JAL-1731 fix JPred4 citation in legacy client code
[jalview.git] / build.xml
1 <?xml version="1.0"?>
2 <!--
3  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
4  * Copyright (C) 2014 The Jalview Authors
5  * 
6  * This file is part of Jalview.
7  * 
8  * Jalview is free software: you can redistribute it and/or
9  * modify it under the terms of the GNU General Public License 
10  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11  *  
12  * Jalview is distributed in the hope that it will be useful, but 
13  * WITHOUT ANY WARRANTY; without even the implied warranty 
14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
15  * PURPOSE.  See the GNU General Public License for more details.
16  * 
17  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
18  * The Jalview Authors are detailed in the 'AUTHORS' file.
19 -->
20 <project name="jalviewX" default="usage" basedir=".">
21   <target name="help" depends="usage" />
22   <target name="usage">
23     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
24     <echo message="Targets include:" />
25     <echo message="usage - default target, displays this message" />
26     <echo message="buildindices - generates JavaHelpSearch from the help files" />
27     <echo message="build - compiles all necessary files for Application" />
28     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
29     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
30     <echo message="              this needs a keystore and key. See docs/building.html for more information." />
31     <echo message="compileApplet - compiles all necessary files for Applet" />
32     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
33     <echo message="See docs/building.html and the comments in build file for other targets." />
34     <echo message="note: compile and makeApplet require the property java118.home to be set to point to a java 1.1.8 jdk." />
35     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
36   </target>
37
38
39   <!-- utils is a class path to additional utilities needed for
40     building docs, jars and webstart stuff -->
41   <!--
42         Userdefined build property defaults
43
44         wsdl.server list (plus namespace mapping info ???)  - also want
45                 ... to make this a dynamically generatable property
46         WebStart Location
47         Build location - provide a temporary root for speed
48         jarsigner keystore and info
49         Jakarta and axis classpath ?
50         Default argument for starting Jalview (if it exists).
51
52 -->
53
54   <target name="init">
55     <path id="axis.classpath">
56       <!-->
57       <fileset dir="/usr/local/axis/lib">
58         <include name="**/*.jar" />
59       </fileset>
60       <fileset dir="/usr/local/jakarta-tomcat-5/webapps/axis/WEB-INF/lib">
61         <include name="**/*.jar"/>
62         <include name="*.jar"/>
63       </fileset> -->
64       </path>
65         
66     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
67     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
68         
69     <property name="INSTALLATION" value="Source" />
70         
71     <!-- 2.4 (VAMSAS)" -->
72     <!-- Include debugging information in javac true or false -->
73     <property name="javac.debug" value="true" />
74
75     <!-- JarSigner Key Store for Webstart Distribution -->
76     <property name="jalview.keystore" value="./keys/.keystore" />
77     <!-- Keystore Password -->
78     <property name="jalview.keystore.pass" value="alignmentisfun" />
79     <!-- Key Name -->
80     <property name="jalview.key" value="jalview" />
81     <!-- Key Password -->
82     <property name="jalview.key.pass" value="alignmentisfun" />
83
84     <!-- Don't change anything below here unless you know what you are doing! -->
85     <!-- Url path for WebStart in JNLP file -->
86     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
87     <!-- Webstart Image - looked for in resources/images -->
88     <property name="WebStartImage" value="JalviewLogo_big.png"/>
89     <!-- J2SE version needed for webstart launch -->
90     <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
91     <property name="j2sev" value="1.7+"/>
92
93     <!-- Permissions for running Java applets and applications. -->
94     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
95     <property name="application.codebase" value="*.jalview.org" />
96     <!-- and allowing the applet to be deployed from any URL -->
97     <!-- note - if you want to make sure LiveConnect works without any warnings, please rebuild and sign your applet jar with your own domain included in the codebase/allowable-codebase properties -->
98     <property name="applet.codebase" value="*.jalview.org *.dundee.ac.uk *" />
99     <property name="applet.caller-codebase" value="${applet.codebase}" />
100
101     <!-- build directory configuration -->
102     <property name="libDir" value="lib" />
103     <property name="resourceDir" value="resources" />
104     <property name="helpDir" value="help" />
105     <property name="docDir" value="doc" />
106     <property name="sourceDir" value="src" />
107     <property name="schemaDir" value="schemas" />
108     <property name="outputDir" value="classes" />
109     <property name="packageDir" value="dist" />
110     <property name="outputJar" value="jalview.jar" />
