Author: clopes
Date: 2011-07-15 10:54:34 -0700 (Fri, 15 Jul 2011)
New Revision: 26192
Added:
csplugins/trunk/toronto/clopes/mcode/build.xml
csplugins/trunk/toronto/clopes/mcode/default.properties
csplugins/trunk/toronto/clopes/mcode/osgi.bnd
csplugins/trunk/toronto/clopes/mcode/pom.xml
csplugins/trunk/toronto/clopes/mcode/src/
csplugins/trunk/toronto/clopes/mcode/src/main/
csplugins/trunk/toronto/clopes/mcode/src/main/java/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEHelpAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEStartAction.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEResources.java
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
csplugins/trunk/toronto/clopes/mcode/src/main/resources/
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/arrow_collapsed.gif
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/arrow_expanded.gif
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo.png
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo1.png
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo2.png
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/note.gif
csplugins/trunk/toronto/clopes/mcode/src/test/
csplugins/trunk/toronto/clopes/mcode/src/test/java/
Modified:
csplugins/trunk/toronto/clopes/mcode/
Log:
MCODE plugin port over to Cytoscape 3 (initial import)
Property changes on: csplugins/trunk/toronto/clopes/mcode
___________________________________________________________________
Added: svn:ignore
+ .settings
local.properties
.classpath
.project
target
Added: csplugins/trunk/toronto/clopes/mcode/build.xml
===================================================================
--- csplugins/trunk/toronto/clopes/mcode/build.xml
(rev 0)
+++ csplugins/trunk/toronto/clopes/mcode/build.xml 2011-07-15 17:54:34 UTC
(rev 26192)
@@ -0,0 +1,31 @@
+<?xml version="1.0"?>
+<project name="MCODE Plugin" basedir="." default="install">
+
+ <!--
+ This file should be created by each user when he/she needs to
override particular values.
+ Do NOT place it under version control.
+ -->
+ <property file="local.properties"/>
+ <!--
+ This file should be placed under version control.
+ -->
+ <property file="default.properties"/>
+
+ <property environment="env"/>
+
+ <property name="build.dir" value="target"/>
+ <property name="cytoscape.plugin.dir" value="${cytoscape.home}/plugins"/>
+
+ <target name="install">
+ <copy todir="${cytoscape.plugin.dir}" overwrite="true">
+ <fileset dir="${build.dir}" includes="*.jar"/>
+ </copy>
+ </target>
+
+ <target name="info">
+
<echo>*******************************************************************</echo>
+ <echo>* This script installs the Cytoscape plugin
*</echo>
+
<echo>*******************************************************************</echo>
+ </target>
+
+</project>
\ No newline at end of file
Added: csplugins/trunk/toronto/clopes/mcode/default.properties
===================================================================
--- csplugins/trunk/toronto/clopes/mcode/default.properties
(rev 0)
+++ csplugins/trunk/toronto/clopes/mcode/default.properties 2011-07-15
17:54:34 UTC (rev 26192)
@@ -0,0 +1,2 @@
+# Overwrite it in your local.properties file
+cytoscape.home=/Applications/Cytoscape_v3.0
\ No newline at end of file
Added: csplugins/trunk/toronto/clopes/mcode/osgi.bnd
===================================================================
--- csplugins/trunk/toronto/clopes/mcode/osgi.bnd
(rev 0)
+++ csplugins/trunk/toronto/clopes/mcode/osgi.bnd 2011-07-15 17:54:34 UTC
(rev 26192)
@@ -0,0 +1,7 @@
+#-----------------------------------------------------------------
+# Use this file to add customized Bnd instructions for the bundle
+#-----------------------------------------------------------------
+
+Import-Package: *
+Private-Package: ${bundle.namespace}.internal.*
+Export-Package: ${bundle.namespace}
Added: csplugins/trunk/toronto/clopes/mcode/pom.xml
===================================================================
--- csplugins/trunk/toronto/clopes/mcode/pom.xml
(rev 0)
+++ csplugins/trunk/toronto/clopes/mcode/pom.xml 2011-07-15 17:54:34 UTC
(rev 26192)
@@ -0,0 +1,137 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0";
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0
http://maven.apache.org/maven-v4_0_0.xsd";>
