Author: kono
Date: 2009-12-03 18:23:36 -0800 (Thu, 03 Dec 2009)
New Revision: 18653
Added:
csplugins/trunk/ucsd/kono/JRubyEngine/build.xml
csplugins/trunk/ucsd/kono/JRubyEngine/images/
csplugins/trunk/ucsd/kono/JRubyEngine/images/ruby.png
csplugins/trunk/ucsd/kono/JRubyEngine/images/ruby22x22.png
csplugins/trunk/ucsd/kono/JRubyEngine/lib/
csplugins/trunk/ucsd/kono/JRubyEngine/lib/ScriptEngineManager.jar
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-complete-1.4.0.jar
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-embed-0.1.3.jar
csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props
csplugins/trunk/ucsd/kono/JRubyEngine/src/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/IRBConsoleDialog.java
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/TextAreaReadLine2.java
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/all_subnetworks.rb
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/ba_model_generator.rb
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/binary_matrix.rb
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/hello_world.rb
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/kegg_relation_mapper.rb
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_multiple_networks.rb
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_networks.rb
csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/
csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
Log:
New JRuby Scripting Engine for Cytoscape 2.7.
Added: csplugins/trunk/ucsd/kono/JRubyEngine/build.xml
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/build.xml
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/build.xml 2009-12-04 02:23:36 UTC
(rev 18653)
@@ -0,0 +1,109 @@
+<?xml version="1.0"?>
+<!--
+
+ Ruby script engine for Cytoscape by Kei Ono
+
+ To build this plugin, you need to download JRuby separately.
+
+-->
+
+<project name="RubyScriptingEngine" default="all" basedir=".">
+
+ <property name="jruby.version" value="jruby-1.4.0" />
+
+ <!-- You need modify this to your Cytoscape -->
+ <property name="cytoscape.dir" value="../workspaceC2/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="RubyScriptingEngine.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="../ScriptEngine1">
+ <include name="ScriptEngineManager.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="${basedir}/lib">
+ <include name="*.jar" />
+ </fileset>
+ </unjar>
+
+ <copy
todir="${build.dir}/classes/edu/ucsd/bioeng/idekerlab/rubyengine"
file="${basedir}/plugin.props" />
+
+ <copy todir="${build.dir}/classes/images">
+ <fileset dir="${basedir}/images" />
+ </copy>
+
+ <copy todir="${build.dir}/classes/utilscripts">
+ <fileset dir="${basedir}/utilscripts" />
+ </copy>
+
+
+
+ <jar destfile="${project.jar}" basedir="${build.dir}/classes">
+
+ <manifest>
+ <attribute name="Cytoscape-Plugin"
value="edu.ucsd.bioeng.idekerlab.rubyengine.RubyEnginePlugin" />
+ </manifest>
+
+ </jar>
+ </target>
+
+ <!-- ==================== Build and test jar
============================== -->
+ <target name="all" depends="jar" />
+
+ <!-- ==================== Prepare Target ==============================
-->
+ <target name="prepare">
+ <!-- Create build directories as needed -->
+ <mkdir dir="${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/JRubyEngine/images/ruby.png
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsd/kono/JRubyEngine/images/ruby.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/JRubyEngine/images/ruby22x22.png
===================================================================
(Binary files differ)
Property changes on: csplugins/trunk/ucsd/kono/JRubyEngine/images/ruby22x22.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/JRubyEngine/lib/ScriptEngineManager.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/JRubyEngine/lib/ScriptEngineManager.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-complete-1.4.0.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-complete-1.4.0.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-embed-0.1.3.jar
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/ucsd/kono/JRubyEngine/lib/jruby-embed-0.1.3.jar
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/plugin.props 2009-12-04 02:23:36 UTC
(rev 18653)
@@ -0,0 +1,22 @@
+# -- The following properties are REQUIRED -- #
+
+# The plugin name that will be displayed to users
+pluginName=RubyScriptingEngine
+
+# 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 jruby 1.4.0 implementation.
The console is now integrated with BioRuby Shell.</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=2.7
+
+# 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/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
===================================================================
---
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/RubyEnginePlugin.java
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,155 @@
+/*
+ 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.rubyengine;
+
+import java.awt.event.ActionEvent;
+import java.beans.PropertyChangeEvent;
+import java.io.IOException;
+import java.lang.reflect.Method;
+
+import javax.swing.AbstractAction;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JMenuItem;
+
+import org.apache.bsf.BSFManager;
+import org.jruby.embed.ScriptingContainer;
+
+import cytoscape.Cytoscape;
+import cytoscape.logger.CyLogger;
+import cytoscape.plugin.CytoscapePlugin;
+import edu.ucsd.bioeng.idekerlab.rubyengine.console.CyIRBConsole;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManagerPlugin;
+import edu.ucsd.bioeng.idekerlab.scriptenginemanager.engine.ScriptingEngine;
+
+
+/**
+ *
+ */
+public class RubyEnginePlugin extends CytoscapePlugin implements
ScriptingEngine {
+ private static final String ENGINE_NAME = "jruby";
+ private static final String ENGINE_DISPLAY_NAME = "Ruby Scripting
Engine (based on JRuby v1.4.0)";
+ private static final Icon ICON = new
ImageIcon(RubyEnginePlugin.class.getResource("/images/ruby.png"));
+ private static final RubyEnginePlugin engine = new RubyEnginePlugin();
+
+ /**
+ * Creates a new RubyEnginePlugin object.
