1
<project name="CDK" default="dist-all" basedir=".">
3
<property file="build.props"/>
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<!-- compile options -->
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<property name="build.sysclasspath" value="ignore" />
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<property name="build.compiler" value="modern" />
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<property name="debug" value="on" />
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<property name="deprecation" value="on" />
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<property name="optimization" value="off" />
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<property name="nowarn" value="off" />
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<property name="compile.batik" value="true" />
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<!-- patches to apply -->
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<!-- where to find some libraries -->
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<property name="pathtojoelib" value="jar/libio" />
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<property name="pathtojmol" value="jar/libio" />
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<property name="jniinchi.jar" value="jniinchi-0.4.jar"/>
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<property name="log4j.jar" value="log4j-1.2.jar"/>
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<property name="build" value="build" />
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<property name="build.src" value="${build}/src" />
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<property name="sourcedist" value="sourcedist" />
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<property name="dist" value="dist" />
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<property name="doc" value="doc" />
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<property name="src" value="src" />
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<property name="lib" value="jar" />
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<property name="devellib" value="develjar" />
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<property name="src.tests" value="${src}/org/openscience/cdk/test" />
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<property name="reports.tests" value="reports" />
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<property name="appjars.dir" value="${dist}/appjars" />
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<property name="metainf" value="${src}/META-INF" />
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<!-- class to run for testing-->
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<property name="testclass" value="CDKTests" />
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<property name="runclass" value="applications.FileConvertor" />
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<property name="arg1" value="" />
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<property name="arg2" value="" />
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<property name="arg3" value="" />
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<property name="arg4" value="" />
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<property environment="env" />
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<target id="info" name="info" depends="check">
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<!-- Gives information about the building process. -->
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<echo message="Platform:" />
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<echo message=" OS: ${os.name}" />
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<echo message=" Architecture: ${os.arch}" />
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<echo message=" Version: ${os.version}" />
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<echo message=" Mac OS/X found: ${isMacOsX}" />
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<echo message="Java/Ant Environment:" />
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<echo message=" Java version: ${java.version}" />
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<echo message=" Java vendor: ${java.vendor}" />
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<echo message=" Java dir: ${java.home}" />
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<echo message=" Java ext dir: ${java.ext.dirs}" />
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<echo message=" Java3: ${isJava13}" />
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<echo message=" Java4: ${isJava14}" />
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<echo message=" Java5: ${isJava15}" />
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<echo message=" Java6: ${isJava16}" />
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<echo message=" Java4+: ${isJava14+}" />
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<echo message=" Java5+: ${isJava15+}" />
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<echo message=" not Java5+: ${isNotJava15+}" />
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<echo message=" Java6: ${isJava16}" />
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<echo message=" Ant version: ${ant.version}" />
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<echo message=" ${ANT_HOME}: ${ant.home}" />
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<echo message=" hasAnt16: ${hasAnt16}" />
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<echo message="CDK Environment:" />
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<echo message=" CDK version: ${version}" />
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<echo message=" build.xml: $Id: build.xml 10282 2008-03-02 15:25:03Z egonw $" />
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<echo message=" Junit found: ${junit.present}" />
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<echo message=" --- required libraries ---" />
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<echo message=" Vecmath found: ${vecmath.present}" />
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<echo message=" Log4j found: ${log4j.present}" />
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<echo message=" JGraphT found: ${jgrapht.present}" />
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<echo message=" --- distributed (but optional) libraries ---" />
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<echo message=" Batik found: ${batik.present}" />
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<echo message=" CMLDOM found: ${cmllibs.present}" />
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<echo message=" DADML found: ${dadml.present}" />
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<echo message=" JAI found: ${jai.present}" />
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<echo message=" XIndice found: ${xindice.present}"/>
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<echo message=" SJava found: ${sjava.present}"/>
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<echo message="JNI-InChI found: ${jniinchi.present}"/>
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<echo message=" --- optional libraries ---" />
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<echo message="Compiling:" />
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<echo message=" for: ${build.compiler}" />
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<echo message=" debug: ${debug}" />
