X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=2425b74fdc02f0a9d929254f2347210481e77cda;hb=refs%2Fheads%2FRelease_2_4_branch;hp=b415140e62f492625ced245bf4d36710c5ca88eb;hpb=3f59e4806e088fd82ef53934dbb4645ac5544bc9;p=jalview.git

diff --git a/build.xml b/build.xml
index b415140..2425b74 100755
--- a/build.xml
+++ b/build.xml
@@ -1,4 +1,22 @@
 <?xml version="1.0"?>
+<!--
+  Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
+  Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+  
+  This program 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 2
+  of the License, or (at your option) any later version.
+  
+  This program 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 this program; if not, write to the Free Software
+  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+-->
 <project name="jalviewX" default="usage" basedir=".">
 	<!-- we use jalopy to format our sources -->
 	<taskdef name="jalopy"
@@ -23,6 +41,8 @@
 		<echo message="compileApplet - compiles all necessary files for Applet"/>
 		<echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
 		<echo message="See docs/building.html and the comments in build file for other targets."/>
+	    <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk."/>
+	    <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation"/>
 	</target>
 
 
@@ -53,7 +73,19 @@
 			</fileset> -->
       </path>
 		<!-- Jalview Version String displayed by application on startup and used to check for updates -->
-      <property name="JALVIEW_VERSION" value="DEVELOPMENT"/>
+    <property name="JALVIEW_VERSION" value="DEVELOPMENT"/> <!-- 2.4 (VAMSAS)" -->
+		<!-- Include debugging information in javac true or false -->
+		<property name="javac.debug" value="true"/>
+		
+		<!-- JarSigner Key Store for Webstart Distribution -->
+		<property name="jalview.keystore" value="./keys/.keystore"/>
+		<!-- Keystore Password -->
+		<property name="jalview.keystore.pass" value="alignmentisfun"/>
+		<!-- Key Name -->
+		<property name="jalview.key" value="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"/>
@@ -67,6 +99,12 @@
 		<property name="outputDir" value="classes" />
 		<property name="packageDir" value="dist" />
 		<property name="outputJar" value="jalview.jar" />
+	  <!-- Jalview Applet JMol Jar Dependency -->
+    <property name="jmolJar" value="Jmol-11.0.2.jar" />
+		<property name="jalviewLiteJar" value="jalviewApplet.jar"/>
+		<!-- switch to indicate if we should obfuscate jalviewLite -->
+		<!--<property name="donotobfuscate" value="true"/> -->
+				
 		<!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 		<property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 		<property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
@@ -85,7 +123,22 @@
 				<include name="*.jar"/>
 				<include name="**/*.jar"/>
 			</fileset>
+			
 		</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="${java.home}/lib/rt.jar"/>
+		-->
+		<!-- the classpath for building the 1.1 applet -->
+		<path id="jalviewlite.deps">
+			<fileset dir="${java118.home}">
+				<include name="lib/classes.zip"/>
+			</fileset>
+	   	<pathelement location="lib/${jmolJar}"/>
+	  </path>
 	</target>
 
 
@@ -146,6 +199,7 @@
 		<javac source="1.4" target="1.4"
         srcdir ="${sourceDir}"
         destdir="${outputDir}"
+				debug="${javac.debug}"
       classpathref="build.classpath">
 			<exclude name="jalview/*applet*"/>
 			<exclude name="com/stevesoft/**"/>
@@ -166,10 +220,10 @@
 	<target name="makefulldist" depends="makedist">
 		<!-- the default keystore details might need to be edited here -->
 		<signjar
-      storepass="alignmentisfun"
-      keypass="alignmentisfun"
-      keystore="keys/.keystore"
-      alias="jalview"
+      storepass="${jalview.keystore.pass}"
+      keypass="${jalview.key.pass}"
+      keystore="${jalview.keystore}"
+      alias="${jalview.key}"
       lazy="false"
       verbose="false"
       >
@@ -181,7 +235,8 @@
 		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties"/>
 
 		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
-		<jnlp toFile="${packageDir}/jalview.jnlp" href="jalview.jnlp"
+		<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
+		<jnlp toFile="${packageDir}/jalview.jnlp" 
       codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
@@ -200,6 +255,7 @@
         <association mime-type="application-x/ext-file" extensions="pfam"/>
         <association mime-type="application-x/ext-file" extensions="aln"/>
         <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
 	-->
 			</information>
 			<resources>
@@ -209,6 +265,7 @@
 				</fileset>
 				<fileset dir="${packageDir}">
 					<include name="*.jar"/>
+					<include name="*_*.jar"/>
 					<exclude name="jalview.jar"/>
 				</fileset>
 				<property name="jalview.version" value="${JALVIEW_VERSION}"/>
@@ -327,86 +384,167 @@
 
 
 