+ */
+ public RubyEnginePlugin() {
+
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() {
+// System.setProperty("jruby.home",
"/Users/kono/Library/jruby-1.4.0");
+ ScriptingContainer container = new ScriptingContainer();
+
+ BSFManager.registerScriptingEngine("jruby",
"org.jruby.embed.bsf.JRubyEngine", new String[] {ENGINE_NAME});
+
+ System.out.println("*JRuby scripting engine loaded!");
+
+ try {
+ final Class<?> engineClass =
Class.forName("edu.ucsd.bioeng.idekerlab.scriptenginemanager.ScriptEngineManager");
+ Method method = engineClass.getMethod("registerEngine",
+ new Class[] {
String.class, ScriptingEngine.class });
+ method.invoke(null, new Object[] { ENGINE_NAME, engine
});
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+
+ final JMenuItem consoleMenuItem = new JMenuItem(new
AbstractAction("Open Ruby Console") {
+ public void actionPerformed(ActionEvent e) {
+ try {
+ CyIRBConsole.showConsole();
+ } catch (IOException e1) {
+
CyLogger.getLogger().error("Ruby Colsone Error", e1);
+ }
+ }
+ });
+
+ consoleMenuItem.setIcon(new
ImageIcon(RubyEnginePlugin.class.getResource("/images/ruby22x22.png")));
+
+
ScriptEngineManagerPlugin.getManager().addConsoleMenu(consoleMenuItem);
+
+ CyLogger.getLogger().info("Ruby scripting engine registered
successfully.");
+ }
+
+ /**
+ * 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/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
===================================================================
---
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/CyIRBConsole.java
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,231 @@
+/*
+ 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.rubyengine.console;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GraphicsEnvironment;
+import java.awt.Insets;
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+import javax.swing.BorderFactory;
+import javax.swing.ImageIcon;
+import javax.swing.JEditorPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextPane;
+import javax.swing.SwingConstants;
+
+import org.jruby.Ruby;
+import org.jruby.RubyInstanceConfig;
+import org.jruby.internal.runtime.ValueAccessor;
+
+import cytoscape.Cytoscape;
+import cytoscape.view.cytopanels.CytoPanelState;
+import edu.ucsd.bioeng.idekerlab.rubyengine.RubyEnginePlugin;
+
+/**
+ * Ruby Console for Cytoscape based on demo code in JRuby distribution.
+ *
+ * @author Keiichiro Ono
+ */
+public class CyIRBConsole extends JPanel {
+ private static CyIRBConsole console = null;
+ private static Ruby runtime = null;
+ private static final ExecutorService consoleService = Executors
+ .newCachedThreadPool();
+ private static final String BIORUBY_SCRIPT_LOCATION =
"/utilscripts/biorubyshell.rb";
+ private static String startScript;
+
+ private static final ImageIcon tabIcon = new ImageIcon(
+
RubyEnginePlugin.class.getResource("/images/ruby22x22.png"));
+
+ /**
+ * Creates a new CyIRBConsole object.
+ *
+ * @param title
+ * DOCUMENT ME!
+ * @throws IOException
+ */
+ public CyIRBConsole(String title) throws IOException {
+ // super(title);
+
+ InputStreamReader in = null;
+ StringBuilder builder = new StringBuilder();
+
+ in = new InputStreamReader(RubyEnginePlugin.class.getResource(
+ BIORUBY_SCRIPT_LOCATION).openStream());
+
+ BufferedReader br = new BufferedReader(in);
+
+ String line;
+
+ while ((line = br.readLine()) != null) {
+ builder.append(line + "\n");
+ }
+
+ br.close();
+ in.close();
+
+ br = null;
+ in = null;
+
+ startScript = builder.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws IOException
+ */
+ public static void showConsole() throws IOException {
+ if (console == null) {
+ // Initialize console
+ if (runtime == null)
+ runtime = Ruby.newInstance();
+
+ console = new CyIRBConsole("Cytoscape-Ruby Interactive
Console");
+ buildConsole(null);
+
+
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST).add(
+ "Cytoscape-BioRuby Console", tabIcon,
console);
+
+
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST).setState(
+ CytoPanelState.DOCK);
+ }
+
+ consoleService.execute(new Runnable() {
+ public void run() {
+ runtime.evalScriptlet(startScript);
+
+
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
+ .remove(console);
+ if
(Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
+ .getCytoPanelComponentCount()
== 0)
+
Cytoscape.getDesktop().getCytoPanel(SwingConstants.EAST)
+
.setState(CytoPanelState.HIDE);
+ runtime.tearDown();
+ console = null;
+ System.out.println("Console terminated!");
+ }
+ });
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param args
+ * DOCUMENT ME!
