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<?xml version="1.0"?>
<projectname="seqcode-core">
<propertyname="src.dir"location="src" />
<propertyname="lib.dir"location="lib" />
<propertyname="build.dir"location="build" />
<propertyname="build.classes.dir"location="${build.dir}/classes" />
<propertyname="build.dist.dir"location="${build.dir}/dist" />
<propertyname="build.unjar.dir"location="${build.dir}/unjar" />
<propertyname="build.compiler"value="javac1.8"/>
<pathid="compile.classpath">
<pathelementlocation="${build.classes.dir}"/>
<filesetdir="${lib.dir}">
<includename="**/*.jar"/>
</fileset>
</path>
<!-- ======================================================================= -->
<!-- Target: init -->
<!-- Depends: -->
<!-- Description: Perform any initialization required to run other targets -->
<!-- ======================================================================= -->
<targetname="init">
<mkdirdir="${build.classes.dir}" />
<mkdirdir="${build.dist.dir}" />
</target>
<!-- ======================================================================= -->
<!-- Target: clean -->
<!-- Depends: init -->
<!-- Description: clean up files produced in the build -->
<!-- ======================================================================= -->
<targetname="clean"depends="init"description="remove build output">
<deletedir="${build.dist.dir}" />
<deletedir="${build.classes.dir}" />
<deletedir="${build.unjar.dir}" />
</target>
<!-- ======================================================================= -->
<!-- Target: compile -->
<!-- Depends: init -->
<!-- Description: Compile the source code -->
<!-- ======================================================================= -->
<targetname="compile"depends="init"description="Compile the code">
<javacsrcdir="${src.dir}"
destdir="${build.classes.dir}"
classpathref="compile.classpath"
debug="true"
debuglevel="lines,vars,source"
deprecation="yes"
compiler="modern"
includeantruntime="false"
verbose="no">
<includename="**/*.java"/>
</javac>
</target>
<!-- ======================================================================= -->
<!-- Target: buildfilecopy -->
<!-- Depends: init -->
<!-- Description: Copies all non-source files required by utils -->
<!-- from the src directory to the build directory -->
<!-- ======================================================================= -->
<targetname="buildfilecopy"depends="init"description="Copy non-src files to the build dir">
<copytodir="${build.classes.dir}">
<filesetdir="${src.dir}">
<includename="**/*.gif"/>
<includename="**/*.html"/>
<includename="**/*.jpg"/>
<includename="**/*.xml"/>
<includename="**/*.txt"/>
<includename="**/*.dtd"/>
<includename="**/*.bat"/>
<includename="**/*.exe"/>
<includename="**/*.ico"/>
<includename="**/*.ser"/>
<includename="**/*.png"/>
<includename="**/*.properties"/>
</fileset>
</copy>
</target>
<!-- ======================================================================= -->
<!-- Target: build -->
<!-- Depends: compile, buildfilecopy -->
<!-- Description: Compiles all the client source files and copies other -->
<!-- required files to the build directory to create a usable -->
<!-- version of the utils module -->
<!-- ======================================================================= -->
<targetname="build"depends="compile, buildfilecopy"
description="build and copy files">
</target>
<targetname="unjarall"unless="build.unjar.dir.present">
<mkdirdir="${build.unjar.dir}.tmp" />
<unjardest="${build.unjar.dir}.tmp">
<filesetdir="${lib.dir}"includes="**/*.jar"/>
</unjar>
<movefile="${build.unjar.dir}.tmp"tofile="${build.unjar.dir}" />
</target>
<targetname="requirepwset">
<failunless="pwset"
message="Must set pwset property. This is a subdir of
pwbasepath (${pwbasepath})."/>
</target>
<targetname="setpwfilespath"depends="init, requirepwset"unless="${pwfiles.path}">
<propertyname="pwfiles.path"value="${pwbasepath}/${pwset}"/>
</target>
<!-- ======================================================================= -->
<!-- Target: makeseqviewjar -->
<!-- Depends: build, unjarall, setpwfilespath -->
<!-- Description: Compiles all the client source files and builds the jar -->
<!-- for the seqview browser. -->
<!-- ant -Dpwbasepath=/storage/group/sam77/default/code/pwfiles -Dpwset=mahonylab makeseqviewjar -->
<!-- ======================================================================= -->
<targetname="makeseqviewjar"depends="build, unjarall, setpwfilespath">