+
+ <properties>
+
<bundle.symbolicName>org.cytoscape.mcode.mcode-plugin</bundle.symbolicName>
+ <bundle.namespace>org.cytoscape.mcode</bundle.namespace>
+ </properties>
+
+ <modelVersion>4.0.0</modelVersion>
+ <groupId>org.cytoscape.mcode</groupId>
+ <artifactId>mcode-plugin</artifactId>
+ <version>1.4.0-alpha1-SNAPSHOT</version>
+
+ <name>${bundle.symbolicName} [${bundle.namespace}]</name>
+
+ <packaging>bundle</packaging>
+
+ <build>
+ <resources>
+ <resource>
+ <directory>src/main/resources</directory>
+ </resource>
+ </resources>
+ <!-- Cytoscape requires Java 1.6 -->
+ <plugins>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-compiler-plugin</artifactId>
+ <configuration>
+ <source>1.6</source>
+ <target>1.6</target>
+ <optimize>true</optimize>
+ <showWarnings>true</showWarnings>
+ <showDeprecation>true</showDeprecation>
+ <compilerArguments>
+ <Xmaxwarns>10000</Xmaxwarns>
+ <Xmaxerrs>10000</Xmaxerrs>
+ </compilerArguments>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.apache.maven.plugins</groupId>
+ <artifactId>maven-surefire-plugin</artifactId>
+ <configuration>
+
<redirectTestOutputToFile>true</redirectTestOutputToFile>
+ </configuration>
+ </plugin>
+ <plugin>
+ <groupId>org.ops4j</groupId>
+ <artifactId>maven-pax-plugin</artifactId>
+ <version>1.5</version>
+ <extensions>true</extensions>
+ </plugin>
+ <!-- Generates the OSGi metadata based on the osgi.bnd
file. -->
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <version>2.3.4</version>
+ <configuration>
+ <instructions>
+
<Bundle-SymbolicName>${bundle.symbolicName}</Bundle-SymbolicName>
+
<Bundle-Version>${project.version}</Bundle-Version>
+ <_include>-osgi.bnd</_include>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+
+ <!-- Links to the Cytoscape Maven repositories. -->
+ <repositories>
+ <repository>
+ <id>cytoscape_snapshots</id>
+ <snapshots>
+ </snapshots>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <name>Cytoscape Snapshots</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/snapshots/</url>
+ </repository>
+ <repository>
+ <id>cytoscape_releases</id>
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <releases>
+ </releases>
+ <name>Cytoscape Releases</name>
+
<url>http://cytoscape.wodaklab.org/nexus/content/repositories/releases/</url>
+ </repository>
+ </repositories>
+
+ <!-- Dependencies needed to compile this project. -->
+ <dependencies>
+ <!-- Cytoscape -->
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>swing-application-api</artifactId>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>session-api</artifactId>
+ <version>3.0.0-alpha6-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>swing-util-api</artifactId>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
+ </dependency>
+
+ <!-- Logging -->
+ <dependency>
+ <groupId>org.ops4j.pax.logging</groupId>
+ <artifactId>pax-logging-api</artifactId>
+ <version>1.5.2</version>
+ <scope>provided</scope>
+ </dependency>
+
+ <!-- Unit Testing -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>4.8.2</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>test-support</artifactId>
+ <version>3.0.0-alpha2</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+
+</project>
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEAboutAction.java
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,78 @@
+package org.cytoscape.mcode.internal;
+
+import java.awt.event.ActionEvent;
+
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.mcode.internal.util.MCODEResources;
+import org.cytoscape.mcode.internal.view.MCODEAboutDialog;
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.util.swing.OpenBrowser;
+
+/**
+ * * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
+ * *
+ * * Code written by: Gary Bader
+ * * Authors: Gary Bader, Ethan Cerami, Chris Sander
+ * *
+ * * 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
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has no obligations to provide maintenance, support,
+ * * updates, enhancements or modifications. In no event shall the
+ * * Memorial Sloan-Kettering Cancer Center
+ * * 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
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has 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.
