initial commit - moved from SVN

org.pathvisio.mappbuilder/.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

org.pathvisio.mappbuilder/.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>MAPPBuilder</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.ManifestBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.pde.SchemaBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.pde.PluginNature</nature>
+	</natures>
+</projectDescription>

org.pathvisio.mappbuilder/META-INF/MANIFEST.MF

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+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: MAPPBuilder plugin
+Bundle-SymbolicName: org.pathvisio.mappbuilder
+Bundle-Version: 1.0.0
+Bundle-Activator: org.pathvisio.mappbuilder.Activator
+Export-Package: org.pathvisio.mappbuilder
+Require-Bundle: org.pathvisio.core;bundle-version="3.0.0",
+ org.pathvisio.desktop;bundle-version="3.0.0",
+ org.pathvisio.gui;bundle-version="3.0.0",
+ org.bridgedb;bundle-version="1.1.0",
+ org.bridgedb.bio;bundle-version="1.1.0",
+ org.pathvisio.jgoodies.forms;bundle-version="1.2.0"
+Import-Package: org.osgi.framework;version="1.5.0"

org.pathvisio.mappbuilder/build.xml

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+<?xml version="1.0"?>
+<project name="org.pathvisio.mappbuilder" default="jar" basedir=".">
+
+	<property name="pathvisio.dir" value="../trunk/"/>
+	<property name="bundle.dest" value="dist"/>
+
+	<target name="prepare-jar-name">
+		<!-- the name of the plug-in jar uses the project name of the calling build file -->
+		<property name="jar.name" value="${bundle.dest}/${ant.project.name}.jar"/>
+	</target>
+
+  	<path id="project.class.path">
+		<fileset dir="${pathvisio.dir}/modules">
+			<include name="org.pathvisio.core.jar"/>
+			<include name="org.pathvisio.desktop.jar"/>
+			<include name="org.pathvisio.gui.jar"/>
+		</fileset>
+		<fileset dir="${pathvisio.dir}/lib">
+			<include name="org.bridgedb.jar"/>
+			<include name="com.springsource.org.jdom-1.1.0.jar"/>
+			<include name="felix.jar"/>
+			<include name="org.pathvisio.jgoodies.forms.jar"/>
+		</fileset>
+	</path>
+
+	<target name="prepare">
+		<mkdir dir="build"/>
+		<mkdir dir="${bundle.dest}"/>
+		<fail message="Can't find ${pathvisio.dir}/modules/org.pathvisio.core.jar, please specify the path to pathvisio with -Dpathvisio.dir=....">
+			<condition>
+				<not><available file="${pathvisio.dir}/modules/org.pathvisio.core.jar"/></not>
+			</condition>
+		</fail>
+	</target>
+
+	<target name="clean">
+		<delete dir="build"/>
+		<delete file="${jar.name}"/>
+	</target>
+
+	<target name="compile" depends="prepare,prepare-jar-name">
+		<echo>Compiling: ${jar.name}</echo>
+		<javac srcdir="src"
+			   includes="**"
+			   destdir="build"
+				  debug="${debug.mode}"
+				  source="1.5">
+			<classpath refid="project.class.path"/>
+		</javac>
+	</target>
+
+	<target name="jar" depends="compile"> 
+		<echo>Creating JAR: ${jar.name}</echo>
+		<jar jarfile="${jar.name}" manifest="META-INF/MANIFEST.MF">
+			<fileset dir="build">
+				<include name="**/*"/>
+			</fileset>
+		</jar>
+	</target>
+
+	<target name="install" depends="jar"> 
+		<copy toDir="${bundle.dest}" flatten="true">
+			<path refid="project.class.path"/>
+		</copy>
+	</target>
+
+	<target name="dist-clean" depends="clean">
+		<delete file="${jar.name}"/>
+		<delete dir="${bundle.dest}"/>
+	</target>
+
+</project>

org.pathvisio.mappbuilder/src/org/pathvisio/mappbuilder/Activator.java

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+// MAPPBuilder plugin for PathVisio
+// Copyright 2016 BiGCaT Bioinformatics
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+package org.pathvisio.mappbuilder;
+
+import org.osgi.framework.BundleActivator;
+import org.osgi.framework.BundleContext;
+import org.pathvisio.desktop.plugin.Plugin;
+
+/**
+ * MAPPBuilder activator class (OSGi)
+ * @author mku
+ *
+ */
+public class Activator implements BundleActivator {
+
+	private MAPPBuilder plugin;
+
+	@Override
+	public void start(BundleContext context) throws Exception {
+		plugin = new MAPPBuilder();
+		context.registerService(Plugin.class.getName(), plugin, null);
+	}
+
+	@Override
+	public void stop(BundleContext context) throws Exception {
+		if (plugin != null) plugin.done();
+	}
+}

org.pathvisio.mappbuilder/src/org/pathvisio/mappbuilder/MAPPBuilder.java

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+// MAPPBuilder plugin for PathVisio
+// Copyright 2016 BiGCaT Bioinformatics
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+package org.pathvisio.mappbuilder;
+
+import java.awt.event.ActionEvent;
+import javax.swing.AbstractAction;
+import javax.swing.JPopupMenu;
+
+import org.pathvisio.core.view.VPathwayElement;
+import org.pathvisio.desktop.PvDesktop;
+import org.pathvisio.desktop.plugin.Plugin;
+import org.pathvisio.gui.PathwayElementMenuListener.PathwayElementMenuHook;
+
+/** 
+ * 
+ * This class is a plug-in for a MAPPBuilder
+ * The user can open a file who contains the list of the genes to draw them
+ * or he can directly type the list of the genes
+ * 
+ */
+public class MAPPBuilder implements Plugin {
+
+	PvDesktop desktop;
+
+	public void init(PvDesktop desktop) {
+		this.desktop = desktop;
+		desktop.registerMenuAction ("Plugins", mappBuilderAction);
+		PathwayElementMenuHook mappBuilderHook = new PathwayElementMenuHook()
+		{
+			private MAPPBuilderAction mapp_action = new MAPPBuilderAction(false);
+			public void pathwayElementMenuHook(VPathwayElement e, JPopupMenu menu) {
+				menu.add(mapp_action);
+			}
+		};
+		desktop.addPathwayElementMenuHook(mappBuilderHook);
+	}
+
+	public void done() {
+		desktop.unregisterMenuAction("Plugins", mappBuilderAction);
+	}
+
+	private final MAPPBuilderAction mappBuilderAction = new MAPPBuilderAction(true);
+
+	private class MAPPBuilderAction extends AbstractAction {
+
+		private boolean n_pv;
+		public MAPPBuilderAction(boolean b) {
+			this.n_pv = b;
+			putValue (NAME, "MAPP Builder");	
+		}
+
+		public void actionPerformed(ActionEvent e) {	
+			MAPPBuilderFrame mappBuilderFrame = new MAPPBuilderFrame(desktop.getFrame(), MAPPBuilder.this, n_pv);
+			mappBuilderFrame.setVisible(true);
+		}
+	}
+}