<deletedir="${build.unjar.dir}/META-INF"/>
<jardestfile="${build.dist.dir}/seqview.${pwset}.jar"manifest="manifests/seqview_manifest.txt">
<filesetdir="${build.classes.dir}"includes="**/*.class"/>
<filesetdir="${build.classes.dir}"includes="**/*.properties"/>
<filesetdir="${build.classes.dir}"includes="**/*.png"/>
<filesetdir="${build.classes.dir}"includes="**/*.txt"/>
<filesetdir="${pwfiles.path}"includes="*"/>
<filesetdir="${build.unjar.dir}"/>
</jar>
<chmodfile="${build.dist.dir}/seqview.${pwset}.jar}"perm="755"/>
</target>
<!-- ======================================================================= -->
<!-- Target: makesigniftestjar -->
<!-- Depends: build, unjarall, setpwfilespath -->
<!-- Description: Compiles all the client source files and builds the jar -->
<!-- for the seqview browser. -->
<!-- ant -Dpwbasepath=/storage/group/sam77/default/code/pwfiles -Dpwset=pughlab makesigniftestjar -->
<!-- ======================================================================= -->
<targetname="makesigniftestjar"depends="build, unjarall, setpwfilespath">
<deletedir="${build.unjar.dir}/META-INF"/>
<jardestfile="${build.dist.dir}/SignificanceTester.${pwset}.jar"manifest="manifests/signiftest_manifest.txt">
<filesetdir="${build.classes.dir}"includes="**/*.class"/>
<filesetdir="${build.classes.dir}"includes="**/*.properties"/>
<filesetdir="${build.classes.dir}"includes="**/*.png"/>
<filesetdir="${build.classes.dir}"includes="**/*.txt"/>
<filesetdir="${pwfiles.path}"includes="*"/>
<filesetdir="${build.unjar.dir}"/>
</jar>
<chmodfile="${build.dist.dir}/SignificanceTester.${pwset}.jar}"perm="755"/>
</target>
<!-- ======================================================================= -->
<!-- Target: makeseqcodejar -->
<!-- Depends: build, unjarall -->
<!-- Description: Compiles all the client source files and builds the jar -->
<!-- for the seqcode jar. -->
<!-- ant -Dpwbasepath=/storage/group/sam77/default/code/pwfiles -Dpwset=mahonylab makeseqcodejar -->
<!-- ======================================================================= -->
<targetname="makeseqcodejar"depends="build, unjarall, setpwfilespath">
<deletedir="${build.unjar.dir}/META-INF"/>
<jardestfile="${build.dist.dir}/seqcode.${pwset}.jar" >
<filesetdir="${build.classes.dir}"includes="**/*.class"/>
<filesetdir="${build.classes.dir}"includes="**/*.properties"/>
<filesetdir="${build.classes.dir}"includes="**/*.png"/>
<filesetdir="${build.classes.dir}"includes="**/*.txt"/>
<filesetdir="${pwfiles.path}"includes="*"/>
<filesetdir="${build.unjar.dir}"/>
</jar>
<chmodfile="${build.dist.dir}/seqcode.${pwset}.jar}"perm="755"/>
</target>
<targetname="unjarcli"unless="build.unjar.dir.present">
<mkdirdir="${build.unjar.dir}.tmp" />
<unjardest="${build.unjar.dir}.tmp">
<filesetdir="${lib.dir}">
<includename="apache-commons/commons-cli-1.5.0.jar"/>
</fileset>
</unjar>
<movefile="${build.unjar.dir}.tmp"tofile="${build.unjar.dir}" />
</target>
<targetname="compilereaddb"depends="init"description="Compile readdb">
<javacsrcdir="${src.dir}"
destdir="${build.classes.dir}"
classpathref="compile.classpath"
debug="true"
debuglevel="lines,vars,source"
deprecation="yes"
compiler="modern"
verbose="no">
<includename="org/seqcode/data/readdb/*.java"/>
</javac>
</target>
<targetname="makereaddbjar"depends="compilereaddb, unjarcli">
<mkdirdir="${build.dir}/javadoc"/>
<javadocdestdir="${build.dir}/javadoc">
<filesetdir="${src.dir}"includes="**/readdb/*.java"/>
</javadoc>
<movefile="${build.unjar.dir}/META-INF/LICENSE.txt"
tofile="${build.unjar.dir}/Apache-Commons-Cli-LICENSE.txt"/>
<movefile="${build.unjar.dir}/META-INF/NOTICE.txt"
tofile="${build.unjar.dir}/Apache-Commons-Cli-NOTICE.txt"/>
<copyfile="${src.dir}/org/seqcode/data/readdb/HOWTO"
tofile="${build.classes.dir}/HOWTO"/>
<copyfile="${src.dir}/org/seqcode/data/readdb/LICENSE"
tofile="${build.classes.dir}/LICENSE"/>
<deletedir="${build.unjar.dir}/META-INF"/>
<jardestfile="${build.dist.dir}/gse-readdb.jar">
<filesetdir="${build.classes.dir}"includes="HOWTO"/>
<filesetdir="${build.classes.dir}"includes="LICENSE"/>
<filesetdir="${build.dir}/javadoc"/>
<filesetdir="${src.dir}"includes="**/readdb/*.java"/>
<filesetdir="${build.classes.dir}"includes="**/readdb/*.class"/>
<filesetdir="${build.unjar.dir}"includes="**org/apache/commons/cli/*.class"/>
<filesetdir="${build.unjar.dir}"includes="*.txt"/>
</jar>
<chmodfile="${build.dist.dir}/gse-readdb.jar"perm="755"/>
</target>
</project>