111     <!-- Jalview Applet JMol Jar Dependency -->
112     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
113     <property name="varnaJar" value="VARNAv3-91.jar" />
114     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
115     <!-- switch to indicate if we should obfuscate jalviewLite -->
116     <!-- <property name="donotobfuscate" value="true"/> -->
117     <!-- switch to exclude associations from generated jnlp files -->
118     <!-- <property name="nojnlpfileassocs" value="true"/> -->
119
120     <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
121     <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
122     <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
123     <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
124     <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
125     <property name="WSInterf" value="MsaWS" />
126     <property name="wsdl.Namespace" value="vamsas" />
127     <property name="wsdl.ClientNS" value="ext.vamsas" />
128     <!-- the class path for building the application -->
129     <path id="build.classpath">
130       <fileset dir="utils">
131         <include name="*.jar" />
132         <include name="**/*.jar" />
133       </fileset>
134       <fileset dir="${libDir}">
135         <include name="*.jar" />
136         <include name="**/*.jar" />
137       </fileset>
138       <fileset dir="${java.home}/lib">
139         <include name="plugin.jar"/>
140       </fileset>
141       <fileset dir="appletlib">
142         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
143                                 -->
144         <include name="${jmolJar}" />
145         <include name="${varnaJar}" />
146       </fileset>
147
148     </path>
149     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
150     <!-- The Location of the java 1.1.8 jdk -->
151     <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
152     <property name="java118.home" value="${java.home}" />
153     <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
154                 -->
155     <!-- jre for 1.4 version -->
156     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
157
158     <!-- the classpath for building the 1.1 applet -->
159     <path id="jalviewlite.deps">
160       <fileset dir="${java118.home}">
161         <include name="lib/classes.zip" />
162       </fileset>
163       <fileset dir="${java.home}/lib">
164         <include name="plugin.jar"/>
165       </fileset>
166       <pathelement location="appletlib/${jmolJar}" />
167       <pathelement location="lib/${varnaJar}" />
168     </path>
169     <!-- default location for outputting javadoc -->
170     <property name="javadocDir" value="${packageDir}/javadoc"/>
171   </target>
172
173
174   <taskdef classpath="utils/roxes-ant-tasks-1.2-2004-01-30.jar" resource="com/roxes/tools/ant/taskdefs.properties" />
175   <target name="buildPropertiesFile" depends="init">
176     <tstamp prefix="build">
177       <format property="date" pattern="dd MMMM yyyy" />
178     </tstamp>
179     <properties file="${outputDir}/.build_properties">
180       <header>
181           ---Jalview Build Details---
182         </header>       
183       <property name="VERSION" value="${JALVIEW_VERSION}" />
184       <property name="INSTALLATION" value="${INSTALLATION}" />
185       <property name="BUILD_DATE" value="${build.date}" />
186     </properties>
187   </target>
188
189
190   <target name="clean" depends="init">
191     <!-- not efficient yet. -->
192     <delete dir="${outputDir}" includes="*,**/*"/>
193   </target>
194
195   <target name="distclean" depends="init, clean">
196
197     <echo message="REMOVING ALL BACKUP/AUTOSAVES!" />
198     <delete>
199       <fileset dir=".">
200         <include name="${outputJar}" />
201         <include name="#*#" />
202         <include name="#*.*#" />
203         <include name="**/#*#" />
204         <include name="**/#*.*#" />
205         <include name="*~" />
206         <include name="*.*~" />
207         <include name="**/*~" />
208         <include name="**/*.*~" />
209       </fileset>
210     </delete>
211   </target>
212
213   <target name="prepare" depends="init">
214     <mkdir dir="${outputDir}" />
215     <copy todir="${outputDir}">
216       <fileset dir=".">
217         <include name="${docDir}/**/*.*" />
218         <include name="${helpDir}/**/*.*" />
219         <include name="${libDir}/*.jar" />
220       </fileset>
221       <fileset dir="${resourceDir}">
222         <include name="**/*.*" />
223       </fileset>
224     </copy>
225   </target>
226
227   <target name="build" depends="prepare">
228     <!-- not efficient yet. -->
229     <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="build.classpath">
230       <exclude name="jalview/*applet*" />
231       <exclude name="jalview/appletgui/**" />
232       <exclude name="com/stevesoft/**" />
233     </javac>
234   </target>
235   <target name="buildindices" depends="init, prepare" unless="help.uptodate">
236     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
237       <arg line="html" />
238     </java>
239   </target>
240
241   <target name="makefulldist" depends="makedist">
242     <copy todir="${packageDir}">
243       <fileset dir="${resourceDir}/images">
244         <include name="${WebStartImage}"/>
245       </fileset>
246     </copy>
247
248     <taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