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<echo message=" nowarn: ${nowarn}" />
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<echo message=" deprecation: ${deprecation}" />
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<echo message=" optimization: ${optimization}" />
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<target id="checkPlatforms" name="checkPlatforms">
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<condition property="isMacOsX">
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<target id="check" name="check" depends="checkPlatforms">
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<!-- Check wether Doclets are compiled and output is generated -->
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<uptodate property="dotjavafiles.uptodate"
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targetfile="${src}/core.javafiles">
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<srcfiles dir="${src}" includes="**/*.java" />
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<condition property="dotjjfiles.uptodate">
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<uptodate property="NomParserJavafiles.uptodate"
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targetfile="${src}/org/openscience/cdk/iupac/parser/NomParser.java">
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<srcfiles dir="${src}" includes="org/openscience/cdk/iupac/parser/NomParser.jj" />
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<!-- Checks which parts of CDK can be build. -->
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<!-- test for optional jars -->
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<available property="vecmath.present" file="${lib}/vecmath1.2-1.14.jar"/>
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<available property="log4j.present" file="${lib}/${log4j.jar}"/>
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<available property="jgrapht.present" file="${lib}/jgrapht.jar"/>
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<available property="cmllibs.present" file="${lib}/jumbo52.jar"/>
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<available property="dadml.present" file="${lib}/dadml.jar"/>
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<available property="sjava-0.68.present" file="${lib}/sjava-0.68.jar"/>
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<available property="jniinchi.present" file="${lib}/${jniinchi.jar}"/>
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<condition property="batik.present">
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<available file="${lib}/batik-awt-util.jar"/>
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<available file="${lib}/batik-dom.jar"/>
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<available file="${lib}/batik-svggen.jar"/>
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<available file="${lib}/batik-util.jar"/>
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<available file="${lib}/batik-xml.jar"/>
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<istrue value="${compile.batik}"/>
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<condition property="jai.present">
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<available file="${lib}/jai_codec.jar"/>
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<available file="${lib}/jai_core.jar"/>
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<available property="junit.present"
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classname="junit.framework.TestCase"
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classpath="${ant.home}/lib/junit.jar"/>
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<condition property="xindice.present">
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<available file="${lib}/xindice.jar"/>
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<available file="${lib}/xmldb.jar"/>
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<!-- test Ant version -->
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<condition property="hasAnt16">
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<contains string="${ant.version}" substring="1.6"/>
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<contains string="${ant.version}" substring="1.7"/>
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<!-- test Java version -->
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<condition property="isJava13">
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<contains string="${java.version}" substring="1.3"/>
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<condition property="isJava14">
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<contains string="${java.version}" substring="1.4"/>
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<condition property="isJava15">
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<contains string="${java.version}" substring="1.5"/>
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<condition property="isJava16">
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<contains string="${java.version}" substring="1.6."/>
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<condition property="isJava14+">
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<contains string="${java.version}" substring="1.4"/>
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<contains string="${java.version}" substring="1.5"/>
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<contains string="${java.version}" substring="1.6"/>
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<condition property="isJava15+">
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<contains string="${java.version}" substring="1.5"/>
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<contains string="${java.version}" substring="1.6"/>
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<condition property="isNotJava15+">
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<contains string="${java.version}" substring="1.5"/>
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<contains string="${java.version}" substring="1.6"/>
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<target id="checkCompilableBlobs" name="checkCompilableBlobs" depends="check">
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<!-- check compilable blobs -->
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<condition property="compile.jai"><and><available file="${build}/jai.javafiles"/><istrue value="${jai.present}"/></and></condition>
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<condition property="compile.dadml"><and><available file="${build}/dadml.javafiles"/><istrue value="${dadml.present}"/></and></condition>
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<condition property="compile.xindice"><and><available file="${build}/xindice.javafiles"/><istrue value="${xindice.present}"/></and></condition>
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<condition property="compile.jumbo52"><and><available file="${build}/jumbo52.javafiles"/><istrue value="${cmllibs.present}"/></and></condition>
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<condition property="compile.r-project"><and><available file="${build}/r-project.javafiles"/><istrue value="${sjava.present}"/></and></condition>
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<condition property="do.compile.batik"><and><available file="${build}/batik.javafiles"/><istrue value="${batik.present}"/></and></condition>
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<condition property="compile.jniinchi"><and><available file="${build}/jniinchi.javafiles"/><istrue value="${jniinchi.present}"/></and></condition>
