Initial commit

.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/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+	<classpathentry kind="src" path="isrc"/>
+	<classpathentry kind="src" path="generated_src"/>
+	<classpathentry kind="lib" path="lib/jetty-all-7.2.2.v20101205.jar"/>
+	<classpathentry kind="lib" path="lib/json.jar"/>
+	<classpathentry kind="lib" path="lib/miglayout15-swing.jar"/>
+	<classpathentry kind="lib" path="lib/poi-3.2-FINAL-20081019.jar"/>
+	<classpathentry kind="lib" path="lib/servlet-api-2.5.jar"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/star_signalsystem_java"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.gitignore

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+*.class
+bin
+build
+.settings

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>stargenetics_java</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>edu.mit.star.builderplugin.starBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>edu.mit.star.builderplugin.StarNature</nature>
+	</natures>
+</projectDescription>

build.xml

@@ -0,0 +1,164 @@
+<?xml version="1.0" encoding="utf-8"?>
+
+<project name="StarGenetics" default="build" basedir=".">
+	<taskdef name="apt" classname="org.apache.tools.ant.taskdefs.Apt" />
+	<taskdef name="jreleaseinfo" classname="ch.oscg.jreleaseinfo.anttask.JReleaseInfoAntTask" classpath="../CommonLibrariesBin/ant-tasks/jreleaseinfo-1.2.0.jar"/>
+
+	<property name="src" value="${basedir}/src" />
+	<property name="isrc" value="${basedir}/isrc" />
+	<property name="build" value="${basedir}/build" />
+
+	<property name="preprocess.dir" value="${basedir}/generated_src" />
+<!--
+	<property name="src.tests" value="${basedir}/tests" />
+	<property name="preprocess.dir.tests" value="${basedir}/generated_tests" />
+-->
+	<path id="apt.classpath">
+		<pathelement path="${basedir}/bin" />
+		<pathelement path="../star_signalsystem_java/bin" />
+		<pathelement path="../Plugin-Commons/bin" />
+		<pathelement path="lib/miglayout15-swing.jar" />
+		<pathelement path="lib/poi-3.2-FINAL-20081019.jar" />
+		<pathelement path="lib/json.jar" />		
+		<pathelement path="lib/jetty-all-7.2.2.v20101205.jar" />		
+		<pathelement path="lib/servlet-api-2.5.jar" />		
+	</path>
+
+	<target name="build" depends="postclean">
+	</target>
+
+	<target name="update_samples">
+		<echo>Downloading samples</echo>		
+		<exec executable="/usr/local/bin/wget" dir="${basedir}/src/resources">
+			<arg value="-r"/>
+			<arg value="--level=1"/>
+			<arg value="http://web.mit.edu/star/genetics/problemsets/samples_body.html"/>
+		</exec>
+	</target>
+
+	<target name="publish" depends="build">
+		<echo>Publishing and signing</echo>
+		<exec executable="scp">
+			<arg value="StarGenetics.jar" />
+			<arg value="[email protected]:/home/star/star/media/uploads/star/jar/genetics3/StarGenetics3.jar" />
+		</exec>
+
+		<exec executable="ssh">
+<!--			<arg value="-ssh" />
+			<arg value="starapp.mit.edu" />
+			<arg value="-l" />
+			<arg value="ceraj" />
+-->
+			<arg value="[email protected]"/>
+			<arg value="/home/star/build/sign_genetics3.sh" />
+		</exec>
+
+	</target>
+
+	<target name="clean" depends="">
+		<echo>Deleting</echo>
+		<mkdir dir="${build}"/>
+		<delete>
+			<fileset dir="${src}">
+				<include name="**/*.class" />
+			</fileset>			
+			<fileset dir="${isrc}">