249
250     <!-- create a dummy jar which will eventually contain the jnlp template -->
251     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
252       <fileset dir="${packageDir}">
253         <include name="jalview.jar" />
254       </fileset>
255     </jar>
256
257     <mkdir dir="${packageDir}/JNLP-INF"/>
258     <antcall target="writejnlpf">
259       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
260       <param name="inih" value="*" />
261       <param name="maxh" value="*"/>
262     </antcall>
263
264     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
265       <fileset dir="${packageDir}">
266         <include name="JNLP-INF"/>
267       </fileset>
268     </jar>
269
270     <antcall target="writejnlpf">
271       <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
272       <param name="inih" value="10M" />
273       <param name="maxh" value="256M"/>
274     </antcall>
275
276     <antcall target="writejnlpf">
277       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
278       <param name="inih" value="128M" />
279       <param name="maxh" value="512M"/>
280     </antcall>
281
282     <antcall target="writejnlpf">
283       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
284       <param name="inih" value="256M" />
285       <param name="maxh" value="1024M"/>
286     </antcall>
287
288     <!-- finally, need to postprocess to add in associations at end of 'information' element 
289                         
290                         <xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
291                 
292                 </xslt>
293                         
294                         
295                         -->
296     <!--
297                                 <association mime-type="application-x/ext-file" extensions="fa"/>
298         <association mime-type="application-x/ext-file" extensions="fasta"/>
299         <association mime-type="application-x/ext-file" extensions="mfa"/>
300         <association mime-type="application-x/ext-file" extensions="fastq"/>
301         <association mime-type="application-x/ext-file" extensions="blc"/>
302         <association mime-type="application-x/ext-file" extensions="msf"/>
303         <association mime-type="application-x/ext-file" extensions="pfam"/>
304         <association mime-type="application-x/ext-file" extensions="aln"/>
305         <association mime-type="application-x/ext-file" extensions="pir"/>
306         <association mime-type="application-x/ext-file" extensions="amsa"/>
307         <association mime-type="application-x/ext-file" extensions="stk"/>
308         <association mime-type="application-x/ext-file" extensions="jar"/>-->
309     <!-- and sign the jars -->
310     <!-- the default keystore details might need to be edited here -->
311     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
312       <fileset dir="${packageDir}">
313         <include name="*.jar" />
314       </fileset>
315     </signjar>
316   </target>
317
318   <target name="runenv" depends="init">
319     <path id="run.classpath">
320       <pathelement location="${outputDir}" />
321       <fileset dir="${outputDir}">
322         <include name="${libDir}/*.jar" />
323       </fileset>
324     </path>
325     <pathconvert targetos="unix" refid="run.classpath" property="run.classpath" />
326
327     <echo>java -classpath ${run.classpath} jalview.bin.Jalview
328       </echo>
329   </target>
330
331   <target name="-generatejnlpf">
332     <presetdef name="jnlpf">
333       <jnlp codebase="${WebStartLocation}">
334         <information>
335           <title>Jalview</title>
336           <vendor>The Barton Group</vendor>
337           <homepage href="http://www.jalview.org" />
338           <description>Jalview Multiple Alignment Editor</description>
339           <description kind="short">Jalview</description>
340           <icon href="${WebStartImage}" />
341           <offline_allowed />
342         </information>
343         <resources>
344           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
345           <fileset dir="${packageDir}">
346             <include name="jalview.jar" />
347           </fileset>
348           <fileset dir="${packageDir}">
349             <include name="*.jar" />
350             <include name="*_*.jar" />
351             <exclude name="jalview.jar" />
352           </fileset>
353           <property name="jalview.version" value="${JALVIEW_VERSION}" />
354         </resources>
355         <application_desc main_class="jalview.bin.Jalview">
356         </application_desc>
357         <security>
358           <all_permissions />
359         </security>
360       </jnlp>
361     </presetdef>
362
363     <jnlpf toFile="${jnlpFile}"/>
364
365   </target>
366
367   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
368     <echo message="Not adding JNLP File Associations"/>
369   </target>
370
371   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
372     <replace file="${jnlpFile}">
373       <replacetoken>
374         <![CDATA[</information>]]></replacetoken>
375       <replacevalue>
376         <![CDATA[
377           <association mime-type="application-x/ext-file" extensions="fa" />
378         <association mime-type="application-x/ext-file" extensions="fasta" />
379         <association mime-type="application-x/ext-file" extensions="mfa" />