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<target id="init" name="init" depends="check, setupBuildDir"/>
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<target id="customize" name="customize" depends="javacc"/>
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<target id="setupBuildDir" name="setupBuildDir">
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<mkdir dir="${build}" />
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<mkdir dir="${sourcedist}" />
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<mkdir dir="${dist}" />
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<mkdir dir="${reports.tests}" />
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<target id="clean" name="clean" description="Removes autogenerated files.">
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<fileset dir="." includes="**/*~" />
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<fileset dir="." includes="*.tar.gz" />
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<fileset dir="." includes="*.zip" />
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<fileset dir="." includes="*.rda" />
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<fileset dir="${src}" includes="*.entitylist" />
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<!-- remove java files generated with JavaCC -->
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<fileset dir="${src}/org/openscience/cdk/iupac/parser" includes="*.java">
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<!-- the next are from CVS -->
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<exclude name="AttachedGroup.java" />
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<exclude name="MoleculeBuilder.java" />
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<fileset dir="${src}">
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<include name="net/sf/cdk/tools/*.class" />
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<delete dir="${build}" />
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<delete dir="${sourcedist}" />
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<delete dir="${dist}" />
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<delete dir="${reports.tests}" />
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<target name="runDoclet" id="runDoclet" depends="check, customize">
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<echo>Not skipping doclet run...</echo>
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<mkdir dir="${build}" />
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<javac includes="net/sf/cdk/tools/MakeJavafilesFiles.java"
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srcdir="${src}" destdir="${build}" optimize="${optimization}"
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debug="${debug}" deprecation="${deprecation}"/>
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<java classpath="${build}" classname="net.sf.cdk.tools.MakeJavafilesFiles">
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<arg value="${src}"/>
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<arg value="${build}"/>
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<javac includes="net/sf/cdk/tools/MakeRequiresfilesFiles.java"
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srcdir="${src}" destdir="${build}" optimize="${optimization}"
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debug="${debug}" deprecation="${deprecation}"/>
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<java classpath="${build}" classname="net.sf.cdk.tools.MakeRequiresfilesFiles">
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<arg value="${src}"/>
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<arg value="${build}"/>
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<target id="compile-needed-test" name="compile-needed-test">
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<condition property="module-uptodate">
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<available file="${build}/${module}.javafiles"/>
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<uptodate property="module-uptodate" targetfile="${dist}/jar/cdk-${module}.jar">
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<srcfiles dir="${src}">
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<includesfile name="${build}/${module}.javafiles"/>
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<target id="compile-info" name="compile-info" depends="init, runDoclet, checkCompilableBlobs">
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<echo message="Determine compilable blobs..."/>
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<echo message="Compile DADML: ${compile.dadml}"/>
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<echo message="Compile JAI: ${compile.jai}"/>
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<echo message="Compile Xindice: ${compile.xindice}"/>
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<echo message="Compile Jumbo52: ${compile.jumbo52}"/>
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<echo message="Compile R Project: ${compile.r-project}"/>
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<echo message="Compile Batik: ${do.compile.batik}"/>
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<echo message="Compile JNI-InChI: ${compile.jniinchi}"/>
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<target id="compile-init" name="compile-init"
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depends="init, runDoclet, checkCompilableBlobs"/>
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<target id="compile-module" name="compile-module"
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depends="init, compile-needed-test, compile-info"
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unless="module-uptodate">
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<echo message="Compiling classes for CDK's ${module} module." />
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<mkdir dir="${dist}/jar" />
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<!-- check for availability for meta info files -->
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<available file="${metainf}/${module}.datafiles" property="module.datafiles.present"/>
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<available file="${metainf}/${module}.extrafiles" property="module.extrafiles.present"/>
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<available file="${metainf}/${module}.buildfiles" property="module.buildfiles.present"/>
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<available file="${metainf}/${module}.cdkdepends" property="module.cdkdepends.present"/>
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<available file="${metainf}/${module}.libdepends" property="module.libdepends.present"/>
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<available file="${metainf}/${module}.devellibdepends" property="module.devellibdepends.present"/>
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<condition property="java14p.javafiles.present"><available file="${build}/java1.4+.javafiles"/></condition>
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<condition property="java15p.javafiles.present"><available file="${build}/java1.5+.javafiles"/></condition>
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<condition property="ant16.javafiles.present"><available file="${build}/ant1.6.javafiles"/></condition>
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<!-- be somewhat informative -->
