File: build.xml

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<?xml version="1.0"?>

<!--

  Ant build file for the entire biojava tree

  see:
  <a href="http://ant.apache.org/">Ant Project Homepage</a>

  targets:

    compile
    compile-tests     compiles JUnit tests
    compile-demos     compiles the demo files
    compile-apps      compiles the application files
    package-biojava   builds the biojava.jar file (default)
    package-demos     builds the demos.jar file
    package-apps      builds the jar.apps file
    runtests          runs all tests (requires Ant 1.6.0 or later)
    runtests-fork     runs all tests in separate virtual machines
    sign              signs the biojava.jar with jarsigner
    javadocs-biojava  builds biojava API documentation
    javadocs-demos    builds demos API documentation
    javadocs-all      builds API documentation for all the above
    clean             cleans up the build & dist directories
    cruise            build target to be used together with CruiseControl
    dist              builds a full BioJava distributions
    dist-src          builds a BioJava source distributions

  The 'runtests' target can be restricted to portions of the tree, e.g.:

       ant -Dtest.subtree=org/biojava/bio/symbol runtests
       ant -Dtest.subtree=org/biojava/bio/seq/** runtests

  author:  Michael Heuer,
           Keith James (JUnit support)
           Greg Cox (fixed documentation)
           Thomas Down (clean up, remove source-copying steps)
           Mark Schreiber
	   Andreas Prlic  (jarsigner, cruise, cleanup)
  version: $Id: build.xml 4675 2008-01-08 03:09:29Z mark_s $

  portions Copyright (c) 1999-2000 The Apache Software Foundation.

-->

<project name="biojava" default="package-biojava" basedir=".">
   
	<!-- Checks environment and setup variables -->
	<target name="init" description="Checks environment and setup variables">
		<tstamp />
		<property name="version"        value="1.7.1" />
		<property name="build.compiler" value="javac1.5" />
		<property name="classpath"      value="/usr/share/java/bytecode.jar:/usr/share/java/commons-cli.jar:/usr/share/java/commons-collections.jar:/usr/share/java/commons-dbcp.jar:/usr/share/java/commons-pool.jar:/usr/share/java/hsqldb.jar:/usr/share/java/jgrapht-0.7.jar:/usr/share/java/junit4.jar" />
		<property name="ant-tasks.path" value="ant-lib/sablecc.jar:ant-lib/anttask.jar" />


		<!-- Check the current system classpath for JUnit -->
		<available classpath="${classpath}"
               classname="junit.framework.TestCase"
               property="junit.present" />

		<!-- Check for XSLT OutputProperty support in Ant (only in Ant >= 1.5) -->
		<available classpath="${java.class.path}"
               classname="org.apache.tools.ant.taskdefs.XSLTProcess$OutputProperty"
               property="outputproperty.support" />

		<!-- Check for JUnit support in Ant (only in >= 1.3) -->
		<available classpath="${java.class.path}"
               classname="org.apache.tools.ant.taskdefs.optional.junit.JUnitTest"
               property="junit.support" />

		<!-- Check for Java 1.4 -->
		<available classpath="${java.class.path}"
               classname="java.nio.Buffer"
               property="java14">
		</available>

		<available classpath="${classpath}"
               classname="org.hsqldb.jdbcDriver"
               property="sqlDriver.hsqldb">
		</available>

		<!-- Echo information -->
		<echo message="Building biojava-${version}" />
		<echo message="Java Home:                       ${java.home}"/>
		<echo message="JUnit present:                   ${junit.present}" />
		<echo message="JUnit supported by Ant:          ${junit.support}" />
		<echo message="HSQLDB driver present:           ${sqlDriver.hsqldb}" />
		<echo message="XSLT support:                    ${outputproperty.support}"/>

		<property name="readme"        value="./README" />
		<property name="license"       value="./LICENSE" />
		<property name="src.dir"       value="./src" />
		<property name="tests.dir"     value="./tests" />
		<property name="demos.dir"     value="./demos" />
		<property name="apps.dir"      value="./apps" />
		<property name="docs.dir"      value="./docs" />
		<property name="doc.css.file"  value="biojava-doc.css" />
		<property name="reports.dir"   value="./reports" />
		<property name="manifest.dir"  value="./manifest" />
		<property name="resources.dir" value="./resources" />
		<property name="signature.dir" value="./selfSignedCertificate" />