+				<include name="**/*.class" />
+			</fileset>
+			<fileset dir="${build}">
+				<include name="**/*.class" />
+			</fileset>						
+			<fileset dir="${preprocess.dir}">
+				<include name="**/*.class" />
+			</fileset>
+			<filename name="StarGenetics.jar"/>			
+		</delete>
+	</target>
+
+	<target name="postclean" depends="apt,compile,jar">
+		<echo>Post build delete</echo>
+		<delete>
+			<fileset dir="${src}">
+				<include name="**/*.class" />
+			</fileset>			
+			<fileset dir="${isrc}">
+				<include name="**/*.class" />
+			</fileset>
+			<fileset dir="${build}">
+				<include name="**/*.class" />
+			</fileset>						
+			<fileset dir="${preprocess.dir}">
+				<include name="**/*.class" />
+			</fileset>						
+		</delete>
+	</target>
+
+
+	<target name="events_apt" depends="clean">
+		<echo>Precompiling</echo>
+		<apt srcdir="${isrc}" classpathref="apt.classpath" debug="on" includes="**/*.java" factory="star.annotations.ProcessorFactory" preprocessdir="${preprocess.dir}" fork="on" target="1.5" />
+	</target>
+
+	<target name="events_compile" depends="events_apt">
+		<echo>Compiling</echo>
+		<!--<javac srcdir="${isrc};${preprocess.dir}" classpathref="apt.classpath" destdir="${build}" debug="on" includes="**/*.java" optimize="on" target="1.5" />-->
+	</target>
+
+	<target name="compile" depends="apt">
+		<echo>Updating build date</echo>
+
+		<jreleaseinfo targetDir="src" packagename="star.genetics" classname="Version" project="StarGenetics">
+		</jreleaseinfo>
+
+		<echo>Compiling</echo>
+		<mkdir dir="${build}"/>
+		<javac srcdir="${src};${isrc};${preprocess.dir}" classpathref="apt.classpath" destdir="${build}" debug="on" includes="**/*.java" optimize="on" target="1.5" />
+	</target>
+
+	<target name="apt"> <!-- depends="events_compile">
+		<echo>Precompiling</echo>
+		<apt srcdir="${src};${isrc};${preprocess.dir}" classpathref="apt.classpath" debug="on" includes="**/*.java" factory="star.annotations.ProcessorFactory" preprocessdir="${preprocess.dir}" fork="on" target="1.5" />
+		-->
+	</target>
+
+	<target name="jar" depends="update_samples">
+		<echo>Creating JAR</echo>
+		<jar destfile="StarGenetics.jar">
+			<fileset dir="build" id="build">
+				<include name="**" />
+				<exclude name=".classpath" />
+				<exclude name=".project" />
+				<exclude name=".settings" />
+				<exclude name=".settings/**" />
+			</fileset>
+			<fileset dir="src" id="pref">
+				<include name="preferences/**" />
+				<include name="resources/**" />
+				<include name="star/genetics/*.properties"/>
+				<exclude name=".settings/**" />
+			</fileset>
+			<fileset dir="../star_signalsystem_java/bin" id="SignalSystem">
+				<include name="**" />
+				<exclude name="**/*.jar*" />
+				<exclude name=".classpath" />
+				<exclude name=".project" />
+				<exclude name=".settings" />
+				<exclude name="**/*.java" />
+				<exclude name="star/junit/**" />
+				<exclude name=".settings/**" />
+			</fileset>
+				<fileset dir="../stargenetics_private_java/bin" id="SignalSystem">
+					<include name="**" />
+					<exclude name="**/*.jar*" />
+					<exclude name=".classpath" />
+					<exclude name=".project" />
+					<exclude name=".settings" />
+					<exclude name="**/*.java" />
+					<exclude name="star/junit/**" />
+					<exclude name=".settings/**" />
+				</fileset>
+
+		</jar>
+	</target>
+
+</project>