+ */
+ public static void buildConsole(final String[] args) {
+ console.setLayout(new BorderLayout());
+ console.setPreferredSize(new Dimension(500, 600));
+
+ final JEditorPane text = new JTextPane();
+ text.setMargin(new Insets(8, 8, 8, 8));
+ text.setCaretColor(new Color(0xa4, 0x00, 0x00));
+ text.setBackground(Color.white);
+ text.setForeground(Color.red);
+
+ final Font font = console.findFont("Monospaced", Font.PLAIN, 14,
+ new String[] { "Monaco", "Andale Mono" });
+ text.setFont(font);
+
+ final JScrollPane pane = new JScrollPane();
+ pane.setViewportView(text);
+ pane.setBorder(BorderFactory.createLineBorder(Color.darkGray));
+ console.add(pane);
+ console.validate();
+
+ final TextAreaReadLine2 tar = new TextAreaReadLine2(text,
+ " Welcome to CyRuby Console \n"
+ + " Starting BioRuby Shell.
Please wait...\n\n");
+
+ final RubyInstanceConfig config = new RubyInstanceConfig() {
+
+ {
+ setInput(tar.getInputStream());
+ setOutput(new
PrintStream(tar.getOutputStream()));
+ setError(new
PrintStream(tar.getOutputStream()));
+ setObjectSpaceEnabled(true); // useful for code
completion
+ // inside the IRB
+ // setArgv(args);
+ }
+ };
+
+ runtime = Ruby.newInstance(config);
+
+ runtime.getGlobalVariables().defineReadonly(
+ "$$",
+ new ValueAccessor(runtime.newFixnum(System
+ .identityHashCode(runtime))));
+ runtime.getLoadService().init(new ArrayList());
+
+ tar.hookIntoRuntime(runtime);
+
+ }
+
+ private Font findFont(String otherwise, int style, int size,
+ String[] families) {
+ String[] fonts =
GraphicsEnvironment.getLocalGraphicsEnvironment()
+ .getAvailableFontFamilyNames();
+ Arrays.sort(fonts);
+
+ Font font = null;
+
+ for (int i = 0; i < families.length; i++) {
+ if (Arrays.binarySearch(fonts, families[i]) >= 0) {
+ font = new Font(families[i], style, size);
+
+ break;
+ }
+ }
+
+ if (font == null)
+ font = new Font(otherwise, style, size);
+
+ return font;
+ }
+}
Added:
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/IRBConsoleDialog.java
===================================================================
---
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/IRBConsoleDialog.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/IRBConsoleDialog.java
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,124 @@
+package edu.ucsd.bioeng.idekerlab.rubyengine.console;
+
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Insets;
+import java.awt.Rectangle;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.JDialog;
+import javax.swing.JScrollPane;
+import javax.swing.JTextPane;
+import javax.swing.SwingUtilities;
+import javax.swing.UIManager;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.JTextComponent;
+
+import org.jruby.Ruby;
+import org.jruby.demo.TextAreaReadline;
+
+import sun.misc.RequestProcessor;
+
+import com.sun.jmx.snmp.tasks.Task;
+
+public class IRBConsoleDialog extends JDialog {
+
+ private boolean finished = true;
+ private JTextPane text;
+
+
+ public void createTerminal() {
+ text = new JTextPane();
+
+ text.setMargin(new Insets(8,8,8,8));
+ text.setCaretColor(new Color(0xa4, 0x00, 0x00));
+ text.setBackground(new Color(0xf2, 0xf2, 0xf2));
+ text.setForeground(new Color(0xa4, 0x00, 0x00));
+
+ // From core/output2/**/AbstractOutputPane
+ Integer i = (Integer) UIManager.get("customFontSize"); //NOI18N
+ int size;
+ if (i != null) {
+ size = i.intValue();
+ } else {
+ Font f = (Font) UIManager.get("controlFont"); // NOI18N
+ size = f != null ? f.getSize() : 11;
+ }
+ text.setFont(new Font ("Monospaced", Font.PLAIN, size)); //NOI18N
+ //setBorder (BorderFactory.createEmptyBorder());
+
+ // Try to initialize colors from NetBeans properties, see core/output2
+ Color c = UIManager.getColor("nb.output.selectionBackground"); //
NOI18N
+ if (c != null) {
+ text.setSelectionColor(c);
+ }
+
+
+
+
+ JScrollPane pane = new JScrollPane();
+ pane.setViewportView(text);
+ pane.setBorder(BorderFactory.createLineBorder(Color.darkGray));
+ add(pane);
+ validate();
+
+ final Ruby runtime = getRuntime(text);
+// startIRB(runtime);
+
+// RequestProcessor.Task task =
RequestProcessor.getDefault().create(new Runnable() {
+// //RequestProcessor.getDefault().post(new Runnable() {
+// public void run() {
+//
+// }
+// });
+// task.addTaskListener(new TaskListener() {
+// public void taskFinished(Task task) {
+// finished = true;
+// //tar.writeMessage(" " +
NbBundle.getMessage(IrbTopComponent.class, "IrbGoodbye") + " "); // NOI18N
+// text.setEditable(false);
+// SwingUtilities.invokeLater(new Runnable() {
+// public void run() {
+// IrbTopComponent.this.close();
+// IrbTopComponent.this.removeAll();
+// text = null;
+// }
+// });
+// }
+// });
+// task.schedule(10);
+
+ }
+
+
+ static Ruby getRuntime(final JTextComponent text) {
+// final TextAreaReadline tar = new TextAreaReadline(text,
+// " " + NbBundle.getMessage(IrbTopComponent.class,
"IrbWelcome") + " \n\n"); // NOI18N
+// // Ensure that ClassPath can find libraries etc.