380         <association mime-type="application-x/ext-file" extensions="fastq" />
381         <association mime-type="application-x/ext-file" extensions="blc" />
382         <association mime-type="application-x/ext-file" extensions="msf" />
383         <association mime-type="application-x/ext-file" extensions="pfam" />
384         <association mime-type="application-x/ext-file" extensions="aln"/>
385         <association mime-type="application-x/ext-file" extensions="pir"/>
386         <association mime-type="application-x/ext-file" extensions="amsa"/>
387         <association mime-type="application-x/ext-file" extensions="stk"/>
388         <association mime-type="application-x/ext-file" extensions="jvp"/>
389       </information>]]></replacevalue>
390   </replace>
391   <echo message="Added file associations to JNLP file"/>
392 </target>
393 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
394 </target>
395
396 <target name="buildextclients" depends="init">
397   <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
398   <condition property="dontextbuild">
399     <equals arg1="n" arg2="${doextbuild.response}" />
400   </condition>
401   <condition property="dontextbuild">
402     <equals arg1="N" arg2="${doextbuild.response}" />
403   </condition>
404   <fail if="dontextbuild">
405         Build External Client Code process aborted by user. Jalview source is unchanged.
406       </fail>
407   <!-- Currently, this doesn't happen automatically.
408      1. Run WSDL2Java as below, which generates an ext.vamsas +
409      vamsas.<datapackages> fileset.
410      2. refactor ext.vamsas.SpecificserviceWS* to
411      ext.vamsas.ServiceclassWS* that implements the ServiceclassWSI interface.
412      3. Update the jalview.ws.*WServices classes to reflect the
413      interface type, and all locations of this wsdl type that Jalview
414      might be using.
415
416 -->
417   <path id="axisbuild">
418     <path refid="build.classpath" />
419   </path>
420   <taskdef resource="axis-tasks.properties" classpathref="axisbuild" />
421   <move todir="./bak">
422     <fileset dir="${sourceDir}" id="client">
423       <include name="${wsdl.ClientNS}/*.*" />
424     </fileset>
425   </move>
426
427   <axis-wsdl2java output="${sourceDir}" verbose="true" url="${wsdl.MsaWS2}" serverside="false" deployscope="Request" debug="false" helpergen="true" all="true">
428     <mappingSet>
429       <mapping namespace="${wsdl.Namespace}" package="${wsdl.ClientNS}" />
430       <mapping namespace="http://dataTypes.vamsas" package="${wsdl.ClientNS}" />
431     </mappingSet>
432   </axis-wsdl2java>
433 </target>
434
435 <target name="makedist" depends="build, buildPropertiesFile, buildindices">
436   <!-- make the package jar if not already existing -->
437   <mkdir dir="${packageDir}" />
438   <!-- clean dir if it already existed -->
439   <delete>
440     <fileset dir="${packageDir}">
441       <include name="*.jar"/>
442     </fileset>
443   </delete>
444   <jar destfile="${packageDir}/${outputJar}" index="true">
445     <manifest>
446       <attribute name="Main-Class" value="jalview.bin.Jalview" />
447       <attribute name="Permissions" value="all-permissions" />
448       <attribute name="Application-Name" value="Jalview Desktop" />
449       <attribute name="Codebase" value="${application.codebase}" />
450     </manifest>
451     <fileset dir="${outputDir}/">
452       <exclude name="cache*/**" />
453       <exclude name="*.jar" />
454       <exclude name="*.jar.*" />
455       <exclude name="**/*.jar" />
456       <exclude name="**/*.jar.*" />
457     </fileset>
458   </jar>
459
460   <copy toDir="${packageDir}" flatten="true">
461     <fileset dir="${outputDir}">
462       <include name="*.jar" />
463       <include name="**/*.jar" />
464     </fileset>
465   </copy>
466 </target>
467
468
469 <!-- jalopy code reformatter -->
470 <target name="sourcescrub" depends="init,build">
471   <jalopy destdir="jsrc" classpathref="run.classpath" convention="jalview-jalopy.xml">
472     <fileset dir="${sourceDir}">
473       <include name="*.java" />
474       <include name="**/*.java" />
475       <include name="**/**/*.java" />
476     </fileset>
477   </jalopy>
478 </target>
479
480
481
482 <!-- Compile, package and obfuscate Jalview Applet -->
483 <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
484
485 <target name="compileApplet" depends="init,clean">
486   <mkdir dir="${outputDir}" />
487   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
488                         classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
489                         excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
490 </target>
491
492 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
493   <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
494   <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
495   <copy todir="${outputDir}/lang">
496     <fileset dir="${resourceDir}/lang">
497       <include name="**.*"/>
498     </fileset>
499   </copy>
500   <jar destfile="in.jar" index="true">
501     <manifest>
502       <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
503       <attribute name="Application-Name" value="JalviewLite" />
504       <attribute name="Codebase" value="${applet.codebase}" />
505     </manifest>
506     <fileset dir="${outputDir}">
507       <include name="com/**" />