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<echo message="Datafiles defined: ${module.datafiles.present}"/>
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<echo message="Extra files defined: ${module.extrafiles.present}"/>
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<echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
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<echo message="Library dependencies defined: ${module.libdepends.present}"/>
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<echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
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<!-- normally javac compiles not just the given files, but also missing
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classes that are in the same src/ directory. By making a copy first,
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we explicitely make it impossible to compile files that are not
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marked for a specific module -->
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<delete dir="${build.src}"/>
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<mkdir dir="${build.src}"/>
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<copy todir="${build.src}">
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<fileset dir="${src}">
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<excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
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<!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
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<!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
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<excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15+"/>
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<excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt16"/>
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<excludesfile name="${build}/jai.javafiles" unless="compile.jai"/>
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<excludesfile name="${build}/dadml.javafiles" unless="compile.dadml"/>
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<excludesfile name="${build}/xindice.javafiles" unless="compile.xindice"/>
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<excludesfile name="${build}/jumbo52.javafiles" unless="compile.jumbo52"/>
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<excludesfile name="${build}/r-project.javafiles" unless="compile.r-project"/>
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<excludesfile name="${build}/batik.javafiles" unless="do.compile.batik"/>
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<excludesfile name="${build}/jniinchi.javafiles" unless="compile.jniinchi"/>
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<includesfile name="${build}/${module}.javafiles"/>
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<!-- ok, now that we have a copy, compile this copy -->
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<javac srcdir="${build.src}" destdir="${build}" optimize="${optimization}"
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debug="${debug}" deprecation="${deprecation}" target="1.3" source="1.3">
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<fileset dir="${lib}" >
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<exclude name="**/*" unless="module.libdepends.present" />
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<includesfile name="${metainf}/${module}.libdepends" if="module.libdepends.present" />
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<fileset dir="${devellib}">
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<exclude name="**/*" unless="module.devellibdepends.present" />
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<includesfile name="${metainf}/${module}.devellibdepends" if="module.devellibdepends.present" />
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<fileset dir="${dist}/jar">
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<exclude name="**/*" unless="module.cdkdepends.present" />
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<includesfile name="${metainf}/${module}.cdkdepends" if="module.cdkdepends.present" />
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<excludesfile name="${build}/java1.4+.javafiles" if="isJava13"/>
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<!-- excludesfile name="${build}/java1.4.javafiles" unless="isJava14"/ -->
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<!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
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<excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15+"/>
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<excludesfile name="${build}/ant1.6.javafiles" unless="hasAnt16"/>
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<excludesfile name="${build}/jai.javafiles" unless="compile.jai"/>
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<excludesfile name="${build}/dadml.javafiles" unless="compile.dadml"/>
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<excludesfile name="${build}/xindice.javafiles" unless="compile.xindice"/>
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<excludesfile name="${build}/jumbo52.javafiles" unless="compile.jumbo52"/>
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<excludesfile name="${build}/r-project.javafiles" unless="compile.r-project"/>
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<excludesfile name="${build}/batik.javafiles" unless="do.compile.batik"/>
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<excludesfile name="${build}/jniinchi.javafiles" unless="compile.jniinchi"/>
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<includesfile name="${build}/${module}.javafiles"/>
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<!-- and then jar things up into the module jar -->
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<jar jarfile="${dist}/jar/cdk-${module}.jar">
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<fileset dir="${build}">
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<includesfile name="${build}/${module}.classes" />
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<excludesfile name="${build}/java1.4+.classes" if="isJava13"/>
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<!-- excludesfile name="${build}/java1.4.classes" unless="isJava14"/ -->
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<!-- excludesfile name="${build}/java1.5.javafiles" unless="isJava15"/ -->
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<excludesfile name="${build}/java1.5+.javafiles" if="isNotJava15+"/>
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<excludesfile name="${build}/ant1.6.classes" unless="hasAnt16"/>
393
<excludesfile name="${build}/jai.javafiles" unless="compile.jai"/>
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<excludesfile name="${build}/dadml.javafiles" unless="compile.dadml"/>
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<excludesfile name="${build}/xindice.javafiles" unless="compile.xindice"/>
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<excludesfile name="${build}/jumbo52.javafiles" unless="compile.jumbo52"/>
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<excludesfile name="${build}/r-project.javafiles" unless="compile.r-project"/>
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<excludesfile name="${build}/batik.javafiles" unless="do.compile.batik"/>
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<excludesfile name="${build}/jniinchi.javafiles" unless="compile.jniinchi"/>
