From dad527c000d951a4c0021f6d828a52021fec258a Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 9 Dec 2014 14:56:56 +0000
Subject: [PATCH] added ant build file -> build/build.xml

---
 .gitignore      |    7 +-
 build/build.xml |  361 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 367 insertions(+), 1 deletion(-)
 create mode 100644 build/build.xml

diff --git a/.gitignore b/.gitignore
index e883e9e..91b6b83 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,11 @@
 .project
 /bin
-/build
+/build/build
+/build/deploy
+/build/dist
+/build/externalLibs
+/build/project
+/build/projectRefs
 .DS_Store
 /.com.apple.timemachine.supported
 .gitattributes
diff --git a/build/build.xml b/build/build.xml
new file mode 100644
index 0000000..5d8a384
--- /dev/null
+++ b/build/build.xml
@@ -0,0 +1,361 @@
+<?xml version="1.0" encoding="UTF-8"?>
+	<project name="JalviewFX" default="do-deploy" basedir="."  xmlns:fx="javafx:com.sun.javafx.tools.ant">
+	<target name="init-fx-tasks">
+		<path id="fxant">
+			<filelist>
+				<file name="${java.home}\..\lib\ant-javafx.jar"/>
+				<file name="${java.home}\lib\jfxrt.jar"/>
+			</filelist>
+		</path>
+	
+		<taskdef resource="com/sun/javafx/tools/ant/antlib.xml"      
+			uri="javafx:com.sun.javafx.tools.ant"
+			classpathref="fxant"/>
+	</target>
+	<target name="setup-staging-area">
+		<delete dir="externalLibs" />
+		<delete dir="project" />
+		<delete dir="projectRefs" />
+		
+		<mkdir dir="externalLibs" />
+		
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="saaj.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="json_simple-1.1.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="mail.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="Jmol-12.2.4.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="miglayout-4.0-swing.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="httpclient-4.0.3.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jalview.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="groovy-all-1.8.2.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="httpcore-4.0.1.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jsoup-1.8.1.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="castor-1.1-cycle-xml.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="min-jabaws-client-2.1.0.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="wsdl4j.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="spring-web-3.0.5.RELEASE.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="axis.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="slf4j-log4j12-1.7.7.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jaxrpc.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="apache-mime4j-0.6.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="commons-discovery.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="xml-apis.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="log4j-to-slf4j-2.0-rc2.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jdas-1.0.4.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="spring-core-3.0.5.RELEASE.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="commons-codec-1.3.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jfreesvg-2.1.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="xercesImpl.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="VARNAv3-91.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jhall.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="jswingreader-0.3.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="JGoogleAnalytics_0.3.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="activation.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="regex.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="commons-logging-1.1.1.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="slf4j-api-1.7.7.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="httpmime-4.0.3.jar"/>	
+			</fileset>
+		</copy>
+		<copy todir="externalLibs">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX/lib">
+				<filename name="vamsas-client.jar"/>	
+			</fileset>
+		</copy>
+		
+		<mkdir dir="project" />
+		<copy todir="project">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX">
+				<include name="src/**" />
+			</fileset>
+		</copy>
+		<copy todir="project">
+			<fileset dir="/Users/tcnofoegbu/Documents/workspace/java/dev/JalviewFX">