		<!-- Main build directory -->
		<property name="build.dir"         value="./ant-build" />
		<property name="build.classes.dir" value="${build.dir}/classes" />

		<!-- Javac properties -->
		<property name="javac.depend"      value="false" />
		<property name="javac.debug"       value="true" />
		<property name="javac.deprecation" value="false" />
		<property name="javac.source"      value="1.5" />
		<property name="javac.target"      value="1.5" />

		<!-- Javadoc properties -->
		<property name="build.dest.docs"     value="${build.dir}/docs" />
		<property name="build.dest.doccheck" value="${build.dir}/docs/check" />
		<property name="packages"            value="org.*" />

		<!-- Subdirectories for main source and classes -->
		<property name="name.biojava"           value="biojava" />
		<property name="Name.biojava"           value="BioJava" />
		<property name="build.dest.biojava"     value="${build.classes.dir}/${name.biojava}" />
		<property name="build.docs.biojava"     value="${build.dest.docs}/${name.biojava}" />
		<property name="build.doccheck.biojava" value="${build.dest.doccheck}/${name.biojava}" />
		<property name="jar.biojava"            value="${build.dir}/${name.biojava}.jar" />
		<property name="manifest.file.biojava"  value="${manifest.dir}/${name.biojava}.txt" />

		<!-- Subdirectories for tests source and classes -->
		<property name="name.tests"       value="tests" />
		<property name="build.dest.tests" value="${build.classes.dir}/${name.tests}" />
		<property name="build.docs.tests" value="${build.dest.docs}/${name.tests}" />
		<property name="reports.tests"    value="./reports/tests" />

		<!-- Subdirectories for demos source and classes -->
		<property name="name.demos"          value="demos" />
		<property name="Name.demos"          value="BioJava Demos" />
		<property name="build.dest.demos"    value="${build.classes.dir}/${name.demos}" />
		<property name="build.docs.demos"    value="${build.dest.docs}/${name.demos}" />
		<property name="jar.demos"           value="${build.dir}/${name.demos}.jar" />
		<property name="manifest.file.demos" value="${manifest.dir}/${name.demos}.txt" />

		<!-- Subdirectories for apps source and classes -->
		<property name="name.apps"          value="apps" />
		<property name="Name.apps"          value="BioJava Applications" />
		<property name="build.dest.apps"    value="${build.classes.dir}/${name.apps}" />
		<property name="build.docs.apps"    value="${build.dest.docs}/${name.apps}" />
		<property name="jar.apps"           value="${build.dir}/${name.apps}.jar" />
		<property name="manifest.file.apps" value="${manifest.dir}/${name.apps}.txt" />

		
		<!-- Subdirectory for creating a distribution -->
		<property name="dist.root"          value="./dist" />
		<property name="dist.dir"           value="${dist.root}/${name.biojava}-${version}" />

	</target>


	<!--
    Prepare each part of the project.

    Each preparation creates working directories and copies files over.
  -->

	<!-- Prepares the basic stuff -->
	<target name="prepare" depends="init" description="creates basic directories">
		<!-- Creates directories -->
		<mkdir dir="${build.dir}" />

		<!-- Copies jars -->
		<copy todir="${build.dir}">
			<fileset dir=".">
				<include name="*.jar" />
			</fileset>
		</copy>

	</target>

	

	<!-- Prepares the biojava source code -->
	<target name="prepare-biojava" depends="prepare"
  description="Prepares biojava source files">
		<!-- Creates directories -->
		<mkdir dir="${build.dest.biojava}" />
		<mkdir dir="${build.docs.biojava}" />
		<mkdir dir="${build.doccheck.biojava}" />
	</target>

	<!-- Prepares the test source code -->
	<target name="prepare-tests" depends="prepare"
  description="Prepares the test source code">

		<!-- Creates directories -->
		<mkdir dir="${build.dest.tests}" />
		<mkdir dir="${build.docs.tests}" />
		<mkdir dir="${reports.tests}" />
	</target>

	<!-- Prepares the demos code -->
	<target name="prepare-demos" depends="prepare"
  description="Prepares the demos code">