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<fileset dir="${build}">
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<include name="${module}.javafiles" />
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<fileset dir="${src}">
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<exclude name="**/*" unless="module.datafiles.present"/>
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<includesfile name="${metainf}/${module}.datafiles" if="module.datafiles.present" />
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<fileset dir="${src}">
409
<exclude name="**/*" unless="module.extrafiles.present"/>
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<includesfile name="${metainf}/${module}.extrafiles" if="module.extrafiles.present" />
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<fileset dir="${build}">
413
<exclude name="**/*" unless="module.buildfiles.present"/>
414
<includesfile name="${metainf}/${module}.buildfiles" if="module.buildfiles.present" />
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<!-- Convert the JavaCC .jj file to the correct .java files for the IUPAC parser -->
420
<target id="javacc" name="javacc" depends="init, check" if="hasAnt16" unless="dotjjfiles.uptodate">
421
<echo message="Compiling Ant 1.6 depending classes." />
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<!-- the IUPAC name parser -->
424
<fileset id="javacc-generated"
425
dir="${src}/org/openscience/cdk/iupac/parser/"
426
includes="NomParser*.java,ParseException.java,SimpleCharStream.java,Token.java,TokenMgrError.java"/>
428
<javacc target="${src}/org/openscience/cdk/iupac/parser/NomParser.jj"
429
outputdirectory="${src}/org/openscience/cdk/iupac/parser/"
430
javacchome="${lib}"/>
433
<target id="dist-java3d" name="dist-java3d" depends="nocompile-java3d, compile-java3d"/>
434
<target id="nocompile-java3d" name="nocompile-java3d" unless="${java3d.present}">
435
<echo message="Java3d is not found. Removed depending functionality. Java3d can be downloaded from http://java.sun.com/."/>
437
<target id="compile-java3d" name="compile-java3d" if="${java3d.present}">
438
<antcall target="compile-module"><param name="module" value="java3d"/></antcall>
441
<target id="dist-optional" name="dist-optional" depends="dist-all"
442
description="Compile CDK modules that require optional libraries">
443
<antcall target="dist-java3d"/>
444
<antcall target="dist-jmol"/>
445
<antcall target="dist-joelib"/>
448
<target id="dist-all" name="dist-all" description="dist-all">
449
<antcall target="compile-init"/>
450
<antcall target="compile-module"><param name="module" value="interfaces"/></antcall>
451
<antcall target="compile-module"><param name="module" value="core"/></antcall>
452
<antcall target="compile-module"><param name="module" value="standard"/></antcall>
453
<antcall target="compile-module"><param name="module" value="data"/></antcall>
454
<antcall target="compile-module"><param name="module" value="render"/></antcall>
455
<antcall target="compile-module"><param name="module" value="io"/></antcall>
456
<antcall target="compile-module"><param name="module" value="valencycheck"/></antcall>
457
<antcall target="compile-module"><param name="module" value="sdg"/></antcall>
458
<antcall target="compile-module"><param name="module" value="control"/></antcall>
459
<antcall target="compile-module"><param name="module" value="datadebug"/></antcall>
460
<antcall target="compile-module"><param name="module" value="nonotify"/></antcall>
461
<antcall target="compile-module"><param name="module" value="structgen"/></antcall>
462
<antcall target="compile-module"><param name="module" value="pdb"/></antcall>
463
<antcall target="compile-module"><param name="module" value="extra"/></antcall>
464
<antcall target="compile-module"><param name="module" value="smiles"/></antcall>
465
<antcall target="compile-module"><param name="module" value="libio-cml"/></antcall>
466
<antcall target="compile-module"><param name="module" value="libio-openbabel"/></antcall>
467
<antcall target="compile-module"><param name="module" value="libiomd"/></antcall>
468
<antcall target="compile-module"><param name="module" value="pdb-cml"/></antcall>
469
<antcall target="compile-module"><param name="module" value="reaction"/></antcall>
470
<antcall target="compile-module"><param name="module" value="charges"/></antcall>
471
<antcall target="compile-module"><param name="module" value="qsar"/></antcall>
472
<antcall target="compile-module"><param name="module" value="qsar-cml"/></antcall>
473
<antcall target="compile-module"><param name="module" value="qsar-pdb"/></antcall>
474
<antcall target="compile-module"><param name="module" value="forcefield"/></antcall>
475
<antcall target="compile-module"><param name="module" value="builder3d"/></antcall>
476
<antcall target="compile-module"><param name="module" value="builder3dtools"/></antcall>
477
<antcall target="compile-module"><param name="module" value="svg"/></antcall>
478
<antcall target="compile-module"><param name="module" value="experimental"/></antcall>
479
<antcall target="compile-module"><param name="module" value="applications"/></antcall>
480
<antcall target="compile-module"><param name="module" value="inchi"/></antcall>
483
<target id="test-dist-all" name="test-dist-all" description="test-dist-all">
484
<antcall target="compile-init"/>
485
<antcall target="compile-module"><param name="module" value="test"/></antcall>
486
<antcall target="compile-module"><param name="module" value="test-core"/></antcall>
487
<antcall target="compile-module"><param name="module" value="test-standard"/></antcall>
488
<antcall target="compile-module"><param name="module" value="test-data"/></antcall>
489
<antcall target="compile-module"><param name="module" value="test-datadebug"/></antcall>
490
<antcall target="compile-module"><param name="module" value="test-nonotify"/></antcall>
491
<antcall target="compile-module"><param name="module" value="test-io"/></antcall>
492
<antcall target="compile-module"><param name="module" value="test-structgen"/></antcall>
493
<antcall target="compile-module"><param name="module" value="test-extra"/></antcall>
494
<antcall target="compile-module"><param name="module" value="test-smiles"/></antcall>
495
<antcall target="compile-module"><param name="module" value="test-reaction"/></antcall>
496
<antcall target="compile-module"><param name="module" value="test-builder3d"/></antcall>
497
<antcall target="compile-module"><param name="module" value="test-forcefield"/></antcall>
498
<antcall target="compile-module"><param name="module" value="test-valencycheck"/></antcall>
499
<antcall target="compile-module"><param name="module" value="test-experimental"/></antcall>
500
<antcall target="compile-module"><param name="module" value="test-qsar"/></antcall>
501
<antcall target="compile-module"><param name="module" value="test-qsarAtomic"/></antcall>
502
<antcall target="compile-module"><param name="module" value="test-qsarBond"/></antcall>
503
<antcall target="compile-module"><param name="module" value="test-qsarMolecular"/></antcall>
504
<antcall target="compile-module"><param name="module" value="test-pdb"/></antcall>
505
<antcall target="compile-module"><param name="module" value="test-osjvmts"/></antcall>
506
<antcall target="compile-module"><param name="module" value="test-inchi"/></antcall>
507
<antcall target="compile-module"><param name="module" value="test-libiomd"/></antcall>
510
<target id="dist-large" name="dist-large" depends="dist-all"
511
description="Builds one big jar file for the CDK, including experimental classes and third-party libraries.">
513
<!-- first unjar the CDK and other jars we need -->
514
