Author: kono
Date: 2009-12-04 12:36:02 -0800 (Fri, 04 Dec 2009)
New Revision: 18656
Added:
csplugins/trunk/ucsd/kono/JythonEnginePlugin/build.xml
csplugins/trunk/ucsd/kono/JythonEnginePlugin/lib/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/lib/ScriptEngineManager.jar
csplugins/trunk/ucsd/kono/JythonEnginePlugin/plugin.props
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/PythonEnginePlugin.java
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/ui/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/ui/PythonConsole.java
csplugins/trunk/ucsd/kono/JythonEnginePlugin/testscripts/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/testscripts/test1.py
csplugins/trunk/ucsd/kono/JythonEnginePlugin/util-scripts/
csplugins/trunk/ucsd/kono/JythonEnginePlugin/util-scripts/message.py
Log:
Added: csplugins/trunk/ucsd/kono/JythonEnginePlugin/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/JythonEnginePlugin/build.xml
(rev 0)
+++ csplugins/trunk/ucsd/kono/JythonEnginePlugin/build.xml 2009-12-04
20:36:02 UTC (rev 18656)
@@ -0,0 +1,126 @@
+<?xml version="1.0"?>
+<!--
+
+ Python Scripting Engine for Cytoscape by Kei Ono
+
+ To build this plugin, you need to download Jython separately.
+
+-->
+
+<project name="PythonScriptingEngine" default="all" basedir=".">
+
+ <!-- Name of jython directory. -->
+ <property name="jython.version" value="jython2.5.1" />
+
+ <!-- You need modify this to your Cytoscape -->
+ <property name="cytoscape.dir" value="../cytoscape" />
+
+ <!-- All files generated by ant go here -->
+ <property name="build.dir" value="${basedir}/build" />
+
+ <!-- The java source directory-->
+ <property name="src.dir" value="${basedir}/src" />
+
+ <property name="project.jar" value="PythonScriptingEngine.jar" />
+
+ <!-- ============ Compilation Control Options =======================
-->
+ <property name="compile.debug" value="true" />
+ <property name="compile.deprecation" value="true" />
+ <property name="compile.optimize" value="true" />
+
+
+ <!-- ==================== Compilation Classpath ======================
-->
+ <path id="compile.classpath">
+ <fileset dir="${cytoscape.dir}">
+ <include name="cytoscape.jar" />
+ </fileset>
+ <fileset dir="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset>
+ <fileset dir="${basedir}/${jython.version}">
+ <include name="jython.jar" />
+ <include name="JyConsole.jar" />
+ </fileset>
+
+ </path>
+
+ <!-- ==================== Clean Target ===============================
-->
+ <target name="clean" description="Deletes all build files and starts
fresh">
+ <delete dir="${build.dir}" />
+ <delete file="${project.jar}" />
+ </target>
+
+ <!-- ==================== Compile Target
==============================-->
+ <target name="compile" depends="prepare" description="Compiles all Java
source files">
+ <mkdir dir="${build.dir}/classes" />
+ <javac srcdir="${src.dir}" source="1.5" target="1.5"
destdir="${build.dir}/classes" debug="${compile.debug}"
deprecation="${compile.deprecation}" optimize="${compile.optimize}">
+ <classpath refid="compile.classpath" />
+ </javac>
+ </target>
+
+ <!-- ==================== Jar Target ============================== -->
+ <target name="jar" depends="compile" description="Creates Plugin Jar:
${project.jar}">
+
+ <unjar dest="${build.dir}/classes">
+ <!--fileset dir="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset-->
+ <fileset dir="${basedir}/${jython.version}">
+ <include name="*.jar" />
+ </fileset>
+ <fileset
dir="${basedir}/JyConsole-1.4-bin/thirdpart/ArtTk">
+ <include name="*.jar" />
+ </fileset>
+ </unjar>
+
+
+ <copy toDir="${build.dir}/script">
+ <fileset dir="${basedir}/JyConsole-1.4-bin/script"
includes="**/*" />
+ </copy>
+
+ <copy toDir="${build.dir}/classes/Lib">
+ <fileset dir="${basedir}/${jython.version}/Lib"
includes="**/*" />
+ </copy>
+
+
+ <copy toDir="${build.dir}/classes/util-scripts">
+ <fileset dir="${basedir}/util-scripts" includes="**/*"
/>
+ </copy>
+ <copy
todir="${build.dir}/classes/edu/ucsd/bioeng/idekerlab/pythonengine"
file="${basedir}/plugin.props" />
+
+ <copy todir="${build.dir}/classes/images">
