<?xml version="1.0"?>
<!--
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
-->
<project name="jalviewX" default="usage" basedir=".">
<!-- we use jalopy to format our sources -->
<!-- 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" />
+ <property name="WebStartImage" value="JalviewLogo_big.png"/>
<!-- J2SE version needed for webstart launch -->
- <property name="j2sev" value="1.6+" />
+ <property name="j2sev" value="1.6+"/>
<!-- Permissions for running Java applets and applications. -->
<!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
<include name="**/*.jar" />
</fileset>
<fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
+ <include name="plugin.jar"/>
</fileset>
<fileset dir="appletlib">
<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages
<!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-->
<!-- jre for 1.4 version -->
- <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
+ <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
<!-- the classpath for building the 1.1 applet -->
<path id="jalviewlite.deps">
<include name="lib/classes.zip" />
</fileset>
<fileset dir="${java.home}/lib">
- <include name="plugin.jar" />
+ <include name="plugin.jar"/>
</fileset>
<pathelement location="appletlib/${jmolJar}" />
</path>
<!-- default location for outputting javadoc -->
- <property name="javadocDir" value="${packageDir}/javadoc" />
+ <property name="javadocDir" value="${packageDir}/javadoc"/>
</target>
<target name="clean" depends="init">
<!-- not efficient yet. -->
- <delete dir="${outputDir}" includes="*,**/*" />
+ <delete dir="${outputDir}" includes="*,**/*"/>
</target>
<target name="distclean" depends="init, clean">
</target>
<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" sigalg="SHA1withRSA">
-
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- </fileset>
- </signjar>
<copy todir="${packageDir}">
<fileset dir="${resourceDir}/images">
- <include name="${WebStartImage}" />
+ <include name="${WebStartImage}"/>
</fileset>
</copy>
<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
- <!-- codebase="http://www.jalview.org/jalview/webstart" -->
- <!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
- <jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org" />
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="${j2sev}" initial_heap_size="10M" />
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="jalview.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- <jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org" />
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="jalview.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
- <jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
- <information>
- <title>Jalview</title>
- <vendor>The Barton Group</vendor>
- <homepage href="http://www.jalview.org" />
- <description>Jalview Multiple Alignment Editor</description>
- <description kind="short">Jalview</description>
- <icon href="${WebStartImage}" />
- <offline_allowed />
- </information>
- <resources>
- <j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
- <fileset dir="${packageDir}">
- <include name="jalview.jar" />
- </fileset>
- <fileset dir="${packageDir}">
- <include name="*.jar" />
- <include name="*_*.jar" />
- <exclude name="jalview.jar" />
- </fileset>
- <property name="jalview.version" value="${JALVIEW_VERSION}" />
- </resources>
- <application_desc main_class="jalview.bin.Jalview">
- </application_desc>
- <security>
- <all_permissions />
- </security>
- </jnlp>
+ <!-- create a dummy jar which will eventually contain the jnlp template -->
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ </jar>
+
+ <mkdir dir="${packageDir}/JNLP-INF"/>
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+ <param name="inih" value="*" />
+ <param name="maxh" value="*"/>
+ </antcall>
+
+ <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+ <fileset dir="${packageDir}">
+ <include name="JNLP-INF"/>
+ </fileset>
+ </jar>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+ <param name="inih" value="10M" />
+ <param name="maxh" value="256M"/>
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+ <param name="inih" value="128M" />
+ <param name="maxh" value="512M"/>
+ </antcall>
+
+ <antcall target="writejnlpf">
+ <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+ <param name="inih" value="256M" />
+ <param name="maxh" value="1024M"/>
+ </antcall>
+
<!-- finally, need to postprocess to add in associations at end of 'information' element
<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
-->
- <!--
+ <!--
<association mime-type="application-x/ext-file" extensions="fa"/>
<association mime-type="application-x/ext-file" extensions="fasta"/>
<association mime-type="application-x/ext-file" extensions="mfa"/>
<association mime-type="application-x/ext-file" extensions="amsa"/>
<association mime-type="application-x/ext-file" extensions="stk"/>
<association mime-type="application-x/ext-file" extensions="jar"/>-->
-
+ <!-- and sign the jars -->
+ <!-- the default keystore details might need to be edited here -->
+ <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ </fileset>