<mkdir dir="${appjars.dir}"/>
515
<unjar dest="${appjars.dir}">
516
<fileset dir="${lib}">
517
<includesfile name="${metainf}/applications.libdepends"/>
518
<includesfile name="${metainf}/builder3d.libdepends"/>
519
<includesfile name="${metainf}/builder3dtools.libdepends"/>
520
<includesfile name="${metainf}/charges.libdepends"/>
521
<includesfile name="${metainf}/core.libdepends"/>
522
<includesfile name="${metainf}/control.libdepends"/>
523
<includesfile name="${metainf}/datadebug.libdepends"/>
524
<includesfile name="${metainf}/data.libdepends"/>
525
<includesfile name="${metainf}/experimental.libdepends"/>
526
<includesfile name="${metainf}/extra.libdepends"/>
527
<includesfile name="${metainf}/io-jmol.libdepends"/>
528
<includesfile name="${metainf}/io.libdepends"/>
529
<includesfile name="${metainf}/libio-cml.libdepends"/>
530
<includesfile name="${metainf}/nonotify.libdepends"/>
531
<includesfile name="${metainf}/pdb-cml.libdepends"/>
532
<includesfile name="${metainf}/pdb.libdepends"/>
533
<includesfile name="${metainf}/qsar.libdepends"/>
534
<includesfile name="${metainf}/qsar-cml.libdepends"/>
535
<includesfile name="${metainf}/qsar-pdb.libdepends"/>
536
<includesfile name="${metainf}/reaction.libdepends"/>
537
<includesfile name="${metainf}/render.libdepends"/>
538
<includesfile name="${metainf}/standard.libdepends"/>
539
<includesfile name="${metainf}/svg.libdepends"/>
540
<includesfile name="${metainf}/valencycheck.libdepends"/>
541
<includesfile name="${metainf}/sdg.libdepends"/>
542
<includesfile name="${metainf}/forcefield.libdepends"/>
543
<includesfile name="${metainf}/inchi.libdepends"/>
545
<fileset dir="${dist}/jar">
546
<include name="cdk-applications.jar"/>
547
<include name="cdk-builder3d.jar"/>
548
<include name="cdk-builder3dtools.jar"/>
549
<include name="cdk-charges.jar"/>
550
<include name="cdk-core.jar"/>
551
<include name="cdk-control.jar"/>
552
<include name="cdk-datadebug.jar"/>
553
<include name="cdk-data.jar"/>
554
<include name="cdk-experimental.jar"/>
555
<include name="cdk-extra.jar"/>
556
<include name="cdk-interfaces.jar"/>
557
<include name="cdk-io.jar"/>
558
<include name="cdk-io-jmol.jar"/>
559
<include name="cdk-libio-cml.jar"/>
560
<include name="cdk-libiomd.jar"/>
561
<include name="cdk-nonotify.jar"/>
562
<include name="cdk-pdb-cml.jar"/>
563
<include name="cdk-pdb.jar"/>
564
<include name="cdk-qsar.jar"/>
565
<include name="cdk-qsar-cml.jar"/>
566
<include name="cdk-qsar-pdb.jar"/>
567
<include name="cdk-reaction.jar"/>
568
<include name="cdk-render.jar"/>
569
<include name="cdk-standard.jar"/>
570
<include name="cdk-structgen.jar"/>
571
<include name="cdk-svg.jar"/>
572
<include name="cdk-valencycheck.jar"/>
573
<include name="cdk-forcefield.jar"/>
574
<include name="cdk-smiles.jar"/>
575
<include name="cdk-sdg.jar"/>
576
<include name="cdk-inchi.jar"/>
580
<!-- then zip up things -->
581
<jar jarfile="${dist}/jar/cdk-${version}.jar">
583
<attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
584
<section name="org.openscience.cdk">
585
<attribute name="Specification-Title" value="The Chemistry Development Kit"/>
586
<attribute name="Specification-Version" value="1.0"/>
587
<attribute name="Specification-Vendor" value="The CDK Project"/>
588
<attribute name="Implementation-Title" value="org.openscience.cdk"/>
589
<attribute name="Implementation-Version" value="${version}"/>
590
<attribute name="Implementation-Vendor" value="The CDK Project"/>
593
<fileset dir="${appjars.dir}">
594
<include name="**/*" />
599
<target id="dist-pure" name="dist-pure" depends="dist-all"
600
description="Builds one big jar file for the CDK, including experimental classes, but excluding third party libraries.">
602
<!-- first unjar the CDK and other jars we need -->
603
<mkdir dir="${appjars.dir}"/>
604
<unjar dest="${appjars.dir}">
605
<fileset dir="${dist}/jar">
606
<include name="cdk-applications.jar"/>
607
<include name="cdk-builder3d.jar"/>
608
<include name="cdk-builder3dtools.jar"/>
609
<include name="cdk-charges.jar"/>
610
<include name="cdk-core.jar"/>
611
<include name="cdk-control.jar"/>
612
<include name="cdk-datadebug.jar"/>
613
<include name="cdk-data.jar"/>
614
<include name="cdk-experimental.jar"/>
615
<include name="cdk-extra.jar"/>
616
<include name="cdk-interfaces.jar"/>
617
<include name="cdk-io.jar"/>
618
<include name="cdk-io-jmol.jar"/>
619
<include name="cdk-libio-cml.jar"/>
620
<include name="cdk-libiomd.jar"/>
621
<include name="cdk-nonotify.jar"/>
622
<include name="cdk-pdb-cml.jar"/>
623
<include name="cdk-pdb.jar"/>
624
<include name="cdk-qsar.jar"/>
625
<include name="cdk-qsar-cml.jar"/>
626
<include name="cdk-qsar-pdb.jar"/>
627
<include name="cdk-reaction.jar"/>
628
<include name="cdk-render.jar"/>
629
<include name="cdk-standard.jar"/>
630
<include name="cdk-structgen.jar"/>
631
<include name="cdk-svg.jar"/>
632
<include name="cdk-valencycheck.jar"/>
633
<include name="cdk-forcefield.jar"/>
634
<include name="cdk-smiles.jar"/>
635
<include name="cdk-sdg.jar"/>
636
<include name="cdk-inchi.jar"/>
640
<!-- then zip up things -->
641
<jar jarfile="${dist}/jar/cdk-pure-${version}.jar">
643
<attribute name="Main-Class" value="org.openscience.cdk.applications.DistLargeInfo"/>
644
<section name="org.openscience.cdk">
645
<attribute name="Specification-Title" value="The Chemistry Development Kit"/>
646
<attribute name="Specification-Version" value="1.0"/>
647
<attribute name="Specification-Vendor" value="The CDK Project"/>
648
<attribute name="Implementation-Title" value="org.openscience.cdk"/>
649
<attribute name="Implementation-Version" value="${version}"/>
650
<attribute name="Implementation-Vendor" value="The CDK Project"/>
653
<fileset dir="${appjars.dir}">
654
<include name="**/*" />
659
<target id="dist-test-large" name="dist-test-large" depends="test-dist-all"
660
description="Builds on big jar file for the CDK test classes.">
662
<!-- first unjar the CDK and other jars we need -->
663
<mkdir dir="${appjars.dir}"/>
664
<unjar dest="${appjars.dir}">
665
<fileset dir="${lib}">
666
<includesfile name="${metainf}/test-core.libdepends"/>
667
<includesfile name="${metainf}/test-data.libdepends"/>
668
<includesfile name="${metainf}/test-datadebug.libdepends"/>
669
<includesfile name="${metainf}/test-experimental.libdepends"/>
670
<includesfile name="${metainf}/test-extra.libdepends"/>
671
<includesfile name="${metainf}/test-builder3d.libdepends"/>
672
<includesfile name="${metainf}/test-forcefield.libdepends"/>
673
<includesfile name="${metainf}/test-inchi.libdepends"/>
674
<includesfile name="${metainf}/test-io.libdepends"/>
675
<includesfile name="${metainf}/test-nonotify.libdepends"/>
676
<includesfile name="${metainf}/test-pdb.libdepends"/>
677
<includesfile name="${metainf}/test-qsarAtomic.libdepends"/>
678
<includesfile name="${metainf}/test-qsarBond.libdepends"/>
679
<includesfile name="${metainf}/test-qsar.libdepends"/>
680
<includesfile name="${metainf}/test-qsarMolecular.libdepends"/>
681
<includesfile name="${metainf}/test-reaction.libdepends"/>
682
<includesfile name="${metainf}/test-smiles.libdepends"/>
683
<includesfile name="${metainf}/test-standard.libdepends"/>
684
<includesfile name="${metainf}/test-structgen.libdepends"/>
685
<includesfile name="${metainf}/test-valencycheck.libdepends"/>
686
<includesfile name="${metainf}/test-libiomd.libdepends"/>
688
<fileset dir="${dist}/jar">
689
<include name="cdk-test-core.jar"/>
690
<include name="cdk-test-data.jar"/>
691
<include name="cdk-test-datadebug.jar"/>
692
<include name="cdk-test-experimental.jar"/>
693
<include name="cdk-test-extra.jar"/>
694
<include name="cdk-test-builder3d.jar"/>
695
<include name="cdk-test-forcefield.jar"/>