+ <fileset dir="${basedir}/images" />
+ </copy>
+
+
+
+ <jar destfile="${project.jar}" basedir="${build.dir}/classes">
+
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="edu.ucsd.bioeng.idekerlab.pythonengine.PythonEnginePlugin" />
+ </manifest>
+
+ </jar>
+ </target>
+
+ <!-- ==================== Build and test jar
============================== -->
+ <target name="all" depends="jar" />
+
+ <!-- ==================== Prepare Target ==============================
-->
+ <target name="prepare">
+ <!-- Create build directories as needed -->
+ <mkdir dir="${build.dir}" />
+ <mkdir dir="${build.dir}/classes" />
+
+ </target>
+
+ <!-- ==================== JUnit Test Target ===========================
-->
+ <target name="test" description="Runs all JUnit tests"
depends="compile">
+ <junit printsummary="yes" fork="yes" haltonfailure="yes">
+ <formatter type="plain" usefile="false" />
+ <test name="cytoscape.test.AllTest" />
+ <classpath refid="compile.classpath" />
+ </junit>
+ </target>
+
+</project>
Added: csplugins/trunk/ucsd/kono/JythonEnginePlugin/lib/ScriptEngineManager.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/JythonEnginePlugin/lib/ScriptEngineManager.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/JythonEnginePlugin/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/JythonEnginePlugin/plugin.props
(rev 0)
+++ csplugins/trunk/ucsd/kono/JythonEnginePlugin/plugin.props 2009-12-04
20:36:02 UTC (rev 18656)
@@ -0,0 +1,22 @@
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=PythonScriptingEngine
+
+# Description used to give users information about the plugin such as what it
does.
+# Html tags are encouraged for formatting purposes.
+pluginDescription=<p>Scripting engine based on Jython 2.5.1 implementation.
This plugin uses JyConsole library by Artenum OpenSource
project.</p><p><strong><font color="red">This plugin is for technology
evaluation purpose ONLY! Totally experimental.</font></strong>
+
+# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
+pluginVersion=0.20
+
+# Compatible Cytoscape version
+cytoscapeVersion=2.6, 2.7
+
+# Category, use one of the categories listed on the website or create your own
+pluginCategory=Communication/Scripting
+
+
+# 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 Department of Medicine
\ No newline at end of file
Added:
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/PythonEnginePlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/PythonEnginePlugin.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/PythonEnginePlugin.java
2009-12-04 20:36:02 UTC (rev 18656)
@@ -0,0 +1,173 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+ */
+package edu.ucsd.bioeng.idekerlab.pythonengine;
+
+import cytoscape.Cytoscape;
+
+import cytoscape.logger.CyLogger;
+
+import cytoscape.plugin.CytoscapePlugin;
+
+import edu.ucsd.bioeng.idekerlab.pythonengine.ui.PythonConsole;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManagerPlugin;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.engine.ScriptingEngine;
+
+import org.apache.bsf.BSFManager;
+
+import java.awt.event.ActionEvent;
+
+import java.beans.PropertyChangeEvent;
+
+import java.io.File;
+
+import java.lang.reflect.Method;
+
+import javax.swing.AbstractAction;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JMenuItem;
+
+
+/**
+ *
+ */
+public class PythonEnginePlugin extends CytoscapePlugin implements
ScriptingEngine {
+ private static final String ENGINE_NAME = "jython";
+ private static final String ENGINE_DISPLAY_NAME = "Python Scripting
Engine (based on Jython v2.5.1)";
+
+ // BSF engine name
+ private static final String ENGINE_CLASS_NAME =
"org.apache.bsf.engines.jython.JythonEngine";
+
+ // Icon of for script runner dialog
+ private static final Icon ICON = new
ImageIcon(PythonEnginePlugin.class.getResource("/images/python.png"));
+
+ // Static instance of this plugin
+ private static final PythonEnginePlugin engine = new
PythonEnginePlugin();
+
+ // private static final JyConsole console = new JyConsole();
+
+ /**
+ * Creates a new RubyEnginePlugin object.