+ </signjar>
</target>
<target name="runenv" depends="init">
<echo>java -classpath ${run.classpath} jalview.bin.Jalview
</echo>
</target>
+ <target name="writejnlpf">
+ <presetdef name="jnlpf">
+ <jnlp codebase="${WebStartLocation}">
+ <information>
+ <title>Jalview</title>
+ <vendor>The Barton Group</vendor>
+ <homepage href="http://www.jalview.org" />
+ <description>Jalview Multiple Alignment Editor</description>
+ <description kind="short">Jalview</description>
+ <icon href="${WebStartImage}" />
+ <offline_allowed />
+ </information>
+ <resources>
+ <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+ <fileset dir="${packageDir}">
+ <include name="jalview.jar" />
+ </fileset>
+ <fileset dir="${packageDir}">
+ <include name="*.jar" />
+ <include name="*_*.jar" />
+ <exclude name="jalview.jar" />
+ </fileset>
+ <property name="jalview.version" value="${JALVIEW_VERSION}" />
+ </resources>
+ <application_desc main_class="jalview.bin.Jalview">
+ </application_desc>
+ <security>
+ <all_permissions />
+ </security>
+ </jnlp>
+ </presetdef>
+ <jnlpf toFile="${jnlpFile}"/>
+ <replace file="${jnlpFile}">
+ <replacetoken><![CDATA[</information>]]></replacetoken>
+ <replacevalue><![CDATA[
+ <association mime-type="application-x/ext-file" extensions="fa" />
+ <association mime-type="application-x/ext-file" extensions="fasta" />
+ <association mime-type="application-x/ext-file" extensions="mfa" />
+ <association mime-type="application-x/ext-file" extensions="fastq" />
+ <association mime-type="application-x/ext-file" extensions="blc" />
+ <association mime-type="application-x/ext-file" extensions="msf" />
+ <association mime-type="application-x/ext-file" extensions="pfam" />
+ <association mime-type="application-x/ext-file" extensions="aln"/>
+ <association mime-type="application-x/ext-file" extensions="pir"/>
+ <association mime-type="application-x/ext-file" extensions="amsa"/>
+ <association mime-type="application-x/ext-file" extensions="stk"/>
+ <association mime-type="application-x/ext-file" extensions="jvp"/>
+ </information>]]></replacevalue>
+ </replace>
+ </target>
<target name="buildextclients" depends="init">
<input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
<condition property="dontextbuild">
<!-- clean dir if it already existed -->
<delete>
<fileset dir="${packageDir}">
- <include name="*.jar" />
+ <include name="*.jar"/>
</fileset>
</delete>
<jar destfile="${packageDir}/${outputJar}" index="true">
<!-- Compile, package and obfuscate Jalview Applet -->
- <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
+ <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/**" />
+ <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="${resourceDir}/lang">
+ <include name="**.*"/>
+ </fileset>
+ </copy>
<jar destfile="in.jar" index="true">
<manifest>
<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
<include name=".build_properties" />
<include name="images/idwidth.gif" />
<include name="images/link.gif" />
+ <include name="lang/**" />
</fileset>
</jar>
</target>
<injar file="in.jar" />
<outjar file="${jalviewLiteJar}" />
<libraryjar refid="obfuscateDeps.path" />
- <dontwarn />
+ <dontwarn/>
<keep access="public" type="class" name="jalview.bin.JalviewLite">
<field access="public" />
<method access="public" />
<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="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" />
<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/*" />
+ <include name="**/*"/>
+ <include name="javascript/*"/>
+ <include name="jmol/*"/>
</fileset>
<fileset dir=".">
<include name="${jalviewLiteJar}" />
</fileset>
<fileset dir="appletlib">
- <include name="**/*" />
+ <include name="**/*"/>
</fileset>
</copy>
-
+ <jar update="true" index="true" jarfile="${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="${applet.caller-codebase}"/>
+ </manifest>
+ </jar>
+ <signjar sigalg="SHA1WithRSA" storepass="${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>
<presetdef name="ap_applet.jar">
<!-- build a signed applet with 'all-permissions' -
Needs 'param name="permissions' value="all-permissions"' in applet tag
</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}"/>
+ <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
<copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
<copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
<ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
<fileset dir="${packageDir}/examples">
<exclude name="u_*.jar"/>
- <include name="*.jar" />
+ <include name="${jalviewLiteJar}" />
+ <include name="${jmolJar}" />
+ <include name="to_${jalviewLiteJar}" />
+ <include name="to_${jmolJar}" />
+ <include name="tl_${jalviewLiteJar}" />
+ <include name="tl_${jmolJar}" />
+ <include name="ap_${jalviewLiteJar}" />
+ <include name="ap_${jmolJar}" />
</fileset>
</signjar>
+ <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+ <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
</target>
<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
<javadoc destdir="${javadocDir}">
</packageset>
</javadoc>
</target>
-
</project>
git://source.jalview.org / jalview.git / blobdiff