508       <include name="MCview/**" />
509       <include name="jalview/**" />
510       <include name=".build_properties" />
511       <include name="images/idwidth.gif" />
512       <include name="images/link.gif" />
513       <include name="lang/**" />
514     </fileset>
515   </jar>
516 </target>
517 <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
518 </target>
519 <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
520   <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
521   <delete file="in.jar" />
522 </target>
523 <target name="-obfuscatereally" unless="donotobfuscate">
524
525   <path id="obfuscateDeps.path">
526     <pathelement location="${applet.jre.tools}" />
527     <pathelement location="appletlib/${jmolJar}" />
528   </path>
529   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
530
531   <proguard>
532     <injar file="in.jar" />
533     <outjar file="${jalviewLiteJar}" />
534     <libraryjar refid="obfuscateDeps.path" />
535     <dontwarn/>
536     <keep access="public" type="class" name="jalview.bin.JalviewLite">
537       <field access="public" />
538       <method access="public" />
539       <constructor access="public" />
540     </keep>
541     <keep access="public" type="class" name="jalview.appletgui.AlignFrame">
542       <field access="public" />
543       <method access="public" />
544       <constructor access="public" />
545     </keep>
546     <!--      -libraryjars "${obfuscateDeps}"
547       -injars      in.jar
548       -outjars     jalviewApplet.jar
549       -keep public class jalview.bin.JalviewLite
550        { public * ; } -->
551   </proguard>
552   <delete file="in.jar" />
553 </target>
554
555 <target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
556   <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
557   <delete>
558     <fileset dir="${sourceDir}/jalview/schemabinding/version2">
559       <include name="*.java" />
560       <include name="descriptors/*.java" />
561     </fileset>
562   </delete>
563   <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
564   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
565   <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
566   <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
567   <!-- 
568                 now build the jalview.binding package with the old schema set
569                 -->
570   <delete>
571     <fileset dir="${sourceDir}/jalview/binding/">
572       <include name="**" />
573     </fileset>
574   </delete>
575   <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
576   <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
577   <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
578 </target>
579 <target name="sourcedist" description="create jalview source distribution" depends="init">
580   <delete file="${source.dist.name}" />
581   <tar destfile="${source.dist.name}" compression="gzip">
582     <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
583       <include name="LICENSE" />
584       <include name="README" />
585       <include name="build.xml" />
586       <include name="jalview-jalopy.xml" />
587       <include name="JalviewApplet.jpx" />
588       <include name="JalviewX.jpx" />
589       <include name="nbbuild.xml"/>
590       <include name="nbproject/genfiles.properties"/>
591       <include name="nbproject/project.properties"/>
592       <include name="nbproject/project.xml"/>
593       <include name="${sourceDir}/*.java" />
594       <include name="${sourceDir}/**/*.java" />
595       <include name="${sourceDir}/**/*.cdr" />
596       <include name="${libDir}/**/*" />
597       <include name="${resourceDir}/**/*" />
598       <include name="${helpDir}/**/*" />
599       <include name="appletlib/${jmolJar}" />
600       <exclude name="**/*locales" />
601       <exclude name="*locales/**" />
602       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
603       <exclude name="utils/InstallAnywhere/**Build*/**" />
604       <exclude name="utils/InstallAnywhere/**Build*/**" />
605       <exclude name="utils/InstallAnywhere/**locale*" />
606       <exclude name="utils/InstallAnywhere/**locale*/**" />
607       <include name="${schemaDir}/**/*" />
608       <include name="utils/**/*" />
609       <include name="${docDir}/**/*" />
610       <include name="examples/**/*" />
611     </tarfileset>
612   </tar>
613 </target>
614 <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
615   <copy todir="${packageDir}/examples">
616     <fileset dir="examples">
617       <include name="**/*"/>
618       <include name="javascript/*"/>
619       <include name="jmol/*"/>
620     </fileset>
621     <fileset dir=".">
622       <include name="${jalviewLiteJar}" />
623     </fileset>
624     <fileset dir="appletlib">
625       <include name="**/*"/>
626     </fileset>
627   </copy>
628   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
629   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
630     <manifest>
631       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
632       <!--          <attribute name="Permissions" value="sandbox" /> -->
633       <!--<attribute name="Trusted-Lib" value="true" /> -->
634       <attribute name="Codebase" value="${applet.codebase}"/>
635       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
636     </manifest>
637   </jar>
638   <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