-	<!-- Compile, package and obfuscate Jalview Applet -->
-	<target name="makeApplet" depends="obfuscate"/>
+  <!-- Compile, package and obfuscate Jalview Applet -->
+  <target name="makeApplet" depends="obfuscate"/>
 
-	<target name="compileApplet" depends="init,clean">
-		<mkdir dir="${outputDir}"/>
+  <target name="compileApplet" depends="init,clean">
+    <mkdir dir="${outputDir}"/>
     <javac source="1.2"
     target="1.1"
     srcdir="${sourceDir}" 
     destdir="${outputDir}"
-    classpath="lib/jmol.jar"
+   	debug="${javac.debug}"
+    classpath="lib/${jmolJar}"
        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">
-			<manifest>
-				<attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
-			</manifest>
-			<fileset dir="${outputDir}">
-				<include name="com/**"/>
-				<include name="MCview/**"/>
-				<include name="jalview/**"/>
-				<include name=".build_properties"/>
-				<include name="images/idwidth.gif"/>
-				<include name="images/link.gif"/>
-			</fileset>
-		</jar>
-	</target>
-
-	<target name="obfuscate" depends="packageApplet">
-		<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
-		<path id="jalviewlite.deps">
-			<pathelement location="${java.home}/lib/rt.jar"/>
-			<pathelement location="lib/jmol.jar"/>
-		</path>
-		<proguard>
-			<libraryjar refid="jalviewlite.deps"/>
+  </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">
+        <manifest>
+            <attribute name="Main-Class" value="jalview.bin.JalviewLite"/>
+        </manifest>
+        <fileset dir="${outputDir}">
+          <include name="com/**"/>
+          <include name="MCview/**"/>
+          <include name="jalview/**"/>
+          <include name=".build_properties"/>
+          <include name="images/idwidth.gif"/>
+          <include name="images/link.gif"/>
+        </fileset>
+      </jar>
+  </target>
+  <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+  </target>
+	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">    
+  	<copy file="in.jar" tofile="${jalviewLiteJar}" />    	
+    <delete file="in.jar"/>
+  </target>
+	<target name="-obfuscatereally" unless="donotobfuscate">
+    
+  	<path id="obfuscateDeps.path">
+    <pathelement location="${applet.jre.tools}"/>
+    <pathelement location="lib/${jmolJar}"/>
+    </path>
+    <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
+  	
+    <proguard>
+      <injar file="in.jar"/>
+      <outjar file="${jalviewLiteJar}"/>
+      <libraryjar refid="obfuscateDeps.path"/>
+      <keep access="public" type="class"
+      name="jalview.bin.JalviewLite">
+        <field access="public"/>
+        <method access="public"/>
+        <constructor access="public"/>
+      </keep>
+<!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
-       { public * ; }
-    </proguard>
-		<delete file="in.jar"/>
-	</target>
+       { public * ; } -->
+      </proguard>
+    <delete file="in.jar"/>
+  </target>
 
 	<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 		<taskdef name="castor-srcgen"
-				  classname="org.exolab.castor.tools.ant.taskdefs.CastorSourceGenTask"
-			      classpathref="build.classpath" />
+			  classname="org.castor.anttask.CastorCodeGenTask"
+		      classpathref="build.classpath" />
 		<delete>
-			<fileset dir="${sourceDir}/jalview/schemabinding/version2/">
-				<filename name="*"/>
+			<fileset dir="${sourceDir}/jalview/schemabinding/version2">
+				<include name="*.java"/>
+				<include name="descriptors/*.java"/>
 			</fileset>
 		</delete>
 		<castor-srcgen file="${schemaDir}/vamsas.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.schemabinding.version2"
-			      warnings="true" 
+			      warnings="false" 
 				  	nodesc="false"
+						verbose="true"
 						properties="${schemaDir}/jalview.properties"
 		/>
 		<castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.schemabinding.version2"
-			      warnings="true" 
+			      warnings="false" 
 				  	nodesc="false"
+						verbose="true"
 						properties="${schemaDir}/jalview.properties"
 		/>
 		<castor-srcgen file="${schemaDir}/jalview.xsd"
 			      todir="${sourceDir}"
 			      package="jalview.schemabinding.version2"
-			      warnings="true" 
+			      warnings="false" 
 					  nodesc="false"
+						verbose="true"
 						properties="${schemaDir}/jalview.properties"
 			
+		/>
+		<!-- 
+		now build the jalview.binding package with the old schema set
+		-->
+		<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="${source.dist.name}"/>
+		<tar destfile="${source.dist.name}" compression="gzip">
+			<tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+				<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="${sourceDir}/*.java"/>
+				<include name="${sourceDir}/**/*.java"/>
+				<include name="${sourceDir}/**/*.cdr"/>
+				<include name="${libDir}/**/*"/>						
+				<include name="${resourceDir}/**/*"/>						
+				<include name="${helpDir}/**/*"/>						
+				<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}/**/*"/>						
+			</tarfileset>
+		</tar>
+	</target>
 </project>