From a4531305fe2f4d43c09bbb8e44ea63d2b8a06eb3 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 18 Sep 2015 13:48:25 +0100
Subject: [PATCH] JAL-1888 JAL-1551 format XML file (2 spaces, no tabs, align
 final > in wrapped tags)

---
 build.xml |  184 +++++++++++++++++++++++++++++++------------------------------
 1 file changed, 93 insertions(+), 91 deletions(-)

diff --git a/build.xml b/build.xml
index a517ec2..73c494d 100755
--- a/build.xml
+++ b/build.xml
@@ -64,12 +64,12 @@
         <include name="*.jar"/>
       </fileset> -->
       </path>
-  	
+
     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
-  	
+
     <property name="INSTALLATION" value="Source" />
-  	
+
     <!-- 2.4 (VAMSAS)" -->
     <!-- Include debugging information in javac true or false -->
     <property name="javac.debug" value="true" />
@@ -82,21 +82,21 @@
     <property name="jalview.key" value="jalview" />
     <!-- Key Password -->
     <property name="jalview.key.pass" value="alignmentisfun" />
-    
-    <property name="testng-groups" value="Functional"/>
+
+    <property name="testng-groups" value="Functional" />
 
     <!-- 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" />
     <!-- 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 -->
     <!-- 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"/>
-  	  	
+    <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" />
@@ -122,9 +122,9 @@
     <property name="jsonSimple" value="json_simple-1.1.jar" />
     <property name="javaJson" value="java-json.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
-	<property name="reportDir" value="test-reports" />
-	<property name="testDir" value="test" />
-	<property name="testOutputDir" value="tests" />
+    <property name="reportDir" value="test-reports" />
+    <property name="testDir" value="test" />
+    <property name="testOutputDir" value="tests" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
     <!-- switch to exclude associations from generated jnlp files -->
@@ -149,7 +149,7 @@
         <include name="**/*.jar" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar"/>
+        <include name="plugin.jar" />
       </fileset>
       <fileset dir="appletlib">
         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
@@ -169,7 +169,7 @@
     <!-- <property name="applet.jre.tools" value="${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">
@@ -177,17 +177,17 @@
         <include name="lib/classes.zip" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar"/>
+        <include name="plugin.jar" />
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
       <pathelement location="lib/${varnaJar}" />
       <pathelement location="lib/${jsoup}" />
       <pathelement location="lib/${jsonSimple}" />
       <pathelement location="lib/${javaJson}" />
-      
+
     </path>
     <!-- default location for outputting javadoc -->
-    <property name="javadocDir" value="${packageDir}/javadoc"/>
+    <property name="javadocDir" value="${packageDir}/javadoc" />
   </target>
 
 
@@ -196,20 +196,20 @@
     <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 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"/>
+      <arg value="rev-parse" />
+      <arg value="--abbrev-ref" />
+      <arg value="HEAD" />
     </exec>
     <properties file="${outputDir}/.build_properties">
       <header>
           ---Jalview Build Details---
-        </header>    	
+        </header>
       <property name="VERSION" value="${JALVIEW_VERSION}" />
       <property name="INSTALLATION" value="${INSTALLATION} git-commit:${git.commit} [${git.branch}]" />
       <property name="BUILD_DATE" value="${build.date}" />
@@ -219,7 +219,7 @@
 
   <target name="clean" depends="init">
     <!-- not efficient yet. -->
-    <delete dir="${outputDir}" includes="*,**/*"/>
+    <delete dir="${outputDir}" includes="*,**/*" />
   </target>
 
   <target name="distclean" depends="init, clean">
@@ -262,10 +262,10 @@
       <exclude name="com/stevesoft/**" />
     </javac>
   </target>
-  
-  
+
+
   <target name="testclean" depends="init">
-    <delete dir="${testOutputDir}" includes="*,**/*"/>
+    <delete dir="${testOutputDir}" includes="*,**/*" />
   </target>
 
   <target name="prepareTests" depends="init,clean">
@@ -298,7 +298,7 @@
   <target name="makefulldist" depends="makedist">
     <copy todir="${packageDir}">
       <fileset dir="${resourceDir}/images">
-        <include name="${WebStartImage}"/>
+        <include name="${WebStartImage}" />
       </fileset>
     </copy>
 
@@ -311,11 +311,11 @@
       </fileset>
     </jar>
 
-    <mkdir dir="${packageDir}/JNLP-INF"/>
+    <mkdir dir="${packageDir}/JNLP-INF" />
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+      <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP" />
       <param name="inih" value="*" />
-      <param name="maxh" value="*"/>
+      <param name="maxh" value="*" />
     </antcall>
 
     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
@@ -325,21 +325,21 @@
     </jar>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+      <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
       <param name="inih" value="10M" />
-      <param name="maxh" value="256M"/>
+      <param name="maxh" value="256M" />
     </antcall>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+      <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
       <param name="inih" value="128M" />
-      <param name="maxh" value="512M"/>
+      <param name="maxh" value="512M" />
     </antcall>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+      <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
       <param name="inih" value="256M" />
-      <param name="maxh" value="1024M"/>
+      <param name="maxh" value="1024M" />
     </antcall>
 
