- <path id="axisbuild">
- <path refid="build.classpath" />
- </path>
- <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
- <move todir="./bak">
- <fileset dir="${sourceDir}" id="client">
- <include name="${wsdl.ClientNS}/*.*" />
- </fileset>
- </move>
-
- <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
- <mappingSet>
- <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
- <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
- </mappingSet>
- </axis-wsdl2java>
- </target>
-
- <target name="makedist" depends="build, buildPropertiesFile, buildindices">
- <!-- make the package jar if not already existing -->
- <mkdir dir="${packageDir}" />
- <!-- clean dir if it already existed -->
- <delete>
- <fileset dir="${packageDir}">
- <include name="*.jar"/>
- </fileset>
- </delete>
- <jar destfile="${packageDir}/${outputJar}" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.Jalview" />
- <attribute name="Permissions" value="all-permissions" />
- <attribute name="Application-Name" value="Jalview Desktop" />
- <attribute name="Codebase" value="${application.codebase}" />
- </manifest>
- <fileset dir="${outputDir}/">
- <exclude name="cache*/**" />
- <exclude name="*.jar" />
- <exclude name="*.jar.*" />
- <exclude name="**/*.jar" />
- <exclude name="**/*.jar.*" />
- </fileset>
- </jar>
-
- <copy toDir="${packageDir}" flatten="true">
- <fileset dir="${outputDir}">
- <include name="*.jar" />
- <include name="**/*.jar" />
- </fileset>
- </copy>
- </target>
-
-
- <!-- jalopy code reformatter -->
- <target name="sourcescrub" depends="init,build">
- <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
- <fileset dir="${sourceDir}">
- <include name="*.java" />
- <include name="**/*.java" />
- <include name="**/**/*.java" />
- </fileset>
- </jalopy>
- </target>
-
-
-
- <!-- Compile, package and obfuscate Jalview Applet -->
- <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
-
- <target name="compileApplet" depends="init,clean">
- <mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}"
- classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
- excludes="ext/**,MCview/**,org/**,vamsas/**" />
- </target>
-
- <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
- <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
- <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
- <copy todir="${outputDir}/lang">
- <fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
- <jar destfile="in.jar" index="true">
- <manifest>
- <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
- <attribute name="Application-Name" value="JalviewLite" />
- <attribute name="Codebase" value="${applet.codebase}" />
- </manifest>
- <fileset dir="${outputDir}">
- <include name="com/**" />
- <include name="MCview/**" />
- <include name="jalview/**" />
- <include name=".build_properties" />
- <include name="images/idwidth.gif" />
- <include name="images/link.gif" />
- <include name="lang/**" />
- </fileset>
- </jar>
- </target>
- <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
- </target>
- <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
- <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
- <delete file="in.jar" />
- </target>
- <target name="-obfuscatereally" unless="donotobfuscate">
-
- <path id="obfuscateDeps.path">
- <pathelement location="${applet.jre.tools}" />
- <pathelement location="appletlib/${jmolJar}" />
- </path>
- <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-
- <proguard>
- <injar file="in.jar" />
- <outjar file="${jalviewLiteJar}" />
- <libraryjar refid="obfuscateDeps.path" />
- <dontwarn/>
- <keep access="public" type="class" name="jalview.bin.JalviewLite">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
- <field access="public" />
- <method access="public" />
- <constructor access="public" />
- </keep>
- <!-- -libraryjars "${obfuscateDeps}"
+ <path id="axisbuild">
+ <path refid="build.classpath" />
+ </path>
+ <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
+ <move todir="./bak">
+ <fileset dir="${sourceDir}" id="client">
+ <include name="${wsdl.ClientNS}/*.*" />
+ </fileset>
+ </move>
+
+ <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
+ <mappingSet>
+ <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
+ <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
+ </mappingSet>
+ </axis-wsdl2java>
+</target>
+
+<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+ <!-- make the package jar if not already existing -->
+ <mkdir dir="${packageDir}" />
+ <!-- clean dir if it already existed -->
+ <delete>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </delete>
+ <jar destfile="${packageDir}/${outputJar}" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Application-Name" value="Jalview Desktop" />
+ <attribute name="Codebase" value="${application.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}/">
+ <exclude name="cache*/**" />
+ <exclude name="*.jar" />
+ <exclude name="*.jar.*" />
+ <exclude name="**/*.jar" />
+ <exclude name="**/*.jar.*" />
+ </fileset>
+ </jar>
+
+ <copy toDir="${packageDir}" flatten="true">
+ <fileset dir="${outputDir}">
+ <include name="*.jar" />
+ <include name="**/*.jar" />
+ </fileset>
+ </copy>
+</target>
+
+
+<!-- jalopy code reformatter -->
+<target name="sourcescrub" depends="init,build">
+ <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
+ <fileset dir="${sourceDir}">
+ <include name="*.java" />
+ <include name="**/*.java" />
+ <include name="**/**/*.java" />
+ </fileset>
+ </jalopy>
+</target>
+
+
+
+<!-- Compile, package and obfuscate Jalview Applet -->
+<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
+
+<target name="compileApplet" depends="init,clean">
+ <mkdir dir="${outputDir}" />
+ <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
+</target>
+
+<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
+ <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
+ <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+ <copy todir="${outputDir}/lang">
+ <fileset dir="${resourceDir}/lang">
+ <include name="**.*" />
+ </fileset>
+ </copy>
+ <jar destfile="in.jar" index="true">
+ <manifest>
+ <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ </manifest>
+ <fileset dir="${outputDir}">
+ <include name="com/**" />
+ <include name="MCview/**" />
+ <include name="jalview/**" />
+ <include name=".build_properties" />
+ <include name="images/idwidth.gif" />
+ <include name="images/link.gif" />
+ <include name="lang/**" />
+ </fileset>
+ </jar>
+</target>
+<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
+</target>
+<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
+ <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
+ <delete file="in.jar" />
+</target>
+<target name="-obfuscatereally" unless="donotobfuscate">
+
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}" />
+ <pathelement location="appletlib/${jmolJar}" />
+ <pathelement location="lib/${varnaJar}" />
+ <pathelement location="appletlib/${jsoup}" />
+ <pathelement location="appletlib/${jsonSimple}" />
+ <pathelement location="appletlib/${javaJson}" />
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar" />
+ </fileset>
+ </path>
+ <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+
+ <proguard verbose="true" >
+ <injar file="in.jar" />
+ <outjar file="${jalviewLiteJar}" />
+ <libraryjar refid="obfuscateDeps.path" />
+ <dontwarn />
+ <keep access="public" type="class" name="jalview.bin.JalviewLite">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+ <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep name="jalview.json.binding**">
+ <constructor/>
+ <method name="*"/>
+ </keep>
+
+ <keep access="public" type="class" name="MCview.PDBfile">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+ <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
+
+
+ <!-- -libraryjars "${obfuscateDeps}"