+ */
+ public PythonEnginePlugin() {
+
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayName() {
+ // TODO Auto-generated method stub
+ return ENGINE_DISPLAY_NAME;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Icon getIcon() {
+ // TODO Auto-generated method stub
+ return ICON;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getIdentifier() {
+ // TODO Auto-generated method stub
+ return ENGINE_NAME;
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static void register() {
+ BSFManager.registerScriptingEngine(ENGINE_NAME,
ENGINE_CLASS_NAME,
+ new String[] { ENGINE_NAME
});
+
+ try {
+ final Class engineClass =
Class.forName("edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManager");
+ Method method = engineClass.getMethod("registerEngine",
+ new Class[] {
String.class, ScriptingEngine.class });
+ Object ret = method.invoke(null, new Object[] {
ENGINE_NAME, engine });
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ final JMenuItem consoleMenuItem = new JMenuItem(new
AbstractAction("Open Python Console...") {
+ public void actionPerformed(ActionEvent e) {
+
PythonConsole.getConsoleFrame().setVisible(true);
+ }
+ });
+
+ consoleMenuItem.setIcon(new
ImageIcon(PythonEnginePlugin.class.getResource("/images/python22x22.png")));
+
+
ScriptEngineManagerPlugin.getManager().addConsoleMenu(consoleMenuItem);
+
+ CyLogger.getLogger().info("Python scripting engine registered
successfully.");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param fileName DOCUMENT ME!
+ */
+ public static void executePythonScript(String fileName) {
+ PythonConsole.getConsoleFrame().setVisible(true);
+ PythonConsole.getConsole().clear();
+ PythonConsole.getConsole().executePythonFile(new
File(fileName));
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void propertyChange(PropertyChangeEvent e) {
+ if
(ScriptEngineManagerPlugin.getManager().getEngine(ENGINE_NAME) != null)
+ return;
+
+ if
(e.getPropertyName().equals(Cytoscape.CYTOSCAPE_INITIALIZED)) {
+ // Register this to ScriptEngineManager.
+ register();
+ }
+ }
+}
Added:
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/ui/PythonConsole.java
===================================================================
---
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/ui/PythonConsole.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/JythonEnginePlugin/src/edu/ucsd/bioeng/idekerlab/pythonengine/ui/PythonConsole.java
2009-12-04 20:36:02 UTC (rev 18656)
@@ -0,0 +1,163 @@
+/*
+ Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
+
+ The Cytoscape Consortium is:
+ - Institute for Systems Biology
+ - University of California San Diego
+ - Memorial Sloan-Kettering Cancer Center
+ - Institut Pasteur
+ - Agilent Technologies
+
+ This library is free software; you can redistribute it and/or modify it
+ under the terms of the GNU Lesser General Public License as published
+ by the Free Software Foundation; either version 2.1 of the License, or
+ any later version.
