVS) -->
+ <property name="cylib" location="../cytoscape" />
+ <property name="lib" location="lib" />
+ <property name="jar" location="jar" />
+ <property name="doc" location="doc" />
+ <property name="projectName" value="shortestPathPlugin2" />
- <path id = "classpath_dev">
- <fileset dir = "${lib.dev}">
- <include name = "**/*.jar"/>
- </fileset>
- </path>
+ <property name="cytoscape.plugin" value="${lib}/plugins" />
- <path id = "classpath_release">
- <fileset dir = "${lib.release}">
- <include name = "**/*.jar"/>
- </fileset>
- </path>
+ <path id="classpath">
+ <fileset dir="${cylib}">
+ <include name="**/*.jar" />
+ </fileset>
+ <fileset dir="${lib}">
+ <include name="**/*.jar" />
+ </fileset>
+ </path>
- <target name="prepare" depends="clean">
- <mkdir dir="${build}"/>
- </target>
+ <target name="prepare" depends="clean">
+ <mkdir dir="${build}" />
+ </target>
- <target name="compile_dev" depends = "prepare" description="Compile with
Cytoscape under development">
- <!-- Compile the java code from ${src} into ${build} -->
- <javac source = "1.5" debug="true" deprecation="true" srcdir = "${src}"
destdir="${build}">
- <classpath refid = "classpath_dev"/>
- </javac>
- </target>
+ <target name="compile" depends="prepare" description="Compile with
Cytoscape under development">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac source="1.5" debug="true" deprecation="true"
srcdir="${src}" destdir="${build}">
+ <classpath refid="classpath" />
+ </javac>
+ </target>
- <target name="compile_release" depends = "prepare" description="Compiles
with current official release of Cytoscape">
- <!-- Compile the java code from ${src} into ${build} -->
- <javac source = "1.5" debug="true" srcdir = "${src}" destdir="${build}">
- <classpath refid = "classpath_release"/>
- </javac>
- </target>
-
- <target name="clean" description="clean up" >
- <!-- Delete the ${build} and ${src} directory trees -->
- <delete dir="${build}"/>
- <delete dir="${jar}"/>
- </target>
+ <target name="clean" description="clean up">
+ <!-- Delete the ${build} and ${src} directory trees -->
+ <delete dir="${build}" />
+ <delete dir="${jar}" />
+ </target>
- <target name="jar_release" depends="compile_release" description="makes a
jar for the current official Cytoscape release">
- <mkdir dir = "${jar}"/>
- <jar jarfile="${jar}/ShortestPath.jar">
- <fileset dir="${build}"/>
- </jar>
- </target>
+ <target name="jar" depends="compile" description="makes a jar for
Cytoscape under development">
+ <mkdir dir="${jar}" />
+ <unzip dest="${build}">
+ <fileset dir="${lib}" includes="*" />
+ </unzip>
+ <copy todir="build/org/cytoscape/view/ui/networkpanel"
file="resources/plugin.props" />
+ <mkdir dir="build/org/cytoscape/view/ui/networkpanel/images"/>
+ <copy todir="build/org/cytoscape/view/ui/networkpanel/images">
+ <fileset dir="images"/>
+ </copy>
+ <jar jarfile="${jar}/${projectName}.jar">
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="org.cytoscape.view.ui.networkpanel.NetworkBrowserPlugin" />
+ </manifest>
+ <fileset dir="${build}" />
+ </jar>
+ </target>
- <target name="jar_dev" depends="compile_dev" description="makes a jar for
Cytoscape under development">
- <mkdir dir = "${jar}"/>
- <jar jarfile="${jar}/ShortestPath.jar">
- <fileset dir="${build}"/>
- </jar>
- </target>
+ <target name="all" depends="jar" />
- <target name = "run_dev" depends="jar_dev" description = "Run under
development">
- <java classname = "cytoscape.CyMain" classpathref = "classpath_dev"
- fork = "true" maxmemory = "1g">
- <arg line = "--JLD"/>
- <arg line = "${jar}/ShortestPath.jar"/>
- <arg line = "-vt"/>
- <arg line = "5000"/>
- </java>
- </target>
+ <target name="run" depends="jar" description="Run under development">
+ <java classname="cytoscape.CyMain" classpathref="classpath"
fork="true" maxmemory="1g">
+ <arg line="--JLD" />
+ <arg line="${jar}/${projectName}.jar" />
+ <arg line="-vt" />
+ <arg line="5000" />
+ </java>
+ </target>
- <target name = "run_release" depends="jar_release" description = "Run
release">
- <java classname = "cytoscape.CyMain" classpathref = "classpath_release"
- fork = "true" maxmemory = "1g">
- <arg line = "--JLD"/>
- <arg line = "${jar}/ShortestPath.jar"/>
- <arg line = "--JLD"/>
- <arg line = "${cytoscape.plugin.release}"/>
- <arg line = "-vt"/>
- <arg line = "5000"/>
- </java>
- </target>
+ <!-- Target to Run JavaDoc -->
+ <target name="doc" description="Runs JavaDoc.">
+ <javadoc packagenames="cytoscape.groups.results.*"
sourcepath="src" source="1.5" destdir="doc" classpathref="classpath_release">
+ <link href="http://java.sun.com/j2se/1.5.0/docs/api/"; />
+ <link href="http://csbi.sourceforge.net/API/"; />
+ <link
href="http://chianti.ucsd.edu/Cyto-2_4_1/javadoc/"; />
+ </javadoc>
+ </target>
- <!-- Target to Run JavaDoc -->
- <target name="doc" description="Runs JavaDoc.">
- <javadoc packagenames="ShortestPath.*" sourcepath="src" source="1.5"
destdir="doc">
- <link href = "http://java.sun.com/j2se/1.4.2/docs/api/"/>
- <link href = "http://csbi.sourceforge.net/API/"/>
- </javadoc>
- </target>
-
</project>
Added: csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
(rev 0)
+++ csplugins/trunk/ucsd/kono/ShortestPath2/resources/plugin.props
2009-07-20 19:37:13 UTC (rev 17489)
@@ -0,0 +1,34 @@
+#plugin.props
+
+# This props file should be filled out and included in the plugin jar file.
