+ <delete>
+ <fileset dir="${sourceDir}/jalview/binding/">
+ <include name="**" />
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+ <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+</target>
+<target name="sourcedist" description="create jalview source distribution" depends="init">
+ <delete file="${source.dist.name}" />
+ <!-- temporary copy of source to update timestamps -->
+ <copy todir="_sourcedist">
+ <fileset dir=".">
+ <include name="LICENSE" />
+ <include name="README" />
+ <include name="build.xml" />
+ <include name="jalview-jalopy.xml" />
+ <include name="JalviewApplet.jpx" />
+ <include name="JalviewX.jpx" />
+ <include name="nbbuild.xml" />
+ <include name="nbproject/genfiles.properties" />
+ <include name="nbproject/project.properties" />
+ <include name="nbproject/project.xml" />
+ <include name="${sourceDir}/*.java" />
+ <include name="${sourceDir}/**/*.java" />
+ <include name="${sourceDir}/**/*.cdr" />
+ <include name="${libDir}/**/*" />
+ <include name="${resourceDir}/**/*" />
+ <include name="${helpDir}/**/*" />
+ <include name="appletlib/${jmolJar}" />
+ <include name="appletlib/${jsonSimple}" />
+ <include name="appletlib/${javaJson}" />
+ <exclude name="**/*locales" />
+ <exclude name="*locales/**" />
+ <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**Build*/**" />
+ <exclude name="utils/InstallAnywhere/**locale*" />
+ <exclude name="utils/InstallAnywhere/**locale*/**" />
+ <include name="${schemaDir}/**/*" />
+ <include name="utils/**/*" />
+ <include name="${docDir}/**/*" />
+ <include name="examples/**/*" />
+ </fileset>
+ </copy>
+
+ <tstamp prefix="build">
+ <format property="year" pattern="yyyy" />
+ </tstamp>
+ <!-- each replacetoken CDATA body must be on one line -
+ otherwise the pattern doesn't match -->
+ <replace value="${JALVIEW_VERSION}">
+ <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+ <fileset dir="_sourcedist">
+ <include name="**/*" />
+ </fileset>
+ </replace>
+ <replace dir="_sourcedist" value="${build.year}">
+ <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+ <fileset dir="_sourcedist">
+ <include name="**/*" />
+ </fileset>
+ </replace>
+
+ <tar destfile="${source.dist.name}" compression="gzip">
+ <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
+ </tarfileset>
+ </tar>
+
+ <delete dir="_sourcedist" />
+</target>
+<target name="prepubapplet_1" depends="makeApplet">
+ <copy todir="${packageDir}/examples">
+ <fileset dir="examples">
+ <include name="**/*" />
+ <include name="javascript/*" />
+ <include name="jmol/*" />
+ </fileset>
+ <fileset dir=".">
+ <include name="${jalviewLiteJar}" />
+ </fileset>
+ <fileset dir="appletlib">
+ <include name="**/*" />
+ </fileset>
+ </copy>
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+ <manifest>
+ <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
+ <!-- <attribute name="Permissions" value="sandbox" /> -->
+ <!--<attribute name="Trusted-Lib" value="true" /> -->
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ </manifest>
+ </jar>
+
+ <presetdef name="ap_applet.jar">
+ <!-- build a signed applet with 'all-permissions' -
+ Needs 'param name="permissions' value="all-permissions"' in applet tag
+ JalviewLite+JmolApplet linked sequence/structure fails
+ Mixed code warnings are raised
+ -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="applet.jar">
+ <!-- build signed applet with sandbox permissions -
+ Needs 'param name="permissions' value="sandbox"' in applet tag
+ Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag
+ -->
+
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="sandbox" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="tl_applet.jar">
+ <!-- build signed applet with trusted library/trusted permissions -
+ Needs 'param name="permissions' value="all-permissions"' in applet tag
+ j1.7_45:
+ No mixed code warnings raised
+ Jmol/JalviewLite sequence/structure example doesn't link structures
+ Raises dialog asking user to allow page to control applet via LiveConnect javascript
+
+ -->
+
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ <attribute name="Trusted-Library" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="to_applet.jar">
+ <!-- not fully test variant (yet) -->
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}" />
+ <attribute name="Trusted-Only" value="true" />
+ </manifest>
+ </jar>
+ </presetdef>
+ <!-- create differently privileged artefacts -->
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
+ <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
+ <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+ <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
+ <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
+ <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
+ <!-- finally, create manifest for original jars -->
+ <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+ <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
+ <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
+
+ <!-- todo - write examples/downloads for alternate versions of the applet
+ probably don't need to do this now since we don't have alternate versions anymore !-->
+</target>
+<target name="-signapplet" depends="prepubapplet_1">
+ <fileset id="signappletjarset" dir="${packageDir}/examples">
+ <exclude name="u_*.jar" />
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="${javaJson}" />
+ <include name="${jsonSimple}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="to_${javaJson}" />
+ <include name="to_${jsonSimple}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="tl_${javaJson}" />
+ <include name="tl_${jsonSimple}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
+ <include name="ap_${javaJson}" />
+ <include name="ap_${jsonSimple}" />
+ </fileset>
+</target>
+<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ <fileset refid="signappletjarset" />
+ </signjar>
+</target>
+
+<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
+ <fileset refid="signappletjarset" />
+ </signjar>
+</target>
+
+<target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+
+<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+ <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+ <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+ <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+ <!-- finally, replace any launchApp servlet tags with a version specification -->
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}"">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp"]]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
+ <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+ <replacetoken>
+ <![CDATA[http://www.jalview.org/services/launchApp']]>
+ </replacetoken>
+ <fileset dir="${packageDir}/examples">
+ <include name="**/*.html" />
+ </fileset>
+ </replace>
+
+</target>
+<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+ <javadoc destdir="${javadocDir}">
+ <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+ </packageset>
+ </javadoc>
+</target>
+<target name="linkcheck" depends="init,prepare">
+ <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+ <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+ <arg file="${helpDir}"/>
+ <arg value="-nointernet"/>
+ </java>
+</target>
+</project>