+
+ This library is distributed in the hope that it will be useful, but
+ WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
+ MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
+ documentation provided hereunder is on an "as is" basis, and the
+ Institute for Systems Biology and the Whitehead Institute
+ have no obligations to provide maintenance, support,
+ updates, enhancements or modifications. In no event shall the
+ Institute for Systems Biology and the Whitehead Institute
+ be liable to any party for direct, indirect, special,
+ incidental or consequential damages, including lost profits, arising
+ out of the use of this software and its documentation, even if the
+ Institute for Systems Biology and the Whitehead Institute
+ have been advised of the possibility of such damage. See
+ the GNU Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public License
+ along with this library; if not, write to the Free Software Foundation,
+ Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
+*/
+package edu.ucsd.bioeng.idekerlab.pythonengine.ui;
+
+import java.awt.BorderLayout;
+
+import javax.swing.JFrame;
+
+import com.artenum.jyconsole.JyConsole;
+
+import edu.ucsd.bioeng.idekerlab.pythonengine.PythonEnginePlugin;
+
+
+/*
+ * PythonConsole.java
+ *
+ * Created on 2008/09/23, 14:42
+ */
+
+/**
+ *
+ * @author kono
+ */
+public class PythonConsole extends javax.swing.JFrame {
+ /** Creates new form PythonConsole */
+ private static final JyConsole console = new JyConsole();
+ private static final PythonConsole pyConsole = new PythonConsole();
+ private static JFrame f;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static JFrame getConsoleFrame() {
+
+ if (f == null) {
+ f = new JFrame("Python Console for Cytoscape");
+ f.setSize(700, 500);
+ f.getContentPane().add(console, BorderLayout.CENTER);
+ f.getContentPane().add(titlePanel, BorderLayout.NORTH);
+ f.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
+ }
+
+ return f;
+ }
+
+ public static JyConsole getConsole() {
+ return console;
+ }
+
+
+ private PythonConsole() {
+ initComponents();
+ }
+
+ /** This method is called from within the constructor to
+ * initialize the form.
+ * WARNING: Do NOT modify this code. The content of this method is
+ * always regenerated by the Form Editor.
+ */
+ @SuppressWarnings("unchecked")
+ // <editor-fold defaultstate="collapsed" desc="Generated Code">
+ private void initComponents() {
+ this.setTitle("Python Console for Cytoscape");
+ this.setDefaultCloseOperation(HIDE_ON_CLOSE);
+
+ titlePanel = new javax.swing.JPanel();
+ pythonIcon = new javax.swing.JLabel();
+ plusLabel = new javax.swing.JLabel();
+ cytoscapeIcon = new javax.swing.JLabel();
+ titleLabel = new javax.swing.JLabel();
+ //consolePanel = new javax.swing.JPanel();
+
+ //JyConsole jyConsole = new JyConsole();
+ //jyConsole.add(jyConsole, BorderLayout.CENTER);
+ //this.getContentPane().add(jyConsole, BorderLayout.CENTER);
+
+
//setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
+ titlePanel.setBackground(new java.awt.Color(255, 255, 255));
+
+ pythonIcon.setBackground(new java.awt.Color(255, 255, 255));
+ pythonIcon.setIcon(new
javax.swing.ImageIcon(PythonEnginePlugin.class.getResource("/images/python.png")));
// NOI18N
+
+ plusLabel.setFont(new java.awt.Font("SansSerif", 1, 24)); //
NOI18N
+ plusLabel.setText("+");
+
+ cytoscapeIcon.setBackground(new java.awt.Color(255, 255, 255));
+ cytoscapeIcon.setIcon(new
javax.swing.ImageIcon(PythonEnginePlugin.class.getResource("/images/icon48.png")));
// NOI18N
+
+ titleLabel.setFont(new java.awt.Font("SansSerif", 1, 18)); //
NOI18N
+ titleLabel.setText("Python Console for Cytoscape");
+
+ org.jdesktop.layout.GroupLayout titlePanelLayout = new
