X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fbuild.xml;h=fd888c35bbd6573ee922016c93119fdf06cc9f76;hb=2af0eeb66b17ef94432816233efce4f976f82517;hp=93ad138352e80b91155e7b60ac4efc5a2dd1d83e;hpb=8954d23c44f161e0282bc6586bc3089a63961da7;p=jalview.git

diff --git a/forester/java/build.xml b/forester/java/build.xml
index 93ad138..fd888c3 100644
--- a/forester/java/build.xml
+++ b/forester/java/build.xml
@@ -5,13 +5,15 @@
 	<property name="classes.dir" value="classes" />
 	<property name="jars.dir" value="resources" />
 	<property name="itextjar" value="${jars.dir}/itextpdf-5.1.0.jar" />
+	<property name="commonscodecjar" value="${jars.dir}/commons-codec-1.5.jar" />
+	<property name="openchartjar" value="${jars.dir}/openchart.jar" />
 	<property name="forester_jar" value="forester.jar" />
 	<property name="archaeopteryx_applets_jar" value="archaeopteryx_applets.jar" />
 
 	<target name="clean" description="Delete all generated files">
-		<delete dir="${classes.dir}" failonerror="false" />
-		<delete file="${forester_jar}" />
-		<delete file="${archaeopteryx_applets_jar}" />
+	    <delete dir="${classes.dir}" failonerror="false" />
+	    <delete file="${forester_jar}" />
+	    <delete file="${archaeopteryx_applets_jar}" />
 	</target>
 
     <target name="copy_resources" description="Copies resources">
@@ -26,14 +28,14 @@
 
 	<target name="compile" description="Compiles the Task" depends="clean">
 		<mkdir dir="${classes.dir}" />
-		<javac source="1.5" target="1.5" debug="true" debuglevel="lines,source" srcdir="${src.dir}" destdir="${classes.dir}" optimize="on" verbose="false" classpath="${itextjar}">
+		<javac source="1.6" target="1.6" debug="true" debuglevel="lines,source" srcdir="${src.dir}" destdir="${classes.dir}" optimize="on" verbose="false" classpath="${itextjar};${commonscodecjar};${openchartjar}">
 			<compilerarg value="-Xlint:deprecation" />
 		</javac> 
 	</target>
 
 	<target name="compile_applets_only" description="Compiles the Task" depends="clean">
 		<mkdir dir="${classes.dir}" />
-		<javac source="1.5" target="1.5" debug="false" srcdir="${src.dir}" destdir="${classes.dir}" optimize="on" verbose="false" classpath="${itextjar}">
+		<javac source="1.6" target="1.6" debug="true" debuglevel="lines,source" srcdir="${src.dir}" destdir="${classes.dir}" optimize="on" verbose="false" classpath="${itextjar};${commonscodecjar};${openchartjar}">
 			<compilerarg value="-Xlint:deprecation" />
 		</javac> 
 	</target>
@@ -47,6 +49,18 @@
                 <exclude name="**/*Test*.class" />
             </patternset>
         </unjar>
+        <unjar src="${commonscodecjar}" dest="${classes.dir}">
+            <patternset>
+                <include name="**/*.class" />
+                <exclude name="**/*Test*.class" />
+            </patternset>
+        </unjar>
+        <unjar src="${openchartjar}" dest="${classes.dir}">
+            <patternset>
+                <include name="**/*.class" />
+                <exclude name="**/*Test*.class" />
+            </patternset>
+        </unjar>
 		<jar level="9" destfile="${forester_jar}" basedir="${classes.dir}" excludes="**/Test.class" duplicate="fail" index="true">
 			<manifest>
 				<attribute name="Main-Class" value="org.forester.archaeopteryx.Archaeopteryx" />
@@ -55,16 +69,28 @@
 	</target>
 
 	<target name="jar_applets_only" description="JARs the classes files" depends="compile_applets_only,copy_resources">
+		<unjar src="${commonscodecjar}" dest="${classes.dir}">
+            <patternset>
+                <include name="**/*.class" />
+                <exclude name="**/*Test*.class" />
+            </patternset>
+        </unjar>
 		<jar level="9" destfile="${archaeopteryx_applets_jar}" basedir="${classes.dir}" excludes="org/forester/application/** 
 			          org/forester/development/**
 			          org/forester/evoinference/**
 			          org/forester/go/**
 			          org/forester/go/etc/**
+			          org/forester/msa_compactor/**
 			          org/forester/pccx/**
 			          org/forester/surfacing/**
 			          org/forester/test/**
-			          org/forester/tools/**
-			          " duplicate="fail" index="true">
+			          org/forester/tools/**"
+			          duplicate="fail" index="true">
+			<manifest>
+                <attribute name="Permissions" value="all-permissions" />
+                <attribute name="Codebase" value="*" />
+                <attribute name="Application-Name" value="Archaeopteryx" />
+            </manifest>
 		</jar>
 	</target>