696
<include name="cdk-test-inchi.jar"/>
697
<include name="cdk-test-io.jar"/>
698
<include name="cdk-test-nonotify.jar"/>
699
<include name="cdk-test-pdb.jar"/>
700
<include name="cdk-test-qsarAtomic.jar"/>
701
<include name="cdk-test-qsarBond.jar"/>
702
<include name="cdk-test-qsar.jar"/>
703
<include name="cdk-test-qsarMolecular.jar"/>
704
<include name="cdk-test-reaction.jar"/>
705
<include name="cdk-test-smiles.jar"/>
706
<include name="cdk-test-standard.jar"/>
707
<include name="cdk-test-structgen.jar"/>
708
<include name="cdk-test-valencycheck.jar"/>
709
<include name="cdk-test-libiomd.jar"/>
713
<!-- then zip up things -->
714
<jar jarfile="${dist}/jar/cdk-test-${version}.jar">
716
<attribute name="Main-Class" value="org.openscience.cdk.test.CDKTests"/>
717
<section name="org.openscience.cdk">
718
<attribute name="Specification-Title" value="The Chemistry Development Kit"/>
719
<attribute name="Specification-Version" value="1.0"/>
720
<attribute name="Specification-Vendor" value="The CDK Project"/>
721
<attribute name="Implementation-Title" value="org.openscience.cdk"/>
722
<attribute name="Implementation-Version" value="${version}"/>
723
<attribute name="Implementation-Vendor" value="The CDK Project"/>
726
<fileset dir="${appjars.dir}">
727
<include name="**/*" />
732
<target id="sourcedist" name="sourcedist" depends="init, runDoclet"
733
description="Builds the source packages.">
734
<property name="package" value="cdk-src+libs-${version}"/>
735
<property name="sourcedist.dir" value="${sourcedist}/${package}"/>
736
<delete dir="${sourcedist.dir}"/>
737
<copy todir="${sourcedist.dir}/${src}">
738
<fileset dir="${build}" includes="*.javafiles" />
739
<fileset dir="${build}" includes="*.classes" />
740
<fileset dir="${build}" includes="*.set" />
741
<fileset dir="${src}" includes="**/*.java" />
742
<fileset dir="${src}" includes="**/*.jj" />
743
<fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
744
<fileset dir="${src}" excludes="org/openscience/cdk/test/**" />
746
<copy todir="${sourcedist.dir}">
747
<fileset dir="." includes="build.props" />
748
<fileset dir="." includes="build.xml" />
749
<fileset dir="." includes="javadoc.xml" />
750
<fileset dir="." includes="README" />
751
<fileset dir="." includes="changelog*" />
753
<copy todir="${sourcedist.dir}/jar">
755
<exclude name="libio/*.jar"/>
758
<copy todir="${sourcedist.dir}/develjar">
759
<fileset dir="develjar">
760
<exclude name="pmd-1.8.jar"/>
761
<exclude name="doccheck.jar"/>
762
<exclude name="dbdoclet*.*"/>
765
<copy todir="${sourcedist.dir}/src/META-INF">
766
<fileset dir="src/META-INF" />
768
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
769
<fileset dir="${src}/org/openscience/cdk/config/data/"
773
file="${src}/org/openscience/cdk/dict/data/chemical.xml"
774
tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
776
file="${src}/org/openscience/cdk/dict/data/elements.xml"
777
tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
778
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
779
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/">
780
<fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
782
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/"/>
783
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/">
784
<fileset dir="${src}/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
786
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/"/>
787
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/">
788
<fileset dir="${src}/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
790
<copy todir="${sourcedist.dir}/${src}/">
791
<fileset dir="${src}/" includes="*.manifest" />
793
<mkdir dir="${sourcedist.dir}/doc/" />
794
<copy todir="${sourcedist.dir}/doc/">
795
<fileset dir="doc/" includes="lgpl.license" />
797
<mkdir dir="${sourcedist.dir}/doc/javadoc" />
798
<!-- the below deteles are a workaround, because the above should not have copied
799
in the src/data and src/org/openscience/cdk/test dirs -->
800
<delete dir="${sourcedist.dir}/src/data"/>
801
<delete dir="${sourcedist.dir}/src/org/openscience/cdk/test"/>
803
<!-- now package things up -->
804
<tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
805
<gzip zipfile="${package}.tar.gz" src="${package}.tar" />
806
<delete file="${package}.tar" />
807
<zip zipfile="${package}.zip" basedir="${sourcedist}/" includes="${package}/**" />
810
<target id="puredist" name="puredist" depends="init, runDoclet"
811
description="Builds the source packages without third-party libaries.">
812
<property name="package" value="cdk-${version}"/>
813
<property name="sourcedist.dir" value="${sourcedist}/${package}"/>
814
<delete dir="${sourcedist.dir}"/>
815
<copy todir="${sourcedist.dir}/${src}">
816
<fileset dir="${src}" includes="**/*.java" />
817
<fileset dir="${src}" includes="**/*.jj" />
818
<fileset dir="${src}" includes="org/openscience/cdk/io/cml/data/**" />
820
<copy todir="${sourcedist.dir}">
821
<fileset dir="." includes="build.props" />
822
<fileset dir="." includes="build.xml" />
823
<fileset dir="." includes="javadoc.xml" />
824
<fileset dir="." includes="README" />
825
<fileset dir="." includes="changelog*" />
827
<copy todir="${sourcedist.dir}/src/data">
828
<fileset dir="src/data" />
830
<copy todir="${sourcedist.dir}/src/META-INF">
831
<fileset dir="src/META-INF" />
833
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/config/data/">
834
<fileset dir="${src}/org/openscience/cdk/config/data/"
838
file="${src}/org/openscience/cdk/dict/data/chemical.xml"
839
tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/chemical.xml" />
841
file="${src}/org/openscience/cdk/dict/data/elements.xml"
842
tofile="${sourcedist.dir}/${src}/org/openscience/cdk/dict/data/elements.xml" />
843
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/"/>
844
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/qsar/model/data/">
845
<fileset dir="${src}/org/openscience/cdk/qsar/model/data/" includes="*.R"/>
847
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/"/>
848
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/forcefield/data/">
849
<fileset dir="${src}/org/openscience/cdk/modeling/forcefield/data/" includes="*.prm"/>
851
<mkdir dir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/"/>
852
<copy todir="${sourcedist.dir}/${src}/org/openscience/cdk/modeling/builder3d/data/">
853
<fileset dir="${src}/org/openscience/cdk/modeling/builder3d/data/" includes="*.gz"/>
855
<copy todir="${sourcedist.dir}/${src}/">
856
<fileset dir="${src}/" includes="*.manifest" />
858
<mkdir dir="${sourcedist.dir}/doc/" />
859
<copy todir="${sourcedist.dir}/doc/">
860
<fileset dir="doc/" includes="lgpl.license" />
862
<mkdir dir="${sourcedist.dir}/doc/javadoc" />
863
<mkdir dir="${sourcedist.dir}/doc/refs" />
864
<copy todir="${sourcedist.dir}/doc/refs">
865
<fileset dir="doc/refs" includes="cheminf.bibx" />
867
<!-- the below deteles are a workaround, because the above should not have copied
868
in the src/data and src/org/openscience/cdk/test dirs -->
869
<delete dir="${sourcedist.dir}/src/data"/>
870
<delete dir="${sourcedist.dir}/src/org/openscience/cdk/test"/>
872
<!-- now package things up -->
873
<tar tarfile="${package}.tar" basedir="${sourcedist}/" includes="${package}/**" />
874
<gzip zipfile="${package}.tar.gz" src="${package}.tar" />
875
<delete file="${package}.tar" />
878
<target id="noJunit" name="noJunit" depends="check" unless="junit.present">
879
<fail message="JUnit is not installed in Ant. Please copy cdk/develjar/junit.jar to ${ant.home}/lib/."/>
882
<target id="test-module" name="test-module" depends="noJunit"
883
description="Performs a full JUnit test for the CDK."