		<!-- Creates directories -->
		<mkdir dir="${build.dest.demos}" />
		<mkdir dir="${build.docs.demos}" />
	</target>

	<!-- Prepares the apps code -->
	<target name="prepare-apps" depends="prepare"
  description="Prepares the apps code">

		<!-- Creates directories -->
		<mkdir dir="${build.dest.apps}" />
		<mkdir dir="${build.docs.apps}" />
	</target>

	<!-- Prepares the javadocs -->
	<target name="prepare-javadocs" depends="prepare" description="Prepares the javadocs">

		<!-- Creates directories -->
		<mkdir dir="${build.dest.docs}" />
	</target>



	<!--
    Compile each part of the project.

    This runs javac or any other tasks necisary to turn the source code into
    .class files.
  -->

	<!-- Compiles the source directory -->
	<target name="compile-biojava" depends="prepare-biojava"
  description="Compiles the source directory">
		<javac
      encoding="ISO-8859-1"
      srcdir="${src.dir}"
      destdir="${build.dest.biojava}"
      depend="${javac.depend}"
      deprecation="${javac.deprecation}"
      source="${javac.source}"
      target="${javac.target}"
      debug="${javac.debug}">
			<classpath>
				<pathelement path="${classpath}" />
			</classpath>
		</javac>
	</target>

	<!-- Compiles the tests directory -->
	<target name="compile-tests" depends="prepare-tests,package-biojava"
  description="Compiles the tests directory">
		<javac
      encoding="ISO-8859-1"
      srcdir="${tests.dir}"
      destdir="${build.dest.tests}"
      depend="${javac.depend}"
      deprecation="${javac.deprecation}"
      source="${javac.source}"
      target="${javac.target}"
      debug="${javac.debug}">
			<classpath>
				<pathelement path="${classpath}" />
				<pathelement path="${jar.biojava}" />
			</classpath>
		</javac>
	</target>

	<!-- Compiles the demos directory -->
	<target name="compile-demos" depends="prepare-demos,package-biojava"
  description="Compiles the demos directory">
		<javac
      encoding="ISO-8859-1"
      srcdir="${demos.dir}"
      destdir="${build.dest.demos}"
      depend="${javac.depend}"
      deprecation="${javac.deprecation}"
      source="${javac.source}"
      target="${javac.target}"
      debug="${javac.debug}">
			<classpath>
				<pathelement path="${classpath}" />
				<pathelement path="${jar.biojava}" />
			</classpath>
		</javac>
	</target>

	<!-- Compiles the apps directory -->
	<target name="compile-apps" depends="prepare-apps,package-biojava"
  description="Compiles the apps directory">
		<javac
      encoding="ISO-8859-1"
      srcdir="${apps.dir}"
      destdir="${build.dest.apps}"
      depend="${javac.depend}"
      deprecation="${javac.deprecation}"
      source="${javac.source}"
      target="${javac.target}"
      debug="${javac.debug}">
			<classpath>
				<pathelement path="${classpath}" />
				<pathelement path="${jar.biojava}" />
			</classpath>
		</javac>
	</target>


	<!--
    Creates the .jar files containing each distributable component.

    This probably just jars up the .class files and any resources as well as
    a manifest for each distributable component.
  -->

	<!-- Creates the biojava package (tests are left in the parallel tree) -->


	<target name="package-biojava" depends="compile-biojava"
  description="create biojava class jar file">
		<jar
      jarfile="${jar.biojava}"
      manifest="${manifest.dir}/biojava.txt"
    >
			<fileset dir="${build.dest.biojava}" />
			<fileset dir="${resources.dir}" />
		</jar>
	</target>

	<!-- Create the demo package -->
	<target name="package-demos" depends="init,package-biojava,compile-demos"
  description="create the demo jar file">
		<jar
      jarfile="${jar.demos}"
      manifest="${manifest.dir}/demos.txt"
    >
			<fileset dir="${build.dest.demos}" />
		</jar>
	</target>

	<!-- Create the apps package -->
	<target name="package-apps" depends="init,package-biojava,compile-apps"
  description="create the apps jar file">
		<jar
      jarfile="${jar.apps}"
      manifest="${manifest.dir}/apps.txt"
    >
			<fileset dir="${build.dest.apps}" />
		</jar>
	</target>


