--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build.xml	Mon Feb 13 22:12:06 2012 -0500
@@ -0,0 +1,112 @@
+<?xml version="1.0" encoding="iso-8859-1"?>
+<project name="java-genomics-toolkit" default="jar" basedir=".">
+  <description>
+    build the toolkit
+  </description>
+  
+  <!-- set global properties for this build -->
+  <property name="version" value="1.1.0"/>
+  <property name="buildnumber" value="1"/>
+  <property name="copyright" value="Copyright &#xa9; 2011 Timothy Palpant"/>
+  
+  <!-- directory variables -->
+  <property name="src" location="src"/>
+  <property name="test" location="test"/>
+  <property name="gui" location="gui"/>
+  <property name="build" location="build"/>
+  <property name="dist" location="dist"/>
+  <property name="lib" location="lib"/>
+
+  <!-- compile all Java code -->
+  <target name="compile" description="compile the scripts">
+    <!-- Create the build directory structure used by compile -->
+    <mkdir dir="${build}"/>
+    
+    <!-- Compile the java code from ${src} into ${build} -->
+    <javac srcdir="${src}" destdir="${build}" source="1.7" target="1.7">
+	  <classpath>
+	    <path id="lib.path.ref">
+	      <fileset dir="lib" includes="*.jar"/>
+	    </path>
+	  </classpath>
+    </javac>
+    
+    <!-- Compile the java code from ${gui} into ${build} -->
+    <javac srcdir="${gui}" destdir="${build}" source="1.7" target="1.7">
+      <classpath>
+  	    <path id="lib.path.ref">
+  	      <fileset dir="lib" includes="*.jar"/>
+  	    </path>
+  	  </classpath>
+	</javac>
+  </target>
+
+  <!-- package all Java code into a JAR file -->
+  <target name="jar" depends="compile" description="generate the jarfile">
+    <!-- Create the distribution directory -->
+    <mkdir dir="${dist}"/>
+
+    <!-- Put everything in ${build} into the jar file -->
+    <jar jarfile="${dist}/${ant.project.name}.jar" manifest="META-INF/MANIFEST.MF">
+      <fileset dir="${build}" />
+    </jar>
+  </target>
+
+  <!-- Package the jar file into a Mac OS X application with jarbundler -->
+  <target name="package-osx" depends="jar" description="Build the application for OS X">
+    <taskdef name="jarbundler"
+             classpath="${lib}/jarbundler-2.2.0.jar" 
+             classname="net.sourceforge.jarbundler.JarBundler"/>
+
+    <jarbundler dir="${dist}" verbose="false" showPlist="false"
+                name="Genomics Toolkit"
+                mainclass="edu.unc.genomics.ToolRunner"
+      			jvmversion="1.7+"
+      			stubfile="stubFile.sh"
+                version="${version}"
+                infostring="${ant.project.name}, ${copyright}"
+                build="${buildnumber}"
+                bundleid="edu.unc.genomics.GenomicsToolkit">
+      
+        <jarfilelist dir="${dist}" files="${ant.project.name}.jar"/>
+        <jarfileset dir="${lib}">
+          <include name="*.jar" />
+          <exclude name="launch4j.jar" />
+          <exclude name="xstream.jar" />
+          <exclude name="jarbundler-2.2.0.jar" />
+        </jarfileset>
+
+	    <!-- Adjust the look, feel and behavior -->
+	    <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
+	    <javaproperty name="apple.awt.brushMetal" value="true"/>
+	    <javaproperty name="apple.awt.showGrowBox" value="false"/>
+      	<javaproperty name="apple.awt.textantialiasing" value="true"/>
+        <javaproperty name="apple.awt.antialiasing" value="true"/>
+	
+	    <!-- Associate document types with this application -->
+	    <documenttype name="Assembly files"
+	      			  extensions="len" 
+	                  role="Viewer" />
+	
+	    <!-- Include resource files -->                
+	    <resourcefilelist dir="." files="README.rdoc"/>
+        <resourcefilelist dir="." files="toolConf.xml"/>
+	    <resourcefileset dir="." includes="resources/assemblies/*.len"/>
+        <javafilelist dir="." files="log4j.properties"/>
+    </jarbundler>
+  </target>
+  
+  <!-- Package the jar file into a Windows application with launch4j -->
+  <target name="package-win" depends="jar" description="Build the application for Windows">
+    <taskdef name="launch4j"
+        classname="net.sf.launch4j.ant.Launch4jTask"
+        classpath="${lib}/launch4j.jar:${lib}/xstream.jar" />
+    
+    <launch4j configFile="launch4j.xml" />
+  </target>
+
+  <target name="clean" description="clean up" >
+    <delete dir="${build}"/>
+    <delete dir="${dist}"/>
+  </target>
+</project>