+// RubyInstallation.getInstance().setJRubyLoadPaths();
+//
+// final PipedInputStream pipeIn = new PipedInputStream();
+// final RubyInstanceConfig config = new RubyInstanceConfig() {{
+// setInput(pipeIn);
+// setOutput(new PrintStream(tar));
+// setError(new PrintStream(tar));
+// setObjectSpaceEnabled(false);
+// //setArgv(args);
+// }};
+// final Ruby runtime = Ruby.newInstance(config);
+//
+// runtime.getGlobalVariables().defineReadonly("$$", new
ValueAccessor(runtime.newFixnum(System.identityHashCode(runtime))));
+// runtime.getLoadService().init(new ArrayList());
+//
+// tar.hookIntoRuntime(runtime);
+// return runtime;
+// }
+//
+// private static void startIRB(final Ruby runtime) {
+// runtime.evalScriptlet("require 'irb'; require 'irb/completion';
IRB.start"); // NOI18N
+// }
+//
+ return null;
+ }
+}
Added:
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/TextAreaReadLine2.java
===================================================================
---
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/TextAreaReadLine2.java
(rev 0)
+++
csplugins/trunk/ucsd/kono/JRubyEngine/src/edu/ucsd/bioeng/idekerlab/rubyengine/console/TextAreaReadLine2.java
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,667 @@
+
+/*
+ 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.rubyengine.console;
+
+import org.jruby.Ruby;
+import org.jruby.RubyModule;
+import org.jruby.RubyString;
+
+import org.jruby.ext.Readline;
+
+import org.jruby.runtime.Arity;
+import org.jruby.runtime.Block;
+import org.jruby.runtime.builtin.IRubyObject;
+import org.jruby.runtime.callback.Callback;
+
+import java.awt.Color;
+import java.awt.EventQueue;
+import java.awt.Point;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.UnsupportedEncodingException;
+
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.concurrent.BlockingQueue;
+import java.util.concurrent.LinkedBlockingQueue;
+
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JComboBox;
+import javax.swing.plaf.basic.BasicComboPopup;
+import javax.swing.text.AbstractDocument;
+import javax.swing.text.AttributeSet;
+import javax.swing.text.BadLocationException;
+import javax.swing.text.DocumentFilter;
+import javax.swing.text.JTextComponent;
+import javax.swing.text.MutableAttributeSet;
+import javax.swing.text.SimpleAttributeSet;
+import javax.swing.text.StyleConstants;
+
+
+/**
+ *
+ */
+public class TextAreaReadLine2 implements KeyListener {
+ private static final String EMPTY_LINE = "";
+ private JTextComponent area;
+ private int startPos;
+ private String currentLine;
+
+ /**
+ *
+ */
+ public volatile MutableAttributeSet promptStyle;
+
+ /**
+ *
+ */
+ public volatile MutableAttributeSet inputStyle;
+
+ /**
+ *
+ */
+ public volatile MutableAttributeSet outputStyle;
+
+ /**
+ *
+ */
+ public volatile MutableAttributeSet resultStyle;
+ private JComboBox completeCombo;
+ private BasicComboPopup completePopup;
+ private int start;
+ private int end;
+ private volatile boolean finished = false;
+ private final InputStream inputStream = new Input();
+ private final OutputStream outputStream = new Output();
+ private volatile BlockingQueue<String> pendingLines = new
LinkedBlockingQueue<String>();
+
+ /**
+ * Creates a new TextAreaReadLine2 object.
+ *
+ * @param area DOCUMENT ME!
+ */
+ public TextAreaReadLine2(JTextComponent area) {
+ this(area, null);
+ }
+
+ /**
+ * Creates a new TextAreaReadLine2 object.
+ *
+ * @param area DOCUMENT ME!
+ * @param message DOCUMENT ME!