639     <fileset dir="${packageDir}/examples">
640       <include name="*.jar" />
641     </fileset>
642   </signjar>
643   <presetdef name="ap_applet.jar">
644     <!-- build a signed applet with 'all-permissions' - 
645                           Needs 'param name="permissions' value="all-permissions"' in applet tag
646                           JalviewLite+JmolApplet linked sequence/structure fails
647                           Mixed code warnings are raised
648                           -->
649     <jar update="true" index="true">
650       <manifest>
651         <attribute name="Application-Name" value="JalviewLite" />
652         <attribute name="Permissions" value="all-permissions" />
653         <attribute name="Codebase" value="${applet.codebase}" />
654         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
655         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
656       </manifest>
657     </jar>
658   </presetdef>
659   <presetdef name="applet.jar">
660     <!-- build signed applet with sandbox permissions -
661                           Needs 'param name="permissions' value="sandbox"' in applet tag
662                          Preserves Pre-Java 1.7_u45 behavior once 'permissions' parameter added to applet tag 
663                         -->
664
665     <jar update="true" index="true">
666       <manifest>
667         <attribute name="Application-Name" value="JalviewLite" />
668         <attribute name="Permissions" value="sandbox" />
669         <attribute name="Codebase" value="${applet.codebase}" />
670         <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
671         <attribute name="Application-Library-Allowable-Codebase" value="${applet.codebase}" />
672       </manifest>
673     </jar>
674   </presetdef>
675   <presetdef name="tl_applet.jar">
676     <!-- build signed applet with trusted library/trusted permissions -
677                                 Needs 'param name="permissions' value="all-permissions"' in applet tag
678                                j1.7_45:
679                                No mixed code warnings raised 
680                                Jmol/JalviewLite sequence/structure example doesn't link structures
681                                Raises dialog asking user to allow page to control applet via LiveConnect javascript
682                                
683                               -->
684
685     <jar update="true" index="true">
686       <manifest>
687         <attribute name="Application-Name" value="JalviewLite" />
688         <attribute name="Permissions" value="all-permissions" />
689         <attribute name="Codebase" value="${applet.codebase}" />
690         <attribute name="Trusted-Only" value="true" />
691         <attribute name="Trusted-Library" value="true" />
692       </manifest>
693     </jar>
694   </presetdef>
695   <presetdef name="to_applet.jar">
696     <!-- not fully test variant (yet) -->
697     <jar update="true" index="true">
698       <manifest>
699         <attribute name="Application-Name" value="JalviewLite" />
700         <attribute name="Permissions" value="all-permissions" />
701         <attribute name="Codebase" value="${applet.codebase}" />
702         <attribute name="Trusted-Only" value="true" />
703       </manifest>
704     </jar>
705   </presetdef>
706   <!-- create differently privileged artefacts -->
707   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
708   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
709   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
710   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
711   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
712   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
713   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
714   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
715   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
716   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
717   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
718   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
719   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
720   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
721   <!-- finally, create manifest for original jars -->
722   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
723   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
724
725   <!-- todo - write examples/downloads for alternate versions of the applet -->
726   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
727
728     <fileset dir="${packageDir}/examples">
729       <exclude name="u_*.jar"/>
730       <include name="${jalviewLiteJar}" />
731       <include name="${jmolJar}" />
732       <include name="to_${jalviewLiteJar}" />
733       <include name="to_${jmolJar}" />
734       <include name="tl_${jalviewLiteJar}" />
735       <include name="tl_${jmolJar}" />
736       <include name="ap_${jalviewLiteJar}" />
737       <include name="ap_${jmolJar}" />
738     </fileset>
739   </signjar>
740   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
741   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
742 </target>
743 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
744   <javadoc destdir="${javadocDir}">
745     <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
746     </packageset>
747   </javadoc>
748 </target>
749 </project>