	<target
    name="package-all"
    depends="package-biojava,package-demos,package-apps"
    description="create all the jar files" />

	<!-- sign the biojava.jar file -->
	<target
    name="sign"
    depends="package-biojava"
    description="sign the biojava.jar file with jarsigner"
    >

		<copy file="${jar.biojava}" tofile="${build.dir}/biojavaUnsigned.jar" />

		<signjar jar="${build.dir}/biojavaUnsigned.jar"
             signedjar="${jar.biojava}"
             keystore="${signature.dir}/selfSignedCertificate.store"
             storepass="biojavaCVS" 
	     alias="biojavaCVS" />

		<!-- to verify that a .jar file is signed: jarsigner -verify biojava.jar -->

		<delete file="${build.dir}/biojavaUnsigned.jar"/>

	</target>

	<!--
    Create Javadoc and other documentation for each distribution package.

    This probably just calls javadoc, but may call other documentation gubbins.
  -->

	

	<!-- Creates the API documentation -->
	<target name="javadocs-biojava" depends="prepare-biojava"
  description="Creates the API documentation">
		<javadoc
      encoding="ISO-8859-1"
      packagenames="${packages}"
      sourcepath="${src.dir}"
      classpath="${classpath}"
      destdir="${build.docs.biojava}"
      author="true"
      version="true"
      use="true"
      source="1.5"
      windowtitle="${Name.biojava}-${version} API"
      doctitle="${Name.biojava}-${version}"
      maxmemory="512m">
			<link href="http://java.sun.com/j2se/1.5.0/docs/api/" offline="false"/>

			<group title="Core biological packages"
              packages="org.biojava.bio:org.biojava.bio.dist:org.biojava.bio.search:org.biojava.bio.seq:org.biojava.bio.seq.db:org.biojava.bio.seq.genomic:org.biojava.bio.seq.io:org.biojava.bio.symbol:org.biojava.bio.alignment:org.biojava.directory:org.biojava.bibliography:org.biojava.bio.taxa:org.biojava.bio.seq.filter" />

			<group title="User interface components"
              packages="org.biojava.bio.gui:org.biojava.bio.gui.glyph:org.biojava.bio.gui.sequence:org.biojava.bio.gui.sequence.tracklayout" />

			<group title="Sequence databases and formats"
              packages="org.biojava.bio.seq.io.agave:org.biojava.bio.program.das:org.biojava.bio.seq.ragbag:org.biojava.bio.seq.db.emblcd:org.biojava.bio.program.xff:org.biojava.bio.seq.dist:org.biojava.bio.seq.io.game:org.biojava.bio.seq.io.game12:org.biojava.bio.seq.db.biofetch:org.biojava.bio.seq.db.flat:org.biojava.bio.seq.db.biosql:org.biojava.bio.program.indexdb:org.biojava.bio.program.das.dasalignment:org.biojava.bio.program.homologene" />

			<group title="Handling output from external tools"
              packages="org.biojava.bio.program:org.biojava.bio.program.gff:org.biojava.bio.program.gff3:org.biojava.bio.program.sax:org.biojava.bio.program.xml:org.biojava.bio.program.blast2html:org.biojava.bio.program.search:org.biojava.bio.program.ssbind:org.biojava.bio.program.phred:org.biojava.bio.program.hmmer:org.biojava.bio.program.sax.blastxml" />

			<group title="Dynamic programming packages"
              packages="org.biojava.bio.dp:org.biojava.bio.dp.onehead:org.biojava.bio.dp.twohead" />

			<group title="Chromatogram and trace file support"
              packages="org.biojava.bio.chromatogram:org.biojava.bio.program.abi:org.biojava.bio.program.scf:org.biojava.bio.chromatogram.graphic" />

			<group title="Macromolecular structure (PDB)"
              packages="org.biojava.bio.structure:org.biojava.bio.structure.io:org.biojava.bio.program.das.dasstructure:org.biojava.bio.structure.align:org.biojava.bio.structure.align.helper:org.biojava.bio.structure.align.pairwise:org.biojava.bio.structure.jama:org.biojava.bio.structure.gui:org.biojava.bio.structure.server" />