+ */
+ public TextAreaReadLine2(JTextComponent area, final String message) {
+ this.area = area;
+
+ area.addKeyListener(this);
+
+ // No editing before startPos
+ if (area.getDocument() instanceof AbstractDocument)
+ ((AbstractDocument)
area.getDocument()).setDocumentFilter(new DocumentFilter() {
+ public void
insertString(DocumentFilter.FilterBypass fb, int offset,
+ String string,
AttributeSet attr)
+ throws BadLocationException {
+ if (offset >= startPos)
+ super.insertString(fb,
offset, string, attr);
+ }
+
+ public void
remove(DocumentFilter.FilterBypass fb, int offset, int length)
+ throws BadLocationException {
+ if (offset >= startPos)
+ super.remove(fb,
offset, length);
+ }
+
+ public void
replace(DocumentFilter.FilterBypass fb, int offset, int length,
+ String text,
AttributeSet attrs)
+ throws BadLocationException {
+ if (offset >= startPos)
+ super.replace(fb,
offset, length, text, attrs);
+ }
+ });
+
+
+ promptStyle = new SimpleAttributeSet();
+ StyleConstants.setForeground(promptStyle, new Color(0xa4, 0x00,
0x00));
+
+ inputStyle = new SimpleAttributeSet();
+ StyleConstants.setForeground(inputStyle, new Color(0x20, 0x4a,
0x87));
+
+ outputStyle = new SimpleAttributeSet();
+ StyleConstants.setForeground(outputStyle, Color.darkGray);
+
+ resultStyle = new SimpleAttributeSet();
+ StyleConstants.setItalic(resultStyle, true);
+ StyleConstants.setForeground(resultStyle, new Color(0x20, 0x4a,
0x87));
+
+ completeCombo = new JComboBox();
+ completeCombo.setRenderer(new DefaultListCellRenderer()); // no
silly ticks!
+ completePopup = new BasicComboPopup(completeCombo);
+
+ if (message != null) {
+ final MutableAttributeSet messageStyle = new
SimpleAttributeSet();
+ StyleConstants.setBackground(messageStyle,
area.getForeground());
+ StyleConstants.setForeground(messageStyle,
area.getBackground());
+ append(message, messageStyle);
+ }
+
+ startPos = area.getDocument().getLength();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public InputStream getInputStream() {
+ return inputStream;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public OutputStream getOutputStream() {
+ return outputStream;
+ }
+
+ private Ruby runtime;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param runtime DOCUMENT ME!
+ */
+ public void hookIntoRuntime(final Ruby runtime) {
+ this.runtime = runtime;
+ /* Hack in to replace usual readline with this */
+ runtime.getLoadService().require("readline");
+
+ RubyModule readlineM = runtime.fastGetModule("Readline");
+
+ readlineM.defineModuleFunction("readline",
+ new Callback() {
+ public IRubyObject execute(IRubyObject recv,
IRubyObject[] args, Block block) {
+ String line =
readLine(args[0].toString());
+
+ if (line != null) {
+ return
RubyString.newUnicodeString(runtime, line);
+ } else {
+ return runtime.getNil();
+ }
+ }
+
+ public Arity getArity() {
+ return Arity.twoArguments();
+ }
+ });
+ }
+
+ protected void completeAction(KeyEvent event) {
+ if (Readline.getCompletor(Readline.getHolder(runtime)) == null)
+ return;
+
+ event.consume();
+
+ if (completePopup.isVisible())
+ return;
+
+ List candidates = new LinkedList();
+ String bufstr = null;
+
+ try {
+ bufstr = area.getText(startPos, area.getCaretPosition()
- startPos);
+ } catch (BadLocationException e) {
+ return;
+ }
+
+ int cursor = area.getCaretPosition() - startPos;
+
+ int position =
Readline.getCompletor(Readline.getHolder(runtime))
+ .complete(bufstr, cursor, candidates);
+
+ // no candidates? Fail.
