Added getValues and write to DistanceMatrix interface for broader use
[jalview.git] / forester / java / build.xml
index f3b4397..43d7046 100644 (file)
@@ -4,7 +4,7 @@
        <property name="src.dir" value="src" />
        <property name="classes.dir" value="classes" />
        <property name="jars.dir" value="resources" />
-       <property name="itextjar" value="${jars.dir}/itextpdf-5.1.0.jar" />
+       <property name="itextjar" value="${jars.dir}/itextpdf-5.5.9.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" />
     <target name="copy_resources" description="Copies resources">
     <mkdir dir="${classes.dir}/resources" />
         <copy verbose="true"
-          file="../resources/phyloxml_schema/1.10/phyloxml.xsd"
-          todir="${classes.dir}/resources"/>
-        <copy verbose="true"
-          file="../resources/synth_laf/synth_look_and_feel_1.xml"
+          file="../resources/phyloxml_schema/1.20/phyloxml.xsd"
           todir="${classes.dir}/resources"/>
     </target>
 
                </javac> 
        </target>
 
-       <target name="compile_applets_only" description="Compiles the Task" depends="clean">
-               <mkdir dir="${classes.dir}" />
-               <javac source="1.8" target="1.8" debug="true" debuglevel="lines,source" srcdir="${src.dir}" destdir="${classes.dir}" optimize="on" verbose="false" classpath="${itextjar};${commonscodecjar};${openchartjar}">
-                       <compilerarg value="-Xlint:deprecation" />
-                       <compilerarg value="-Xlint:unchecked" />
-               </javac> 
-       </target>
-
        <target name="jar" description="JARs the classes files" depends="compile,copy_resources">
                <unjar src="${itextjar}" dest="${classes.dir}">
             <patternset>
                </jar>
        </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">
-                       <manifest>
-                <attribute name="Permissions" value="all-permissions" />
-                <attribute name="Codebase" value="*" />
-                <attribute name="Application-Name" value="Archaeopteryx" />
-            </manifest>
-               </jar>
-       </target>
-
        <target name="all" description="" depends="jar">
        </target>
 
-       <target name="applets_only" description="" depends="jar_applets_only">
-       </target>
 
 </project>