			<group title="Utilities and developers' packages"
              packages="org.biojava.utils.process:org.biojava.bio.seq.impl:org.biojava.bio.seq.projection:org.biojava.utils:org.biojava.utils.cache:org.biojava.utils.xml:org.biojava.utils.stax:org.biojava.utils.io:org.biojava.utils.math:org.biojava.utils.net:org.biojava.utils.candy:org.biojava.bio.seq.io.filterxml:org.biojava.bio.program.tagvalue:org.biojava.ontology:org.biojava.ontology.io:org.biojava.utils.automata:org.biojava.utils.regex:org.biojava.naming:org.biojava.utils.walker" />

			<group title="Molecular biology packages"
              packages = "org.biojava.bio.proteomics:org.biojava.bio.proteomics.aaindex:org.biojava.bio.molbio" />

			<group title="Ontology packages"
              packages = "org.biojava.bio.ontology:org.biojava.bio.ontology.io"/>

			<group title="Experimental packages"
              packages="org.biojava.stats.svm:org.biojava.stats.svm.tools:org.biojava.bio.seq.homol:org.biojava.utils.lsid:org.biojava.bio.program.unigene:org.biojava.bio.program.ssaha:org.biojava.bio.seq.distributed:org.biojava.bio.annodb:org.biojava.bio.program.formats" />

			<group title="Biojava extension (biojavax) packages"
              packages="org.biojavax:org.biojavax.bio:org.biojavax.bio.db:org.biojavax.bio.db.biosql:org.biojavax.bio.db.ncbi:org.biojavax.bio.seq:org.biojavax.bio.seq.io:org.biojavax.bio.taxa:org.biojavax.bio.taxa.io:org.biojavax.ontology:org.biojavax.utils" />

			<group title="Genetic Algorithm Framework"
              packages="org.biojavax.ga:org.biojavax.ga.exception:org.biojavax.ga.functions:org.biojavax.ga.impl:org.biojavax.ga.util" />
			<group title="Experimental Phylogeny packages"
              packages="org.biojavax.bio.phylo:org.biojavax.bio.phylo.io:org.biojavax.bio.phylo.io.nexus:org.biojavax.bio.phylo.io.phylip:org.biojavax.bio.phylo.tree" />

			
		</javadoc>
	</target>

	<!-- Create demos API documentation -->
	<target name="javadocs-demos" depends="prepare-demos,compile-biojava"
  description="Create the demos API documentation">
		<javadoc
      encoding="ISO-8859-1"
      packagenames="**"
      sourcepath="${demos.dir}"
      classpath="${classpath}:${build.dest.biojava}"
      destdir="${build.docs.demos}"
      author="true"
      version="true"
      use="true"
      source="1.5"
      windowtitle="${Name.demos} API"
      doctitle="${Name.demos}"
      maxmemory="512m">
			<link href="http://java.sun.com/j2se/1.5.0/docs/api/" offline="false"/>
			<link href="../biojava" offline="true" packagelistLoc="${build.docs.biojava}/package-list}"/>
		</javadoc>
	</target>

	<!-- Create apps API documentation -->
	<target name="javadocs-apps" depends="prepare-apps,compile-biojava"
  description="Create the apps API documentation">
		<javadoc
      encoding="ISO-8859-1"
      packagenames="org.*"
      sourcepath="${apps.dir}"
      classpath="${classpath}:${build.dest.biojava}"
      destdir="${build.docs.apps}"
      author="true"
      version="true"
      use="true"
      source="1.5"
      windowtitle="${Name.apps} API"
      doctitle="${Name.apps}"
      maxmemory="512m">
			<link href="http://java.sun.com/j2se/1.5.0/docs/api/" offline="false"/>
			<link href="../biojava" offline="true" packagelistLoc="${build.docs.biojava}/package-list}"/>
			
		</javadoc>
	</target>



	<target
    name="javadocs-all"
    depends="javadocs-biojava,javadocs-demos,javadocs-apps"
    description="Creates the javadocs for all components"
  />