This props file will be used
+# to put information into the Plugin Manager about the plugin
+
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=networkBrowser
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=Displays a list of groups created in a results panel.
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=1.0
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Other
+
+# -- The following properties are OPTIONAL -- #
+
+# URL to a website that gives more information about your plugin, Ex.
http://my-lab-site.org
+projectURL=http://cytoscape.org
+
+# List of authors. Note each author and institution pair are separated by a :
(colon)
+# each additional author institution pair must be separated from other pairs
bye a ; (semicolon)
+pluginAuthorsIntsitutions=Keiichiro Ono:UCSD
+
+# Date this plugin/plugin version was released
+releaseDate=July 1, 2009
Copied: csplugins/trunk/ucsd/kono/ShortestPath2/src/org (from rev 17487,
csplugins/trunk/ucsd/kono/ShortestPath2/org)
Deleted:
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathDialog.java
===================================================================
---
csplugins/trunk/ucsd/kono/ShortestPath2/org/cytoscape/analysis/shortestpath/ShortestPathDialog.java
2009-07-20 19:27:41 UTC (rev 17487)
+++
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathDialog.java
2009-07-20 19:37:13 UTC (rev 17489)
@@ -1,100 +0,0 @@
-package org.cytoscape.analysis.shortestpath;
-
-
-
-import java.awt.event.ActionEvent;
-
-import javax.swing.*;
-import javax.swing.WindowConstants.*;
-import javax.swing.border.*;
-import java.awt.Frame;
-import java.awt.GridLayout;
-import java.awt.event.*;
-
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-import cytoscape.view.CyNetworkView;
-import cytoscape.plugin.CytoscapePlugin;
-
-/**
- * Plugin for Cytoscape to find the shortest path between 2 nodes in a network.
- * It is possible to find the shortest path in directed and undirected networks
- *
- * @author mrsva
- *
- */
-public class ShortestPathDialog extends JDialog implements ActionListener {
- String selectedAttribute = null;
- JCheckBox dirButton;
- JCheckBox logButton;
-
- public ShortestPathDialog (Frame parent, String attribute) {
- super(parent, false);
- this.selectedAttribute = attribute;
- setDefaultCloseOperation(DISPOSE_ON_CLOSE);
- setTitle("Find Shorted Path using "+selectedAttribute);
-
- JPanel dataPanel = new JPanel();
- BoxLayout layout = new BoxLayout(dataPanel,
BoxLayout.PAGE_AXIS);
- dataPanel.setLayout(layout);
-
- JPanel checkBoxes = new JPanel(new GridLayout(2,1));
- // Set up our radio buttons (Directed vs Undirected)
- dirButton = new JCheckBox("Calculate path assuming directed
edges");
- dirButton.setSelected(false);
- checkBoxes.add(dirButton);
-
- logButton = new JCheckBox("Weights are expectation values (will
use negative log)");
- {
- logButton.setSelected(false);
- checkBoxes.add(logButton);
- // Is the negative log option available?
