<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
<!-- Key Password -->
<property name="jalview.key.pass" value="alignmentisfun" />
+
+
<!-- Don't change anything below here unless you know what you are doing! -->
<!-- Url path for WebStart in JNLP file -->
<property name="WebStartLocation" value="http://www.jalview.org/webstart" />
+ <!-- Webstart Image - looked for in resources/images -->
+ <property name="WebStartImage" value="JalviewLogo_big.png"/>
+ <!-- J2SE version needed for webstart launch -->
+ <property name="j2sev" value="1.6+"/>
+
+ <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
+ <property name="application.codebase" value="*.jalview.org"/>
+ <property name="applet.codebase" value="*.jalview.org"/>
+ <property name="applet.caller-codebase" value="${applet.codebase}"/>
+
<!-- build directory configuration -->
<property name="libDir" value="lib" />
<property name="resourceDir" value="resources" />
<property name="packageDir" value="dist" />
<property name="outputJar" value="jalview.jar" />
<!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
<property name="jalviewLiteJar" value="jalviewApplet.jar" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!--<property name="donotobfuscate" value="true"/> -->
</fileset>
<pathelement location="appletlib/${jmolJar}" />
</path>
+ <!-- default location for outputting javadoc -->
+ <property name="javadocDir" value="${packageDir}/javadoc"/>
</target>
<target name="clean" depends="init">
<!-- not efficient yet. -->
- <delete dir="${outputDir}" />
+ <delete dir="${outputDir}" includes="*,**/*"/>
</target>
<target name="distclean" depends="init, clean">
<target name="makefulldist" depends="makedist">
<!-- the default keystore details might need to be edited here -->
- <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
<fileset dir="${packageDir}">
<include name="*.jar" />
</fileset>
</signjar>
+ <copy todir="${packageDir}">
+ <fileset dir="${resourceDir}/images">
+ <include name="${WebStartImage}"/>
+ </fileset>
+ </copy>
+
<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
<!-- codebase="http://www.jalview.org/jalview/webstart" -->
<homepage href="http://www.jalview.org" />
<description>Jalview Multiple Alignment Editor</description>
<description kind="short">Jalview</description>
- <icon href="logo_big.gif" />
- <offline_allowed />
- <!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- -->
+ <icon href="${WebStartImage}" />
+ <offline_allowed/>
</information>
<resources>
- <j2se version="1.5+" initial_heap_size="10M" />
+ <j2se version="${j2sev}" initial_heap_size="10M" />
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
<security>
<all_permissions />
</security>
- </jnlp>
- <!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
+ </jnlp>
<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
<information>
<title>Jalview</title>
<homepage href="http://www.jalview.org" />
<description>Jalview Multiple Alignment Editor</description>
<description kind="short">Jalview</description>
- <icon href="logo_big.gif" />
+ <icon href="${WebStartImage}" />
<offline_allowed />
- <!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- -->
</information>
<resources>
- <j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
+ <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
<homepage href="http://www.jalview.org" />
<description>Jalview Multiple Alignment Editor</description>
<description kind="short">Jalview</description>
- <icon href="logo_big.gif" />
+ <icon href="${WebStartImage}" />
<offline_allowed />
- <!--
- <association mime-type="application-x/ext-file" extensions="fa"/>
- <association mime-type="application-x/ext-file" extensions="fasta"/>
- <association mime-type="application-x/ext-file" extensions="fastq"/>
- <association mime-type="application-x/ext-file" extensions="blc"/>
- <association mime-type="application-x/ext-file" extensions="msf"/>
- <association mime-type="application-x/ext-file" extensions="pfam"/>
- <association mime-type="application-x/ext-file" extensions="aln"/>
- <association mime-type="application-x/ext-file" extensions="pir"/>
- <association mime-type="application-x/ext-file" extensions="amsa"/>
- -->
</information>
<resources>
- <j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
+ <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
<fileset dir="${packageDir}">
<include name="jalview.jar" />
</fileset>
<all_permissions />
</security>
</jnlp>
-
+ <!-- finally, need to postprocess to add in associations at end of 'information' element
+
+ <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+
+ </xslt>
+
+
+ -->
+ <!--
+ <association mime-type="application-x/ext-file" extensions="fa"/>
+ <association mime-type="application-x/ext-file" extensions="fasta"/>
+ <association mime-type="application-x/ext-file" extensions="fastq"/>
+ <association mime-type="application-x/ext-file" extensions="blc"/>
+ <association mime-type="application-x/ext-file" extensions="msf"/>
+ <association mime-type="application-x/ext-file" extensions="pfam"/>
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jar"/>-->
+
</target>
<target name="runenv" depends="init">
<include name="*.jar"/>
</fileset>
</delete>
- <jar destfile="${packageDir}/${outputJar}">
+ <jar destfile="${packageDir}/${outputJar}" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <attribute name="Permissions" value="all-permissions" />
+ <!--<attribute name="Trusted-Lib" value="true" /> -->
+ <attribute name="Application-Name" value="Jalview Desktop"/>
+ <attribute name="Codebase" value="${application.codebase}"/>
</manifest>
<fileset dir="${outputDir}/">
<exclude name="cache*/**" />
<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" />
- <jar destfile="in.jar">
+ <jar destfile="in.jar" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite Applet"/>
+ <!-- <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>
<fileset dir="${outputDir}">
<include name="com/**" />
<injar file="in.jar" />
<outjar file="${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 "${obfuscateDeps}"
-injars in.jar
-outjars jalviewApplet.jar
<copy todir="${packageDir}/examples">
<fileset dir="examples">
<include name="**/*"/>
+ <include name="javascript/*"/>
+ <include name="jmol/*"/>
</fileset>
<fileset dir=".">
<include name="jalviewApplet.jar"/>
<include name="**/*"/>
</fileset>
</copy>
-
+ <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+ <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>
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+
+ <fileset dir="${packageDir}/examples">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
+ </target>
+ <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+ <javadoc destdir="${javadocDir}">
+ <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+ </packageset>
+ </javadoc>
</target>
+
</project>