	<!-- Runs tests if the Ant optional JUnit support is available -->
	<target name="runtests" 
  	  depends="compile-tests"
  	  description="Run all tests, can be quite slow">
		<property name="test.subtree" value="**" />
		<echo message="Running tests:           ${test.subtree}" />
		<junit maxmemory="512m" printsummary="yes" haltonfailure="no" reloading="no">
			<formatter type="plain" usefile="true" />
			<classpath>
				<!-- main classes from build -->
				<pathelement path="${build.dest.biojava}" />
				<!-- resources -->
				<pathelement path="${resources.dir}" />
				<!-- test classes from build -->
				<pathelement path="${build.dest.tests}" />
				<!-- test data from build -->
				<pathelement path="${tests.dir}/files" />
				<!-- currently the move isn't complete -->
				<pathelement path="${tests.dir}" />
				<!-- classes specified in this file -->
				<pathelement path="${classpath}" />
				<!-- classes specified in system classpath -->
				<pathelement path="${java.class.path}" />
			</classpath>
			<!-- The junit task doesn't support 'if' so we test for JUnit here -->
			<batchtest fork="no" todir="${reports.tests}" if="junit.present">
				<fileset dir="${build.dest.tests}">
					<include name="${test.subtree}/*Test.class" />
					<include name="${test.subtree}/*TestSuite.class" />
					<exclude name="**/Abstract*Test.class" />
				</fileset>
			</batchtest>
		</junit>
	</target>

	<target name="doccheck-biojava" depends="prepare-biojava"
    description="Checks the API documentation">
		<javadoc
      encoding="ISO-8859-1"
      doclet="com.sun.tools.doclets.doccheck.DocCheck"
      docletpath="doccheck.jar"
      packagenames="${packages}"
      sourcepath="${src.dir}"
      classpath="${classpath}"
      destdir="${build.doccheck.biojava}"
      source="1.5"
      maxmemory="512m">
		</javadoc>
	</target>

	<!-- Runs the CruiseControl checks only needed for admins who want to trace the compile state of biojava -->
	<!-- does the same as runtests, but with XML output, so CruiseControl can parse the outcome -->
	<target name="cruise" 
          depends="clean,package-biojava,compile-tests"
          description="Run clean, build and tests for CruiseControl">
		<property name="test.subtree" value="**" />
		<echo message="Running tests:           ${test.subtree}" />
		<junit 	maxmemory="512m" 
    		printsummary="yes" 
		haltonfailure="no" 
		reloading="no"
		errorProperty="test.failed"
		>
			<formatter type="xml" />
			<classpath>
				<!-- main classes from build -->
				<pathelement path="${build.dest.biojava}" />
				<!-- resources -->
				<pathelement path="${resources.dir}" />
				<!-- test classes from build -->
				<pathelement path="${build.dest.tests}" />
				<!-- test data from build -->
				<pathelement path="${tests.dir}/files" />
				<!-- currently the move isn't complete -->
				<pathelement path="${tests.dir}" />
				<!-- classes specified in this file -->
				<pathelement path="${classpath}" />
				<!-- classes specified in system classpath -->
				<pathelement path="${java.class.path}" />
			</classpath>
			<!-- The junit task doesn't support 'if' so we test for JUnit here -->
			<batchtest fork="no" todir="${reports.tests}" if="junit.present">
				<fileset dir="${build.dest.tests}">
					<include name="${test.subtree}/*Test.class" />
					<include name="${test.subtree}/*TestSuite.class" />
					<exclude name="**/Abstract*Test.class" />
				</fileset>
			</batchtest>
		</junit>
		<fail message="Tests failed: check test reports." if="test.failed" />
	</target>


	<!-- Cleans everything -->
	<target name="clean" 
  	  depends="init"
  	  description="Cleans everything">
		<delete dir="${build.dir}" />
		<delete dir="${reports.tests}" />
	</target>

	<!-- Cleans the dist directory -->
	<target name="clean-dist" depends="init" description="Cleans the dist root directory">
		<delete dir="${dist.root}" />
	</target>


	<!-- This task is mainly for BioJava admins to build a distribution, not needed for normal use -->
	<target name="dist" depends="clean-dist, init, javadocs-all, package-all" description="copy all the files for a distribution">
		<mkdir dir="${dist.root}"/>
		<mkdir dir="${dist.dir}"/>