org.jdesktop.layout.GroupLayout(titlePanel);
+ titlePanel.setLayout(titlePanelLayout);
+
titlePanelLayout.setHorizontalGroup(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(titlePanelLayout.createSequentialGroup()
+
.addContainerGap()
+
.add(pythonIcon)
+
.addPreferredGap(org.jdesktop.layout.LayoutStyle.RELATED)
+
.add(plusLabel)
+
.add(18, 18, 18)
+
.add(cytoscapeIcon)
+
.add(18, 18, 18)
+
.add(titleLabel)
+
.addContainerGap(51,
+
Short.MAX_VALUE)));
+
titlePanelLayout.setVerticalGroup(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.LEADING)
+
.add(titlePanelLayout.createSequentialGroup()
+
.addContainerGap()
+
.add(titlePanelLayout.createParallelGroup(org.jdesktop.layout.GroupLayout.BASELINE)
+
.add(pythonIcon)
+
.add(plusLabel)
+
.add(cytoscapeIcon)
+
.add(titleLabel))
+
.addContainerGap(org.jdesktop.layout.GroupLayout.DEFAULT_SIZE,
+
Short.MAX_VALUE)));
+
+ pack();
+ } // </editor-fold>
+
+ // Variables declaration - do not modify
+ //private javax.swing.JPanel jyConsole;
+ private javax.swing.JLabel cytoscapeIcon;
+ private javax.swing.JLabel plusLabel;
+ private javax.swing.JLabel pythonIcon;
+ private javax.swing.JLabel titleLabel;
+ private static javax.swing.JPanel titlePanel;
+
+ // End of variables declaration
+}
Added: csplugins/trunk/ucsd/kono/JythonEnginePlugin/testscripts/test1.py
===================================================================
--- csplugins/trunk/ucsd/kono/JythonEnginePlugin/testscripts/test1.py
(rev 0)
+++ csplugins/trunk/ucsd/kono/JythonEnginePlugin/testscripts/test1.py
2009-12-04 20:36:02 UTC (rev 18656)
@@ -0,0 +1,61 @@
+from cytoscape import Cytoscape
+
+import cytoscape.layout.CyLayouts as CyLayouts
+import java.lang.Integer as Integer
+import random
+
+ORIGINAL_NODES = 2
+MAX_LOOP = 1000 - ORIGINAL_NODES
+EACH_TRIAL = 2
+
+# Create network
+graph = Cytoscape.createNetwork("Barabasi-Albert generated by Python Script");
+
+#Create seed graph
+node1 = Cytoscape.getCyNode("Seed 1", True)
+node2 = Cytoscape.getCyNode("Seed 2", True)
+nodes = [node1, node2]
+
+graph.addNode(node1)
+graph.addNode(node2)
+edge = Cytoscape.getCyEdge(node1, node2, "interaction", "-", True);
+graph.addEdge(edge);
+
+degree = 0.0
+prob = 0.0
+i = 0
+
+# Grow the seed graph
+print "\n\n============Barabasi-Albert Random Graph Generator ============"
+print "\nGenerating network (1000 nodes). Please wait..."
+
+while (i<MAX_LOOP) :
+ newNode = Cytoscape.getCyNode(Integer.toString(i), True)
+ graph.addNode(newNode)
+
+ j = 0
+ while (j<EACH_TRIAL):
+ created = False
+ while (created == False):
+ idx = random.random() * len(nodes)
+ selectedNode = nodes[int(idx)]
+ degree = graph.getDegree(selectedNode)
+ prob = (degree + 1.0) / (graph.getNodeCount() +
graph.getEdgeCount() - 1.0)
+ if prob >= random.random() and newNode.getIdentifier !=
selectedNode.getIdentifier:
+ created = True;
+
+ edge = Cytoscape.getCyEdge(newNode, selectedNode, "interaction", "-",
True)
+ graph.addEdge(edge)
+ nodes.append(newNode)
+ j = j+1
+
+ i = i+1
+
+# Layout nodes
+
+print "Network generated. Start layout..."
+
+CyLayouts.getLayout("force-directed").doLayout();
+Cytoscape.getCurrentNetworkView().redrawGraph(False, True);
+
+print "\n\nDone!"
\ No newline at end of file
Added: csplugins/trunk/ucsd/kono/JythonEnginePlugin/util-scripts/message.py
===================================================================
--- csplugins/trunk/ucsd/kono/JythonEnginePlugin/util-scripts/message.py
(rev 0)
+++ csplugins/trunk/ucsd/kono/JythonEnginePlugin/util-scripts/message.py
2009-12-04 20:36:02 UTC (rev 18656)
@@ -0,0 +1 @@
+print "============= Finished! ==============="
\ No newline at end of file
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