- CyAttributes EdgeAttributes =
Cytoscape.getEdgeAttributes();
- byte type = EdgeAttributes.getType(selectedAttribute);
- if(type == EdgeAttributes.TYPE_INTEGER) {
- // No
- logButton.setEnabled(false);
- }
- }
- checkBoxes.add(logButton);
- checkBoxes.setBorder(new CompoundBorder(
- BorderFactory.createEtchedBorder(EtchedBorder.LOWERED),
- new EmptyBorder(10,10,10,10)));
-
- dataPanel.add(checkBoxes);
-
- // Create the button box
- JPanel buttonBox = new JPanel();
- JButton doneButton = new JButton("Done");
- doneButton.setActionCommand("done");
- doneButton.addActionListener(this);
-
- JButton findButton = new JButton("Find Shortest Path");
- findButton.setActionCommand("find");
- findButton.addActionListener(this);
- buttonBox.add(doneButton);
- buttonBox.add(findButton);
-
buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
-
- dataPanel.add(buttonBox);
- setContentPane(dataPanel);
- }
-
- public void actionPerformed(ActionEvent e) {
- if ("done".equals(e.getActionCommand())) {
- setVisible(false);
- } else if ("find".equals(e.getActionCommand())) {
- ShortestPath sp = new ShortestPath();
- if (logButton.isSelected()) {
- sp.setNegativeLog(true);
- } else {
- sp.setNegativeLog(false);
- }
- if (dirButton.isSelected()) {
- sp.calculate(true,selectedAttribute);
- } else {
- sp.calculate(false,selectedAttribute);
- }
- }
- }
-}
Modified:
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/ShortestPath2/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
2009-07-20 19:27:41 UTC (rev 17487)
+++
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/ShortestPathPlugin.java
2009-07-20 19:37:13 UTC (rev 17489)
@@ -12,6 +12,8 @@
import javax.swing.SwingUtilities;
import javax.swing.JOptionPane;
+import org.cytoscape.analysis.shortestpath.internal.ShortestPathDialog;
+
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.view.CyNetworkView;
Copied:
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
(from rev 17487,
csplugins/trunk/ucsd/kono/ShortestPath2/org/cytoscape/analysis/shortestpath/ShortestPathDialog.java)
===================================================================
---
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/ShortestPath2/src/org/cytoscape/analysis/shortestpath/internal/ShortestPathDialog.java
2009-07-20 19:37:13 UTC (rev 17489)
@@ -0,0 +1,103 @@
+package org.cytoscape.analysis.shortestpath.internal;
+
+
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.*;
+import javax.swing.WindowConstants.*;
+import javax.swing.border.*;
+
+import org.cytoscape.analysis.shortestpath.ShortestPath;
+
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.event.*;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.view.CyNetworkView;
+import cytoscape.plugin.CytoscapePlugin;
+
+/**
+ * Plugin for Cytoscape to find the shortest path between 2 nodes in a network.
+ * It is possible to find the shortest path in directed and undirected networks
+ *
+ * @author mrsva
+ *
+ */
+public class ShortestPathDialog extends JDialog implements ActionListener {
+ String selectedAttribute = null;
+ JCheckBox dirButton;
+ JCheckBox logButton;
+
+ public ShortestPathDialog (Frame parent, String attribute) {
+ super(parent, false);
+ this.selectedAttribute = attribute;
+ setDefaultCloseOperation(DISPOSE_ON_CLOSE);
+ setTitle("Find Shorted Path using "+selectedAttribute);
+
+ JPanel dataPanel = new JPanel();
+ BoxLayout layout = new BoxLayout(dataPanel,
BoxLayout.PAGE_AXIS);
+ dataPanel.setLayout(layout);
+
+ JPanel checkBoxes = new JPanel(new GridLayout(2,1));
+ // Set up our radio buttons (Directed vs Undirected)
+ dirButton = new JCheckBox("Calculate path assuming directed
edges");
+ dirButton.setSelected(false);
+ checkBoxes.add(dirButton);
+
+ logButton = new JCheckBox("Weights are expectation values (will
use negative log)");
+ {
+ logButton.setSelected(false);
+ checkBoxes.add(logButton);
+ // Is the negative log option available?
+ CyAttributes EdgeAttributes =
Cytoscape.getEdgeAttributes();
+ byte type = EdgeAttributes.getType(selectedAttribute);
+ if(type == EdgeAttributes.TYPE_INTEGER) {
+ // No
+ logButton.setEnabled(false);
+ }
+ }
+ checkBoxes.add(logButton);
+ checkBoxes.setBorder(new CompoundBorder(
+ BorderFactory.createEtchedBorder(EtchedBorder.LOWERED),
+ new EmptyBorder(10,10,10,10)));
+
+ dataPanel.add(checkBoxes);
+
+ // Create the button box
+ JPanel buttonBox = new JPanel();
+ JButton doneButton = new JButton("Done");
+ doneButton.setActionCommand("done");
+ doneButton.addActionListener(this);
+
+ JButton findButton = new JButton("Find Shortest Path");
+ findButton.setActionCommand("find");
+ findButton.addActionListener(this);
+ buttonBox.add(doneButton);
+ buttonBox.add(findButton);
+
buttonBox.setBorder(BorderFactory.createEtchedBorder(EtchedBorder.LOWERED));
+
+ dataPanel.add(buttonBox);
+ setContentPane(dataPanel);
+ }
+
+ public void actionPerformed(ActionEvent e) {
+ if ("done".equals(e.getActionCommand())) {
+ setVisible(false);
+ } else if ("find".equals(e.getActionCommand())) {
+ ShortestPath sp = new ShortestPath();
+ if (logButton.isSelected()) {
+ sp.setNegativeLog(true);
+ } else {
+ sp.setNegativeLog(false);
+ }
+ if (dirButton.isSelected()) {
+ sp.calculate(true,selectedAttribute);
+ } else {
+ sp.calculate(false,selectedAttribute);
+ }
+ }
+ }
+}
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