+ if (candidates.isEmpty())
+ return;
+
+ if (candidates.size() == 1) {
+ replaceText(startPos + position,
area.getCaretPosition(), (String) candidates.get(0));
+
+ return;
+ }
+
+ start = startPos + position;
+ end = area.getCaretPosition();
+
+ Point pos = area.getCaret().getMagicCaretPosition();
+
+ // bit risky if someone changes completor, but useful for
method calls
+ int cutoff = bufstr.substring(position).lastIndexOf('.') + 1;
+ start += cutoff;
+
+ if (candidates.size() < 10)
+
completePopup.getList().setVisibleRowCount(candidates.size());
+ else
+ completePopup.getList().setVisibleRowCount(10);
+
+ completeCombo.removeAllItems();
+
+ for (Iterator i = candidates.iterator(); i.hasNext();) {
+ String item = (String) i.next();
+
+ if (cutoff != 0)
+ item = item.substring(cutoff);
+
+ completeCombo.addItem(item);
+ }
+
+ completePopup.show(area, pos.x, pos.y +
area.getFontMetrics(area.getFont()).getHeight());
+ }
+
+ protected void backAction(KeyEvent event) {
+ if (area.getCaretPosition() <= startPos)
+ event.consume();
+ }
+
+ protected void upAction(KeyEvent event) {
+ event.consume();
+
+ if (completePopup.isVisible()) {
+ int selected = completeCombo.getSelectedIndex() - 1;
+
+ if (selected < 0)
+ return;
+
+ completeCombo.setSelectedIndex(selected);
+
+ return;
+ }
+
+ if (!Readline.getHistory(Readline.getHolder(runtime)).next())
// at end
+ currentLine = getLine();
+ else
+
Readline.getHistory(Readline.getHolder(runtime)).previous(); // undo check
+
+ if
(!Readline.getHistory(Readline.getHolder(runtime)).previous())
+ return;
+
+ String oldLine =
Readline.getHistory(Readline.getHolder(runtime)).current().trim();
+ replaceText(startPos, area.getDocument().getLength(), oldLine);
+ }
+
+ protected void downAction(KeyEvent event) {
+ event.consume();
+
+ if (completePopup.isVisible()) {
+ int selected = completeCombo.getSelectedIndex() + 1;
+
+ if (selected == completeCombo.getItemCount())
+ return;
+
+ completeCombo.setSelectedIndex(selected);
+
+ return;
+ }
+
+ if (!Readline.getHistory(Readline.getHolder(runtime)).next())
+ return;
+
+ String oldLine;
+
+ if (!Readline.getHistory(Readline.getHolder(runtime)).next())
// at end
+ oldLine = currentLine;
+ else {
+
Readline.getHistory(Readline.getHolder(runtime)).previous(); // undo check
+ oldLine =
Readline.getHistory(Readline.getHolder(runtime)).current().trim();
+ }
+
+ replaceText(startPos, area.getDocument().getLength(), oldLine);
+ }
+
+ protected void replaceText(int start, int end, String replacement) {
+ try {
+ area.getDocument().remove(start, end - start);
+ area.getDocument().insertString(start, replacement,
inputStyle);
+ } catch (BadLocationException e) {
+ e.printStackTrace();
+ }
+ }
+
+ protected String getLine() {
+ try {
+ return area.getText(startPos,
area.getDocument().getLength() - startPos);
+ } catch (BadLocationException e) {
+ e.printStackTrace();
+ }
+
+ return null;
+ }
+
+ protected void enterAction(KeyEvent event) {
+ event.consume();
+
+ if (completePopup.isVisible()) {
+ if (completeCombo.getSelectedItem() != null)
+ replaceText(start, end, (String)
completeCombo.getSelectedItem());
+
+ completePopup.setVisible(false);
+
+ return;
+ }
+
+ append("\n", null);
+
+ if (!finished) {
+ String line = getLine();
+ startPos = area.getDocument().getLength();
+ pendingLines.offer(line);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param prompt DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String readLine(final String prompt) {
+ if (EventQueue.isDispatchThread()) {
+ throw runtime.newThreadError("Cannot call readline from
event dispatch thread");
+ }
+
+ EventQueue.invokeLater(new Runnable() {
+ public void run() {
+ append(prompt.trim(), promptStyle);
+ append(" ", inputStyle); // hack to get
right style for input
+
area.setCaretPosition(area.getDocument().getLength());
+ startPos =
area.getDocument().getLength();
+
Readline.getHistory(Readline.getHolder(runtime)).moveToEnd();
+ }
+ });
+
+ try {
+ String line = pendingLines.take();
+
+ if (line.length() > 0) {
+ return line.trim();
+ } else {
+ if (finished) {
+ pendingLines.offer(EMPTY_LINE);
+ }
+
+ return null;
+ }
+ } catch (InterruptedException e) {
+ Thread.currentThread().interrupt();
+
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param event DOCUMENT ME!