     <!-- finally, need to postprocess to add in associations at end of 'information' element 
@@ -406,16 +406,16 @@
             <include name="*.jar" />
             <include name="*_*.jar" />
             <exclude name="jalview.jar" />
-          	<exclude name="*jnilib.jar"/>
+            <exclude name="*jnilib.jar" />
           </fileset>
-      	</resources>
+        </resources>
         <resources os="Mac OS X">
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
-        	<fileset dir="${packageDir}">
-        		<include name="*quaqua*.jnilib.jar"/>
-        	</fileset>
+          <fileset dir="${packageDir}">
+            <include name="*quaqua*.jnilib.jar" />
+          </fileset>
         </resources>
-      	
+
         <application_desc main_class="jalview.bin.Jalview">
         </application_desc>
         <security>
@@ -424,12 +424,12 @@
       </jnlp>
     </presetdef>
 
-    <jnlpf toFile="${jnlpFile}"/>
+    <jnlpf toFile="${jnlpFile}" />
 
   </target>
 
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
-    <echo message="Not adding JNLP File Associations"/>
+    <echo message="Not adding JNLP File Associations" />
   </target>
 
   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
@@ -452,7 +452,7 @@
         <association mime-type="application-x/ext-file" extensions="jvp"/>
       </information>]]></replacevalue>
   </replace>
-  <echo message="Added file associations to JNLP file"/>
+  <echo message="Added file associations to JNLP file" />
 </target>
 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 </target>
@@ -502,7 +502,7 @@
   <!-- clean dir if it already existed -->
   <delete>
     <fileset dir="${packageDir}">
-      <include name="*.jar"/>
+      <include name="*.jar" />
     </fileset>
   </delete>
   <jar destfile="${packageDir}/${outputJar}" index="true">
@@ -544,13 +544,11 @@
 
 
 <!-- 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="${outputDir}" />
-  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
-			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-			excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -558,7 +556,7 @@
   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
   <copy todir="${outputDir}/lang">
     <fileset dir="${resourceDir}/lang">
-      <include name="**.*"/>
+      <include name="**.*" />
     </fileset>
   </copy>
   <jar destfile="in.jar" index="true">
@@ -598,7 +596,7 @@
     <injar file="in.jar" />
     <outjar file="${jalviewLiteJar}" />
     <libraryjar refid="obfuscateDeps.path" />
-    <dontwarn/>
+    <dontwarn />
     <keep access="public" type="class" name="jalview.bin.JalviewLite">
       <field access="public" />
       <method access="public" />
@@ -652,10 +650,10 @@
       <include name="jalview-jalopy.xml" />
       <include name="JalviewApplet.jpx" />
       <include name="JalviewX.jpx" />
-      <include name="nbbuild.xml"/>
-      <include name="nbproject/genfiles.properties"/>
-      <include name="nbproject/project.properties"/>
-      <include name="nbproject/project.xml"/>
+      <include name="nbbuild.xml" />
+      <include name="nbproject/genfiles.properties" />
+      <include name="nbproject/project.properties" />
+      <include name="nbproject/project.xml" />
       <include name="${sourceDir}/*.java" />
       <include name="${sourceDir}/**/*.java" />
       <include name="${sourceDir}/**/*.cdr" />
@@ -680,27 +678,27 @@
 <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/${javaJson}"/>
-  <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}" />
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}" />
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}" />
   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
     <manifest>
-      <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+      <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)" />
       <!--          <attribute name="Permissions" value="sandbox" /> -->
       <!--<attribute name="Trusted-Lib" value="true" /> -->
-      <attribute name="Codebase" value="${applet.codebase}"/>
-      <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+      <attribute name="Codebase" value="${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="${jalview.key}" lazy="false" verbose="false">
@@ -773,13 +771,13 @@
   </presetdef>
   <!-- create differently privileged artefacts -->
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
-  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
-  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
-  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
-  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
-  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
-  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
+  <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
@@ -810,7 +808,7 @@
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 
     <fileset dir="${packageDir}/examples">
-      <exclude name="u_*.jar"/>
+      <exclude name="u_*.jar" />
       <include name="${jalviewLiteJar}" />
       <include name="${jmolJar}" />
       <include name="${javaJson}" />
@@ -831,19 +829,23 @@
   </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_${jmolJar}" overwrite="true" />
-	<!-- finally, replace any launchApp servlet tags with a version specification -->
-	<replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
-		<replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
-		<fileset dir="${packageDir}/examples">
-			<include name="**/*.html"/>
-		</fileset>
-	</replace>
-	<replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
-		<replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
-		<fileset dir="${packageDir}/examples">
-			<include name="**/*.html"/>
-		</fileset>
-	</replace>
+  <!-- finally, replace any launchApp servlet tags with a version specification -->
+  <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
+    <replacetoken>
+      <![CDATA[http://www.jalview.org/services/launchApp"]]>
+    </replacetoken>
+    <fileset dir="${packageDir}/examples">
+      <include name="**/*.html" />
+    </fileset>
+  </replace>
+  <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+    <replacetoken>
+      <![CDATA[http://www.jalview.org/services/launchApp']]>
+    </replacetoken>
+    <fileset dir="${packageDir}/examples">
+      <include name="**/*.html" />
+    </fileset>
+  </replace>
 
 </target>
 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
-- 
1.7.10.2