+ * *
+ * * User: Gary Bader
+ * * Date: Jun 25, 2004
+ * * Time: 5:38:52 PM
+ * * Description: The action to show the About dialog box
+ */
+
+/**
+ * The action to show the About dialog box
+ */
+public class MCODEAboutAction extends AbstractCyAction {
+
+ private static final long serialVersionUID = -8445425993916988045L;
+
+ private final CySwingApplication swingApplication;
+ private final OpenBrowser openBrowser;
+ private final MCODEResources resources;
+
+ public MCODEAboutAction(final String menuTitle,
+ final
CyApplicationManager applicationManager,
+ final
CySwingApplication swingApplication,
+ final OpenBrowser
openBrowser,
+ final MCODEResources
resources) {
+ super(menuTitle, applicationManager);
+ this.swingApplication = swingApplication;
+ this.openBrowser = openBrowser;
+ this.resources = resources;
+ setPreferredMenu("Plugins.MCODE");
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ //display about box
+ MCODEAboutDialog aboutDialog = new
MCODEAboutDialog(swingApplication, openBrowser, resources);
+ aboutDialog.pack();
+ aboutDialog.setVisible(true);
+ }
+}
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEHelpAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEHelpAction.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEHelpAction.java
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,67 @@
+package org.cytoscape.mcode.internal;
+
+import java.awt.event.ActionEvent;
+
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.session.CyApplicationManager;
+import org.cytoscape.util.swing.OpenBrowser;
+
+/**
+ * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
+ * *
+ * * Code written by: Gary Bader
+ * * Authors: Gary Bader, Ethan Cerami, Chris Sander
+ * *
+ * * 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
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has no obligations to provide maintenance, support,
+ * * updates, enhancements or modifications. In no event shall the
+ * * Memorial Sloan-Kettering Cancer Center
+ * * 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
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has 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.
+ * *
+ * * User: vukpavlovic
+ * * Date: Jan 10, 2007
+ * * Time: 5:55:40 PM
+ * * Description: Opens a browser with the MCODE wiki page.
+ */
+
+/**
+ * Opens a browser with the MCODE wiki page.
+ */
+
+public class MCODEHelpAction extends AbstractCyAction {
+
+ private static final long serialVersionUID = -8129187221346920847L;
+
+ private final OpenBrowser openBrowser;
+
+ public MCODEHelpAction(final String menuTitle,
+ final CyApplicationManager
applicationManager,
+ final OpenBrowser
openBrowser) {
+ super(menuTitle, applicationManager);
+ this.openBrowser = openBrowser;
+ setPreferredMenu("Plugins.MCODE");
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent) {
+ openBrowser.openURL("http://www.baderlab.org/Software/MCODE/";);
+ }
+}
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEStartAction.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEStartAction.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/MCODEStartAction.java
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,27 @@
+package org.cytoscape.mcode.internal;
+
+import java.awt.event.ActionEvent;
+
+import javax.swing.JOptionPane;
+
+import org.cytoscape.application.swing.AbstractCyAction;
+import org.cytoscape.session.CyApplicationManager;
+
+/**
+ * Creates a new menu item under Plugins menu section.
+ */
+public class MCODEStartAction extends AbstractCyAction {
+
+ private static final long serialVersionUID = 3521389398662580589L;
+
+ public MCODEStartAction(final String menuTitle, final
CyApplicationManager applicationManager) {
+ super(menuTitle, applicationManager);
+ setPreferredMenu("Plugins.MCODE");
+ }
+
+ @Override
+ public void actionPerformed(ActionEvent e) {
+ // TODO...