+ */
+ public void keyPressed(KeyEvent event) {
+ int code = event.getKeyCode();
+
+ switch (code) {
+ case KeyEvent.VK_TAB:
+ completeAction(event);
+
+ break;
+
+ case KeyEvent.VK_LEFT:
+ case KeyEvent.VK_BACK_SPACE:
+ backAction(event);
+
+ break;
+
+ case KeyEvent.VK_UP:
+ upAction(event);
+
+ break;
+
+ case KeyEvent.VK_DOWN:
+ downAction(event);
+
+ break;
+
+ case KeyEvent.VK_ENTER:
+ enterAction(event);
+
+ break;
+
+ case KeyEvent.VK_HOME:
+ event.consume();
+ area.setCaretPosition(startPos);
+
+ break;
+ }
+
+ if (completePopup.isVisible() && (code != KeyEvent.VK_TAB) &&
(code != KeyEvent.VK_UP)
+ && (code != KeyEvent.VK_DOWN))
+ completePopup.setVisible(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public void keyReleased(KeyEvent arg0) {
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ */
+ public void keyTyped(KeyEvent arg0) {
+ }
+
+ /** Output methods **/
+ protected void append(String toAppend, AttributeSet style) {
+ try {
+
area.getDocument().insertString(area.getDocument().getLength(), toAppend,
style);
+ } catch (BadLocationException e) {
+ }
+ }
+
+ private void writeLineUnsafe(final String line) {
+ if (line.startsWith("=>"))
+ append(line, resultStyle);
+ else
+ append(line, outputStyle);
+
+ startPos = area.getDocument().getLength();
+ }
+
+ private void writeLine(final String line) {
+ if (EventQueue.isDispatchThread()) {
+ writeLineUnsafe(line);
+ } else {
+ EventQueue.invokeLater(new Runnable() {
+ public void run() {
+ writeLineUnsafe(line);
+ }
+ });
+ }
+ }
+
+ private class Input extends InputStream {
+ private byte[] bytes = null;
+ private int offset = 0;
+
+ @Override
+ public synchronized int available() {
+ if (bytes != null) {
+ return bytes.length - offset;
+ } else {
+ return 0;
+ }
+ }
+
+ private boolean ensureBytes() throws IOException {
+ if (bytes == null) {
+ String line;
+
+ try {
+ line = pendingLines.take();
+ } catch (InterruptedException e) {
+ IOException ioEx = new
IOException("Interrupted");
+ ioEx.initCause(e);
+ throw ioEx;
+ }
+
+ if (line.length() > 0) {
+ try {
+ bytes = line.getBytes("UTF-8");
+ } catch (UnsupportedEncodingException
e) {
+ bytes = line.getBytes();
+ }
+ } else if (finished) {
+ pendingLines.offer(EMPTY_LINE);
+ }
+ }
+
+ return bytes != null;
+ }
+
+ @Override
+ public synchronized int read() throws IOException {
+ if (EventQueue.isDispatchThread()) {
+ throw new IOException("Cannot call read from
event dispatch thread");
+ }
+
+ if (ensureBytes()) {
+ assert bytes.length > 0;
+
+ int b = bytes[offset];
+
+ if (++offset == bytes.length) {
+ offset = 0;
+ bytes = null;
+ }
+
+ return b;
+ } else {
+ return -1;
+ }
+ }
+
+ @Override
+ public synchronized int read(byte[] b, int off, int len) throws
IOException {
+ if (EventQueue.isDispatchThread()) {
+ throw new IOException("Cannot call read from
event dispatch thread");
+ }
+
+ if (b == null) {
+ throw new NullPointerException();
+ }
+
+ if ((off < 0) || (len < 0) || ((off + len) > b.length))
{
+ throw new IndexOutOfBoundsException();
+ }
+
+ if (len == 0) {
+ return 0;
+ }
+
+ if (ensureBytes()) {
+ final int remaining = bytes.length - offset;
+
+ if (len > remaining) {
+ len = remaining;
+ }
+
+ System.arraycopy(bytes, offset, b, off, len);
+ offset += len;
+
+ if (len == remaining) {
+ offset = 0;
+ bytes = null;
+ }
+
+ return len;
+ } else {
+ return -1;
+ }
+ }
+
+ @Override
+ public synchronized void close() {
+ offset = 0;
+ bytes = null;
+ finished = true;
+ pendingLines.clear();
+ pendingLines.offer(EMPTY_LINE);
+ }
+ }
+
+ private class Output extends OutputStream {
+ @Override
+ public void write(int b) throws IOException {
+ writeLine("" + b);
+ }
+
+ @Override
+ public void write(byte[] b, int off, int len) {
+ try {
+ writeLine(new String(b, off, len, "UTF-8"));
+ } catch (UnsupportedEncodingException ex) {
+ writeLine(new String(b, off, len));
+ }
+ }
+
+ @Override
+ public void write(byte[] b) {
+ try {
+ writeLine(new String(b, "UTF-8"));
+ } catch (UnsupportedEncodingException ex) {
+ writeLine(new String(b));
+ }
+ }
+ }
+}
Added: csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/all_subnetworks.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/all_subnetworks.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/all_subnetworks.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,16 @@
+require 'java'
+
+include_class 'cytoscape.Cytoscape'
+include_class 'cytoscape.CyNetwork'
+include_class 'java.util.ArrayList'
+
+# Nodes in current network
+net = Cytoscape.getCurrentNetwork
+nodes = Cytoscape.getCurrentNetwork.nodesList
+subnet = ArrayList.new
+
+nodes.each do |node|
+
+ subnet.add(node)
+ puts net.getConnectingEdges(subnet)
+end
\ No newline at end of file
Added: csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/ba_model_generator.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/ba_model_generator.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/ba_model_generator.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,60 @@
+require 'java'
+
+include_class 'cytoscape.Cytoscape'
+include_class 'cytoscape.CyNode'
+include_class 'cytoscape.CyEdge'
+include_class 'cytoscape.CyNetwork'
+include_class 'cytoscape.layout.CyLayouts'