		<!-- copy the biojava-jar -->
		<copy file="${jar.biojava}" tofile="${dist.dir}/${name.biojava}-${version}.jar"/>

		<!-- copy the apps-jar -->
		<copy file="${jar.apps}" tofile="${dist.dir}/apps-${version}.jar"/>

		<!-- copy the demos.jar -->
		<copy file="${jar.demos}" tofile="${dist.dir}/demos-${version}.jar"/>

		<!-- copy the other jars -->
		<copy todir="${dist.dir}">
			<fileset dir=".">
				<include name="*.jar" />
			</fileset>
		</copy>

		<!-- copy the docs -->
		<copy todir="${dist.dir}/doc">
			<fileset dir="${build.dest.docs}"/>
		</copy>

		<!-- copy biojava src -->
		<copy todir="${dist.dir}/src">
			<fileset dir="${src.dir}"/>
		</copy>

		<!-- copy READMEs -->
		<copy tofile="${dist.dir}/README" file="./README"/>
		<copy tofile="${dist.dir}/README.biosql" file="./README.biosql"/>

		<!-- copy tests -->
		<copy todir="${dist.dir}/tests">
			<fileset dir="${tests.dir}"/>
		</copy>

		<!-- copy demo src -->
		<copy todir="${dist.dir}/demos">
			<fileset dir="${demos.dir}"/>
		</copy>

		<!-- copy apps src -->
		<copy todir="${dist.dir}/apps">
			<fileset dir="${apps.dir}"/>
		</copy>

		<!-- copy licenses -->
		<copy tofile="${dist.dir}/LICENSE" file="./LICENSE"/>

		<!-- why do this need this license? isn't all of BioJava LGPL? -->
		<copy tofile="${dist.dir}/LICENSE.COMMONS" file="./LICENSE.COMMONS"/>

		<!-- copy manifest -->
		<copy todir="${dist.dir}/manifest">
			<fileset dir="${manifest.dir}"/>
		</copy>

		<!-- copy dtd -->
		<copy todir="${dist.dir}/dtd">
			<fileset dir="./dtd"/>
		</copy>

		<!-- copy resources -->
		<copy todir="${dist.dir}/resources">
			<fileset dir="${resources.dir}"/>
		</copy>

		<!-- copy this build file -->
		<copy file="${ant.file}" tofile="${dist.dir}/build.xml"/>

	</target>

	<target name="dist-src" depends="clean-dist, init, prepare"
  	        description="create a jar file of the biojava source">

		<mkdir dir="${dist.root}"/>
		<mkdir dir="${dist.dir}"/>

		<!-- copy biojava src -->
		<copy todir="${dist.dir}/src">
			<fileset dir="${src.dir}"/>
		</copy>

		<!-- copy resources -->
		<copy todir="${dist.dir}/resources">
			<fileset dir="${resources.dir}"/>
		</copy>

		<!-- copy this build file -->
		<copy file="${ant.file}" tofile="${dist.dir}/build.xml"/>

		<!-- copy licenses -->
		<copy tofile="${dist.dir}/LICENSE" file="./LICENSE"/>		

		<!-- copy manifest -->
		<copy todir="${dist.dir}/manifest">
			<fileset dir="${manifest.dir}"/>
		</copy>


		<!-- copy READMEs -->
		<copy tofile="${dist.dir}/README" file="./README"/>
		<copy tofile="${dist.dir}/README.biosql" file="./README.biosql"/>

		<!-- copy tests -->
		<copy todir="${dist.dir}/tests">
			<fileset dir="${tests.dir}"/>
		</copy>

		<!-- copy the docs -->
		<copy todir="${dist.dir}/doc">
			<fileset dir="${build.dest.docs}"/>
		</copy>
		
		<!-- jarsign -->
		<copy todir="${dist.dir}/selfSignedCertificate">
			<fileset dir="${signature.dir}"/>
		</copy>


		<!-- copy the jar files -->
		<copy todir="${dist.dir}">
			<fileset dir=".">
				<include name="*.jar" />
			</fileset>
		</copy>


		<jar
	      jarfile="${build.dir}/biojava-src.jar"
    	  manifest="${manifest.dir}/biojava.txt">
			
			<fileset dir="${dist.dir}" />

		</jar>

	</target>

</project>