generated_src/star/genetics/Applet_generated.java

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+/* Generated by star.annotations.GeneratedClass, all changes will be lost */
+
+package star.genetics;
+
+abstract class Applet_generated extends javax.swing.JApplet implements star.event.EventController
+{
+	private star.event.Adapter adapter;
+	private java.lang.Exception errorMessage;
+	private java.util.prefs.Preferences preferences = loadPreferences();
+	private static final long serialVersionUID = 1L;
+
+	public Applet_generated() throws java.awt.HeadlessException
+	{
+		super();
+	}
+
+	public void addNotify()
+	{
+		super.addNotify();
+	}
+
+	public star.event.Adapter getAdapter()
+	{
+		if (adapter == null)
+		{
+			adapter = new star.event.Adapter(this);
+		}
+		return adapter;
+	}
+
+	public java.lang.Exception getErrorMessage()
+	{
+		return this.errorMessage;
+	}
+
+	java.util.prefs.Preferences getPreferences(java.lang.String name)
+	{
+		try
+		{
+			plugin.preferences.Preferences pref = (plugin.preferences.Preferences) plugin.Loader.getDefaultLoader().getPlugin(plugin.preferences.Preferences.class.getName(), plugin.preferences.PreferencesImplementation.class.getName());
+			this.preferences = pref.getPreferences(name);
+		}
+		catch (plugin.PluginException ex)
+		{
+			ex.printStackTrace();
+		}
+		if (preferences == null)
+		{
+			return java.util.prefs.Preferences.userRoot().node(name);
+		}
+		return preferences;
+	}
+
+	java.util.prefs.Preferences getPreferences()
+	{
+		if (preferences == null)
+		{
+			try
+			{
+				plugin.preferences.Preferences pref = (plugin.preferences.Preferences) plugin.Loader.getDefaultLoader().getPlugin(plugin.preferences.Preferences.class.getName(), plugin.preferences.PreferencesImplementation.class.getName());
+				this.preferences = pref.getPreferences("star.genetics.Applet");
+			}
+			catch (plugin.PluginException ex)
+			{
+				ex.printStackTrace();
+			}
+		}
+		if (preferences == null)
+		{
+			return java.util.prefs.Preferences.userRoot().node("star.genetics.Applet");
+		}
+		return preferences;
+	}
+
+	java.util.prefs.Preferences loadPreferences()
+	{
+		try
+		{
+			plugin.preferences.Preferences pref = (plugin.preferences.Preferences) plugin.Loader.getDefaultLoader().getPlugin(plugin.preferences.Preferences.class.getName(), plugin.preferences.PreferencesImplementation.class.getName());
+			java.util.Properties prop = new java.util.Properties();
+			prop.load(this.getClass().getClassLoader().getResourceAsStream("resources/default.properties"));
+			pref.setApplication("StarGenetics", prop);
+		}
+		catch (Throwable ex)
+		{
+			ex.printStackTrace();
+		}
+		return getPreferences();
+	}
+
+	public void removeNotify()
+	{
+		super.removeNotify();
+	}
+
+	protected void setErrorMessage(java.lang.Exception errorMessage)
+	{
+		this.errorMessage = errorMessage;
+	}
+
+}

generated_src/star/genetics/CommandLineFileOpener_generated.java

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+/* Generated by star.annotations.GeneratedClass, all changes will be lost */
+
+package star.genetics;
+
+abstract class CommandLineFileOpener_generated extends java.lang.Object implements star.event.EventController, star.genetics.events.OpenModelRaiser
+{
+	private star.event.Adapter adapter;
+	private static final long serialVersionUID = 1L;
+
+	public  CommandLineFileOpener_generated()
+	{
+		super();
+	}
+
+	public void addNotify()
+	{
+	}
+
+	public star.event.Adapter getAdapter()
+	{
+		if( adapter == null )
+		{
+			adapter = new star.event.Adapter(this);
+		}
+		return adapter;
+	}
+
+	public void raise_OpenModelEvent()
+	{
+		(new star.genetics.events.OpenModelEvent(this)).raise();
+	}
+
+	public void removeNotify()
+	{
+	}
+
+}

generated_src/star/genetics/events/ErrorDialogEvent.java

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+/* Generated by star.annotations.GeneratedClass, all changes will be lost */
+
+package star.genetics.events;
+
+public class ErrorDialogEvent extends star.event.Event
+{
+	private static final long serialVersionUID = 1L;
+
+	public  ErrorDialogEvent(star.event.Raiser raiser, boolean valid)
+	{
+		super( raiser , valid ) ;
+	}
+
+	public  ErrorDialogEvent(star.genetics.events.ErrorDialogEvent event)
+	{
+		super( event ) ;
+	}
+
+	public  ErrorDialogEvent(star.genetics.events.ErrorDialogRaiser raiser)
+	{
+		super( raiser ) ;
+	}
+
+}