+include_class 'java.lang.Integer'
+
+ORIGINAL_NODES = 2
+MAX_LOOP = 1000 - ORIGINAL_NODES
+EACH_TRIAL = 2
+
+# Create network
+graph = Cytoscape.createNetwork("Barabasi-Albert Scale Free Network");
+
+nodes = Array.new
+
+#Create seed graph
+node1 = Cytoscape.getCyNode("Seed 1", true)
+node2 = Cytoscape.getCyNode("Seed 2", true)
+nodes << node1
+nodes << 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
+while i<MAX_LOOP do
+ newNode = Cytoscape.getCyNode("Node " + Integer.toString(i), true)
+ graph.addNode(newNode)
+
+ j = 0
+ while j<EACH_TRIAL do
+ created = false
+ while created == false do
+ selectedNode = nodes[rand(nodes.length)]
+ degree = graph.getDegree(selectedNode)
+ prob = (degree + 1.0) / (graph.getNodeCount() +
graph.getEdgeCount() - 1.0)
+ if prob >= rand && newNode.getIdentifier !=
selectedNode.getIdentifier
+ created = true;
+ end
+ end
+
+ edge = Cytoscape.getCyEdge(newNode, selectedNode,
"interaction", "-", true);
+ graph.addEdge(edge);
+ nodes << newNode
+ j = j+1
+ end
+ i = i+1
+end
+
+# Layout nodes
+CyLayouts.getLayout("force-directed").doLayout();
+Cytoscape.getCurrentNetworkView().redrawGraph(false, true);
Added: csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/binary_matrix.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/binary_matrix.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/binary_matrix.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,32 @@
+require 'java'
+
+include_class 'cytoscape.Cytoscape'
+include_class 'cytoscape.CyNetwork'
+include_class 'cytoscape.CyNode'
+
+net = Cytoscape.getCurrentNetwork
+source = net.nodesList
+
+line = ','
+source.each do |column|
+ line << column.getIdentifier << ','
+end
+
+fileName = net.getTitle + "_matrix.csv"
+File.open(fileName, "w") {|file|
+
+ file.puts line
+
+ source.each do |s|
+ line = s.getIdentifier + ','
+ targets = net.nodesList
+ targets.each do |t|
+ if net.edgeExists(s, t)
+ line << '1,'
+ else
+ line << '0,'
+ end
+ end
+ file.puts line
+ end
+}
Added: csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/hello_world.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/hello_world.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/hello_world.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,7 @@
+$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/gems/1.8/gems/bio-1.3.1/lib'
+puts "LOAD_PATH: " + $:.inspect
+
+
+require 'csv'
+require 'bio'
+puts 'Hello, Cytoscape.'
\ No newline at end of file
Added: csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/kegg_relation_mapper.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/kegg_relation_mapper.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/kegg_relation_mapper.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,3 @@
+pathway_id = ARGV.sift
+
+puts 'Got ID: ' + pathway_id
Added:
csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_multiple_networks.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_multiple_networks.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_multiple_networks.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,19 @@
+require 'java'
+
+include_class 'cytoscape.Cytoscape'
+include_class 'cytoscape.layout.CyLayouts'
+include_class 'cytoscape.layout.LayoutAlgorithm'
+include_class 'cytoscape.CytoscapeInit'
+
+include_class
'edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableMappingParameters'
+include_class
'edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableReader'
+include_class 'java.net.URL'
+
+props = CytoscapeInit.getProperties
+props.setProperty("layout.default", "force-directed")
+
+Dir::glob("sampleData/*.table").each {|f|
+ puts "Loading: " + f
+ Cytoscape.createNetworkFromFile f
+ Cytoscape.getCurrentNetworkView.redrawGraph(false, true)
+}
Added: csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_networks.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_networks.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/testscripts/load_networks.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,7 @@
+require 'java'
+
+include_class
'edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableMappingParameters'
+include_class
'edu.ucsd.bioeng.coreplugin.tableImport.reader.NetworkTableReader'
+include_class 'java.net.URL'
+
+
Added: csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
===================================================================
--- csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
(rev 0)
+++ csplugins/trunk/ucsd/kono/JRubyEngine/utilscripts/biorubyshell.rb
2009-12-04 02:23:36 UTC (rev 18653)
@@ -0,0 +1,30 @@
+$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/1.8'
+$LOAD_PATH << ENV['JRUBY_HOME'] + '/lib/ruby/gems/1.8/gems/bio-1.3.1/lib'
+
+#puts "LOAD_PATH: " + $:.inspect
+
+require 'bio'
+require 'bio/shell'
+
+include Java
+include Bio::Shell
+
+include_class 'cytoscape.Cytoscape'
+
+Bio::Shell::Setup.new
+Bio::Shell.load_session
+
+
+if Bio::Shell.cache[:rails]
+ Bio::Shell.cache[:rails].join
+else
+ Signal.trap("SIGINT") do
+ Bio::Shell.cache[:irb].signal_handle
+ end
+
+ catch(:IRB_EXIT) do
+ Bio::Shell.cache[:irb].eval_input
+ end
+end
+
+Bio::Shell.save_session
--
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