<?xml version="1.0"?>
<!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
-->
<project name="jalviewX" default="usage" basedir=".">
<!-- we use jalopy to format our sources -->
<!-- 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="*"/>
+ <property name="applet.caller-codebase" value="${applet.codebase}"/>
+
<!-- build directory configuration -->
<property name="libDir" value="lib" />
<property name="resourceDir" value="resources" />
<property name="packageDir" value="dist" />
<property name="outputJar" value="jalview.jar" />
<!-- Jalview Applet JMol Jar Dependency -->
- <property name="jmolJar" value="JmolApplet-12.1.13.jar" />
+ <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
<property name="jalviewLiteJar" value="jalviewApplet.jar" />
<!-- switch to indicate if we should obfuscate jalviewLite -->
<!--<property name="donotobfuscate" value="true"/> -->
<include name="*.jar" />
<include name="**/*.jar" />
</fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </fileset>
<fileset dir="appletlib">
<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
-->
</path>
<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
<!-- The Location of the java 1.1.8 jdk -->
- <property name="java118.home" value="C:\Sun\jdk1.1.8" />
- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
- <!-- jre for 1.4 version
- <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+ <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
-->
+ <property name="java118.home" value="${java.home}" />
+ <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+ --><!-- jre for 1.4 version -->
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+
<!-- the classpath for building the 1.1 applet -->
<path id="jalviewlite.deps">
<fileset dir="${java118.home}">
<include name="lib/classes.zip" />
</fileset>
+ <fileset dir="${java.home}/lib">
+ <include name="plugin.jar"/>
+ </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}/${outputJar}" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.Jalview" />
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Application-Name" value="Jalview Desktop"/>
+ <attribute name="Codebase" value="${application.codebase}"/>
</manifest>
<fileset dir="${outputDir}/">
<exclude name="cache*/**" />
<!-- Compile, package and obfuscate Jalview Applet -->
- <target name="makeApplet" depends="obfuscate" />
+ <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
<target name="compileApplet" depends="init,clean">
<mkdir dir="${outputDir}" />
- <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpath="appletlib/${jmolJar}" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
+ <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="${outputDir}/images/link.gif" />
- <jar destfile="in.jar">
+ <jar destfile="in.jar" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
+ <attribute name="Application-Name" value="JalviewLite"/>
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}"/>
</manifest>
<fileset dir="${outputDir}">
<include name="com/**" />
</fileset>
</jar>
</target>
- <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+ <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
</target>
<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
<copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
<injar file="in.jar" />
<outjar file="${jalviewLiteJar}" />
<libraryjar refid="obfuscateDeps.path" />
+ <dontwarn/>
<keep access="public" type="class" name="jalview.bin.JalviewLite">
<field access="public" />
<method access="public" />
<constructor access="public" />
</keep>
+ <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+ <field access="public" />
+ <method access="public" />
+ <constructor access="public" />
+ </keep>
<!-- -libraryjars "${obfuscateDeps}"
-injars in.jar
-outjars jalviewApplet.jar
<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="${sourceDir}/**/*.cdr" />
<include name="${schemaDir}/**/*" />
<include name="utils/**/*" />
<include name="${docDir}/**/*" />
+ <include name="examples/**/*" />
</tarfileset>
</tar>
</target>
+ <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+ <copy todir="${packageDir}/examples">
+ <fileset dir="examples">
+ <include name="**/*"/>
+ <include name="javascript/*"/>
+ <include name="jmol/*"/>
+ </fileset>
+ <fileset dir=".">
+ <include name="${jalviewLiteJar}"/>
+ </fileset>
+ <fileset dir="appletlib">
+ <include name="**/*"/>
+ </fileset>
+ </copy>
+ <presetdef name="applet.jar">
+ <jar update="true" index="true">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite"/>
+ <attribute name="Permissions" value="all-permissions"/>
+ <attribute name="Codebase" value="${applet.codebase}"/>
+ <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
+ <!--
+ <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}"/>
+ -->
+<!-- <attribute name="Trusted-Only" value="true"/>
+-->
+<!-- <attribute name="Trusted-Library" value="true"/>
+-->
+ </manifest>
+ </jar>
+ </presetdef>
+ <presetdef name="applet_tl.jar">
+ <jar update="true" index="true" jarfile="@{jarfile}">
+ <manifest>
+ <attribute name="Application-Name" value="JalviewLite"/>
+ <attribute name="Permissions" value="all-permissions" />
+ <attribute name="Codebase" value="${applet.codebase}"/>
+ <attribute name="Trusted-Only" value="true"/>
+ <attribute name="Trusted-Library" value="true"/>
+ </manifest>
+ </jar>
+
+ </presetdef>
+ <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}"/>
+ <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+ <applet_tl.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}"/>
+ <applet.jar jarfile="${packageDir}/examples/${jmolJar}"/>
+ <applet_tl.jar jarfile="${packageDir}/examples/tl_${jmolJar}"/>
+ <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>
git://source.jalview.org / jalview.git / blobdiff