+ JOptionPane.showMessageDialog(null, "TODO...");
+ }
+}
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEResources.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEResources.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/util/MCODEResources.java
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,31 @@
+package org.cytoscape.mcode.internal.util;
+
+import java.net.URL;
+
+public class MCODEResources {
+
+ public static enum Image {
+ LOGO("/img/logo1.png"),
+ LOGO_SMALL("/img/logo2.png"),
+ LOGO_SIMPLE("/img/logo.png"),
+ ARROW_EXPANDED("/img/arrow_expanded.gif"),
+ ARROW_COLLAPSED("/img/arrow_collapsed.gif"),
+ NOTE("/img/note.gif");
+
+ private final String name;
+
+ private Image(final String name) {
+ this.name = name;
+ }
+
+ @Override
+ public String toString() {
+ return name;
+ }
+ }
+
+ public URL getUrl(Image img) {
+ return this.getClass().getResource(img.toString());
+ }
+
+}
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/java/org/cytoscape/mcode/internal/view/MCODEAboutDialog.java
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,122 @@
+package org.cytoscape.mcode.internal.view;
+
+import java.awt.Insets;
+import java.net.URL;
+
+import javax.swing.JDialog;
+import javax.swing.JEditorPane;
+import javax.swing.event.HyperlinkEvent;
+import javax.swing.event.HyperlinkListener;
+import javax.swing.text.html.HTMLEditorKit;
+
+import org.cytoscape.application.swing.CySwingApplication;
+import org.cytoscape.mcode.internal.util.MCODEResources;
+import org.cytoscape.mcode.internal.util.MCODEResources.Image;
+import org.cytoscape.util.swing.OpenBrowser;
+
+/**
+ * * Copyright (c) 2004 Memorial Sloan-Kettering Cancer Center
+ * *
+ * * Code written by: Gary Bader
+ * * Authors: Gary Bader, Ethan Cerami, Chris Sander
+ * *
+ * * 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
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has no obligations to provide maintenance, support,
+ * * updates, enhancements or modifications. In no event shall the
+ * * Memorial Sloan-Kettering Cancer Center
+ * * 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
+ * * Memorial Sloan-Kettering Cancer Center
+ * * has 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.
+ * *
+ * * User: Gary Bader
+ * * Date: Jun 25, 2004
+ * * Time: 5:47:31 PM
+ * * Description: An about dialog box for MCODE
+ */
+
+/**
+ * An about dialog box for MCODE
+ */
+public class MCODEAboutDialog extends JDialog {
+
+ private static final long serialVersionUID = 635333288924094273L;
+
+ private final OpenBrowser openBrowser;
+ private final MCODEResources resources;
+
+ /** Main panel for dialog box */
+ private JEditorPane mainContainer;
+
+ public MCODEAboutDialog(final CySwingApplication swingApplication,
+ final OpenBrowser
openBrowser,
+ final MCODEResources
resources) {
+ super(swingApplication.getJFrame(), "About MCODE", false);
+ this.openBrowser = openBrowser;
+ this.resources = resources;
+
+ setResizable(false);
+ setContentPane(getMainContainer());
+ }
+
+ private JEditorPane getMainContainer() {
+ if (mainContainer == null) {
+ mainContainer = new JEditorPane();
+ mainContainer.setMargin(new Insets(10, 10, 10, 10));
+ mainContainer.setEditable(false);
+ mainContainer.setEditorKit(new HTMLEditorKit());
+ mainContainer.addHyperlinkListener(new
HyperlinkAction());
+
+ URL logoURL = resources.getUrl(Image.LOGO);
+ String logoCode = "";
+
+ if (logoURL != null) {
+ logoCode = "<center><img src='" + logoURL +
"'></center>";
+ }
+
+ String text = "<html><body>" +
+ logoCode +
+ "<P align=center><b>MCODE
(Molecular Complex Detection) v1.32 (Jun 2011)</b><BR>" +
+ "A Cytoscape PlugIn<BR><BR>" +
+
+ "Version 1.32 by <a
href='http://www.baderlab.org/'>Bader Lab</a>, University of Toronto<BR>" +
+ "Version 1.2 by Vuk Pavlovic
(<a href='http://www.baderlab.org/'>Bader Lab</a>, University of Toronto)<BR>" +
+ "Version 1.1 and 1.0 by Gary
Bader (while in the <a href='http://cbio.mskcc.org/'>Sander Lab</a>,<BR>" +
+ "Memorial Sloan-Kettering
Cancer Center)<BR><BR>" +
+
+ "If you use this plugin in
your research, please cite:<BR>" +
+ "Bader GD, Hogue CW<BR>" +
+ "<a
href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract'>An
automated method for finding molecular complexes<BR>" +
+ "in large protein interaction
networks.</a><BR>" +
+ "<i>BMC Bioinformatics</i>.