886
<echo message="Testing classes for CDK's ${module} module." />
888
<!-- check for availability for meta info files -->
889
<available file="${metainf}/test-${module}.cdkdepends" property="module.cdkdepends.present"/>
890
<available file="${metainf}/test-${module}.libdepends" property="module.libdepends.present"/>
891
<available file="${metainf}/test-${module}.devellibdepends" property="module.devellibdepends.present"/>
893
<!-- be somewhat informative -->
894
<echo message="CDK dependencies defined: ${module.cdkdepends.present}"/>
895
<echo message="Library dependencies defined: ${module.libdepends.present}"/>
896
<echo message="Developer Library dependencies defined: ${module.devellibdepends.present}"/>
898
<mkdir dir="${reports.tests}"/>
899
<junit printsummary="yes" haltonfailure="no" fork="yes" maxmemory="256m">
901
<fileset dir="${lib}" >
902
<exclude name="**/*" unless="module.libdepends.present" />
903
<includesfile name="${metainf}/test-${module}.libdepends" if="module.libdepends.present" />
905
<fileset dir="${devellib}">
906
<exclude name="**/*" unless="module.devellibdepends.present" />
907
<includesfile name="${metainf}/test-${module}.devellibdepends" if="module.devellibdepends.present" />
909
<fileset dir="${dist}/jar">
910
<exclude name="**/*" unless="module.cdkdepends.present" />
911
<includesfile name="${metainf}/test-${module}.cdkdepends" if="module.cdkdepends.present" />
912
<include name="cdk-test-${module}.jar" />
915
<test name="org.openscience.cdk.test.M${module}Tests"
917
todir="${reports.tests}"
918
outfile="result-${module}">
919
<formatter type="brief" />
924
<target id="test-all" name="test-all" depends="noJunit, dist-all, test-dist-all"
925
description="Performs a full JUnit test for the CDK."
927
<antcall target="test-module"><param name="module" value="core"/></antcall>
928
<antcall target="test-module"><param name="module" value="data"/></antcall>
929
<antcall target="test-module"><param name="module" value="datadebug"/></antcall>
930
<antcall target="test-module"><param name="module" value="nonotify"/></antcall>
931
<antcall target="test-module"><param name="module" value="standard"/></antcall>
932
<antcall target="test-module"><param name="module" value="io"/></antcall>
933
<antcall target="test-module"><param name="module" value="extra"/></antcall>
934
<antcall target="test-module"><param name="module" value="builder3d"/></antcall>
935
<antcall target="test-module"><param name="module" value="forcefield"/></antcall>
936
<antcall target="test-module"><param name="module" value="valencycheck"/></antcall>
937
<antcall target="test-module"><param name="module" value="reaction"/></antcall>
938
<antcall target="test-module"><param name="module" value="smiles"/></antcall>
939
<antcall target="test-module"><param name="module" value="experimental"/></antcall>
940
<antcall target="test-module"><param name="module" value="qsar"/></antcall>
941
<antcall target="test-module"><param name="module" value="qsarAtomic"/></antcall>
942
<antcall target="test-module"><param name="module" value="qsarBond"/></antcall>
943
<antcall target="test-module"><param name="module" value="qsarMolecular"/></antcall>
944
<antcall target="test-module"><param name="module" value="pdb"/></antcall>
945
<antcall target="test-module"><param name="module" value="inchi"/></antcall>
946
<antcall target="test-module"><param name="module" value="structgen"/></antcall>
947
<antcall target="test-module"><param name="module" value="libiomd"/></antcall>
950
<target id="limitations" name="limitations" depends="noJunit, dist-all"
951
description="Performs a JUnit tests that indicate limitations of certain CDK algorithms/classes.">
952
<junit printsummary="yes" haltonfailure="yes" fork="yes">
954
<fileset dir="${dist}/jar">
955
<include name="cdk-*.jar" />
957
<fileset dir="${lib}">
958
<include name="*.jar" />
960
<fileset dir="${devellib}">
961
<include name="*.jar" />
963
<fileset dir="${lib}/libio">
964
<include name="*.jar" />
967
<test name="org.openscience.cdk.test.limitations.AlgorithmLimitations"
969
todir="${reports.tests}"
970
outfile="limitations">
971
<formatter type="brief" />
976
<target id="run-test" name="run-test" depends="dist-all,test-dist-all"
977
description="Runs one specific JUnit test suite (org.openscience.cdk.test.<class>) as a standalone application with -Dtestclass=<class>.">
978
<echo message="Running test class: testclass=${testclass}"/>
979
<java classname="org.openscience.cdk.test.${testclass}" fork="yes" maxmemory="512m">
980
<jvmarg value="-Dcdk.debugging=true"/>
982
<fileset dir="${dist}/jar/">
983
<include name="*.jar" />
985
<fileset dir="${lib}">
986
<include name="*.jar" />
988
<fileset dir="${devellib}">
989
<include name="*.jar" />
991
<fileset dir="${lib}/libio">
992
<include name="*.jar" />
998
<target id="junit-test" name="junit-test" depends="dist-all,test-dist-all,noJunit"
999
description="Runs one specific JUnit test suite (org.openscience.cdk.test.<class>) with -Dtestclass=<class>.">
1000
<echo message="JUnit tests class: testclass=${testclass}"/>
1001
<junit printsummary="yes" haltonfailure="no" fork="yes">
1002
<jvmarg value="-Dcdk.debugging=true"/>
1003
<jvmarg value="-Dcdk.debug.stdout=true"/>
1005
<fileset dir="${dist}/jar/">
1006
<include name="*.jar" />
1008
<pathelement path="${java.class.path}" />
1009
<pathelement location="." />
1010
<fileset dir="${lib}">
1011
<include name="*.jar" />
1013
<fileset dir="${devellib}">
1014
<include name="*.jar" />
1016
<fileset dir="${lib}/libio">
1017
<include name="*.jar" />
1020
<test name="org.openscience.cdk.test.${testclass}"
1022
todir="${reports.tests}"
1023
outfile="result.${testclass}">
1024
<formatter type="brief" />
1029
<target id="run" name="run" depends="dist-all"
1030
description="Runs an application (org.openscience.cdk.<class>) with -Drunclass=<class>.">
1031
<java classname="org.openscience.cdk.${runclass}" fork="yes" >
1032
<!--jvmarg value="-Dcdk.debugging=true"/>
1033
<jvmarg value="-Dcdk.debug.stdout=true"/-->
1035
<arg value="${arg1}" />
1036
<arg value="${arg2}" />
1037
<arg value="${arg3}" />
1038
<arg value="${arg4}" />
1040
<fileset dir="${dist}/jar">
1041
<include name="*.jar" />
1043
<fileset dir="${lib}">
1044
<include name="*.jar" />
1046
<fileset dir="${lib}/libio">
1047
<include name="*.jar" />
added
removed
build.xml
