JAL-1880 updated mapping tests to ensure they handle subsequence offsets

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index dbf1df3..bb743d6 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -89,7 +89,10 @@
     <!-- J2SE version needed for webstart launch -->
     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
     <property name="j2sev" value="1.7+"/>
-
+       <!-- Java Compilation settings - source and target javac version -->
+       <property name="javac.source" value="1.7"/>
+       <property name="javac.target" value="1.7"/>
+               
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
     <property name="application.codebase" value="*.jalview.org" />
@@ -109,8 +112,8 @@
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
-    <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
-    <property name="varnaJar" value="VARNAv3-91.jar" />
+    <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+    <property name="varnaJar" value="VARNAv3-93.jar" />
     <property name="jsoup" value="jsoup-1.8.1.jar" />
     <property name="jsonSimple" value="json_simple-1.1.jar" />
     <property name="javaJson" value="java-json.jar" />
@@ -186,12 +189,22 @@
     <tstamp prefix="build">
       <format property="date" pattern="dd MMMM yyyy" />
     </tstamp>
+    <exec executable="/usr/bin/git" outputproperty="git.commit"  failifexecutionfails="false">
+      <arg value="rev-parse"/>
+      <arg value="--short"/>
+      <arg value="HEAD"/>
+    </exec>
+    <exec executable="/usr/bin/git" outputproperty="git.branch" failifexecutionfails="false">
+      <arg value="rev-parse"/>
+      <arg value="--abbrev-ref"/>
+      <arg value="HEAD"/>
+    </exec>
     <properties file="${outputDir}/.build_properties">
       <header>
           ---Jalview Build Details---
         </header>      
       <property name="VERSION" value="${JALVIEW_VERSION}" />
-      <property name="INSTALLATION" value="${INSTALLATION}" />
+      <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
       <property name="BUILD_DATE" value="${build.date}" />
     </properties>
   </target>
@@ -236,7 +249,7 @@
 
   <target name="build" depends="prepare">
     <!-- not efficient yet. -->
-    <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
+    <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
       <exclude name="jalview/*applet*" />
       <exclude name="jalview/appletgui/**" />
       <exclude name="com/stevesoft/**" />
@@ -263,12 +276,10 @@
   </target>  
   
   <target name="buildTests" depends="prepareTests">
-       <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${testOutputDir}"
-               debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
-               <exclude name="jalview/*applet*" />
-               <exclude name="jalview/appletgui/**" />
+       <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${testOutputDir}"
+               debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >               
        </javac>
-       <javac source="1.5" target="1.5" srcdir="${testDir}" destdir="${testOutputDir}"
+       <javac source="${javac.source}" target="${javac.target}" srcdir="${testDir}" destdir="${testOutputDir}"
                debug="${javac.debug}" classpathref="build.classpath" includeantruntime="false" >
        </javac>
   </target>
@@ -316,7 +327,7 @@
 
     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
       <fileset dir="${packageDir}">
-        <include name="JNLP-INF"/>
+        <include name="JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
       </fileset>
     </jar>
 
@@ -544,9 +555,9 @@
 
 <target name="compileApplet" depends="init,clean">
   <mkdir dir="${outputDir}" />
-  <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
                        classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-                       excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
+                       excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">