2003 Jan 13;4(1):2</P></body></html>";
+
+ mainContainer.setText(text);
+ }
+
+ return mainContainer;
+ }
+
+ private class HyperlinkAction implements HyperlinkListener {
+
+ public void hyperlinkUpdate(HyperlinkEvent event) {
+ if (event.getEventType() ==
HyperlinkEvent.EventType.ACTIVATED) {
+ openBrowser.openURL(event.getURL().toString());
+ }
+ }
+ }
+}
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,43 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:osgi="http://www.springframework.org/schema/osgi";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/osgi
+ http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
+ default-lazy-init="false">
+
+
+ <!-- ================= Import =========================== -->
+
+ <!-- Import OSGi service from service registry -->
+ <!--
+ <osgi:reference id="pluginAdapterServiceRef"
+ interface="org.cytoscape.plugin.CyPluginAdapter" />
+ -->
+
+ <osgi:reference id="cyApplicationManagerServiceRef"
+ interface="org.cytoscape.session.CyApplicationManager" />
+
+ <osgi:reference id="cySwingApplicationServiceRef"
+ interface="org.cytoscape.application.swing.CySwingApplication"
/>
+
+ <osgi:reference id="openBrowserServiceRef"
+ interface="org.cytoscape.util.swing.OpenBrowser" />
+
+
+ <!-- ================= Export =========================== -->
+
+ <!-- Export the instance as an OSGi service -->
+ <osgi:service id="startMenuActionService" ref="startMenuAction"
+ interface="org.cytoscape.application.swing.CyAction" />
+
+ <osgi:service id="helpMenuActionService" ref="helpMenuAction"
+ interface="org.cytoscape.application.swing.CyAction" />
+
+ <osgi:service id="aboutMenuActionService" ref="aboutMenuAction"
+ interface="org.cytoscape.application.swing.CyAction" />
+
+
+</beans>
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
(rev 0)
+++
csplugins/trunk/toronto/clopes/mcode/src/main/resources/META-INF/spring/bundle-context.xml
2011-07-15 17:54:34 UTC (rev 26192)
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans";
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance";
xmlns:context="http://www.springframework.org/schema/context";
+ xsi:schemaLocation="
+ http://www.springframework.org/schema/beans
+ http://www.springframework.org/schema/beans/spring-beans-2.5.xsd
+ http://www.springframework.org/schema/context
+
http://www.springframework.org/schema/context/spring-context-2.5.xsd";>
+
+ <!-- Create an instance (bean) of the class -->
+
+ <!--<bean id="plugin" class="org.cytoscape.mcode.internal.MCODEPlugin">
+ <constructor-arg ref="pluginAdapterServiceRef" />
+ <constructor-arg ref="openBrowserServiceRef" />
+ <constructor-arg ref="resources" />
+ </bean>-->
+
+ <bean id="startMenuAction"
class="org.cytoscape.mcode.internal.MCODEStartAction">
+ <constructor-arg value="Start MCODE" />
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ </bean>
+
+ <bean id="helpMenuAction"
class="org.cytoscape.mcode.internal.MCODEHelpAction">
+ <constructor-arg value="Help" />
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="openBrowserServiceRef" />
+ </bean>
+
+ <bean id="aboutMenuAction"
class="org.cytoscape.mcode.internal.MCODEAboutAction">
+ <constructor-arg value="About" />
+ <constructor-arg ref="cyApplicationManagerServiceRef" />
+ <constructor-arg ref="cySwingApplicationServiceRef" />
+ <constructor-arg ref="openBrowserServiceRef" />
+ <constructor-arg ref="resources" />
+ </bean>
+
+ <bean id="resources"
class="org.cytoscape.mcode.internal.util.MCODEResources" />
+
+</beans>
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/arrow_collapsed.gif
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/arrow_collapsed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/arrow_expanded.gif
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/arrow_expanded.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo.png
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo1.png
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo1.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo2.png
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/logo2.png
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/note.gif
===================================================================
(Binary files differ)
Property changes on:
csplugins/trunk/toronto/clopes/mcode/src/main/resources/img/note.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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