+				<include name="resources/**" />
+			</fileset>
+		</copy>
+		
+		<mkdir dir="projectRefs" />
+	</target>
+	<target name='do-compile'>
+		<delete dir="build" />
+		<mkdir dir="build/src" />
+		<mkdir dir="build/libs" />
+		<mkdir dir="build/classes" />
+	
+		<!-- Copy project-libs references -->
+		<copy todir="build/libs">
+			<fileset dir="externalLibs">
+				<include name="jaxrpc.jar"/>
+				<include name="jswingreader-0.3.jar"/>
+				<include name="regex.jar"/>
+				<include name="activation.jar"/>
+				<include name="groovy-all-1.8.2.jar"/>
+				<include name="miglayout-4.0-swing.jar"/>
+				<include name="JGoogleAnalytics_0.3.jar"/>
+				<include name="apache-mime4j-0.6.jar"/>
+				<include name="commons-logging-1.1.1.jar"/>
+				<include name="jsoup-1.8.1.jar"/>
+				<include name="commons-discovery.jar"/>
+				<include name="Jmol-12.2.4.jar"/>
+				<include name="axis.jar"/>
+				<include name="castor-1.1-cycle-xml.jar"/>
+				<include name="jdas-1.0.4.jar"/>
+				<include name="spring-web-3.0.5.RELEASE.jar"/>
+				<include name="httpclient-4.0.3.jar"/>
+				<include name="slf4j-api-1.7.7.jar"/>
+				<include name="httpmime-4.0.3.jar"/>
+				<include name="wsdl4j.jar"/>
+				<include name="commons-codec-1.3.jar"/>
+				<include name="xercesImpl.jar"/>
+				<include name="vamsas-client.jar"/>
+				<include name="json_simple-1.1.jar"/>
+				<include name="xml-apis.jar"/>
+				<include name="jhall.jar"/>
+				<include name="spring-core-3.0.5.RELEASE.jar"/>
+				<include name="saaj.jar"/>
+				<include name="jfreesvg-2.1.jar"/>
+				<include name="mail.jar"/>
+				<include name="VARNAv3-91.jar"/>
+				<include name="httpcore-4.0.1.jar"/>
+				<include name="log4j-to-slf4j-2.0-rc2.jar"/>
+				<include name="jalview.jar"/>
+				<include name="slf4j-log4j12-1.7.7.jar"/>
+				<include name="min-jabaws-client-2.1.0.jar"/>
+			</fileset>
+		</copy>
+	
+		<!-- Copy project references -->
+	
+		<!-- Copy project sources itself -->
+		<copy todir="build/src">
+			<fileset dir="project/src">
+				<include name="**/*"/>
+			</fileset>
+		</copy>
+		<copy todir="build/src">
+			<fileset dir="project/resources">
+				<include name="**/*"/>
+			</fileset>
+		</copy>
+	
+		<javac includeantruntime="false" source="1.8" target="1.8" srcdir="build/src" destdir="build/classes" encoding="UTF-8">
+			<classpath>
+				<fileset dir="build/libs">
+					<include name="*"/>
+				</fileset>
+			</classpath>
+		</javac>
+		
+		<!-- Copy over none Java-Files -->
+		<copy todir="build/classes">
+		<fileset dir="project/src">
+			<exclude name="**/*.java"/>
+		</fileset>
+		<fileset dir="project/resources">
+			<exclude name="**/*.java"/>
+		</fileset>
+		</copy>
+	
+	
+	</target>
+	<target name="do-deploy" depends="setup-staging-area, do-compile, init-fx-tasks">
+		<delete file="dist"/>
+		<delete file="deploy" />
+		
+		<mkdir dir="dist" />
+		<mkdir dir="dist/libs" />
+		
+		<copy todir="dist/libs">
+			<fileset dir="externalLibs">
+				<include name="*" />
+			</fileset>
+		</copy>
+		
+		
+		<fx:resources id="appRes">
+			<fx:fileset dir="dist" includes="JalviewFX.jar"/>
+			<fx:fileset dir="dist" includes="libs/*"/>
+		</fx:resources> 
+		
+		<fx:application id="fxApplication"
+			name="JalviewFx"
+			mainClass="application.App"
+		/>
+	
+		<mkdir dir="build/classes/META-INF" />
+		
+		
+		
+		<fx:jar destfile="dist/JalviewFX.jar">
+			<fx:application refid="fxApplication"/>
+			<fileset dir="build/classes">
+			</fileset>
+			<fx:resources refid="appRes"/>
+			
+			<manifest>
+				<attribute name="Implementation-Vendor" value="Charles"/>
+				<attribute name="Implementation-Title" value="JalviewFx"/>
+				<attribute name="Implementation-Version" value="1.0"/>
+				<attribute name="JavaFX-Feature-Proxy" value="None"/>
+			</manifest>
+		</fx:jar>
+		
+	
+		<mkdir dir="deploy" />
+		<!-- Need to use ${basedir} because somehow the ant task is calculating the directory differently -->
+		<fx:deploy
+			embedJNLP="true"
+			extension="false"
+			width="500" height="500" 
+			includeDT="true"
+			offlineAllowed="true"
+			outdir="${basedir}/deploy"
+			outfile="JalviewFX" nativeBundles="all"
+			updatemode="background" >
+	
+			<fx:info title="JalviewFX" vendor="Charles"/>
+			<fx:application refId="fxApplication"/>
+			<fx:resources refid="appRes"/>
+		</fx:deploy>
+		
+		
+	</target>
+</project>
-- 
1.7.10.2