<property name="outputDir" value="classes" />
<property name="packageDir" value="dist" />
<property name="outputJar" value="jalview.jar" />
+ <!-- Jalview Applet JMol Jar Dependency -->
+ <property name="jmolJar" value="Jmol-11.0.2.jar" />
<!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
<property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
<property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
</path>
<!-- The Location of the java 1.1.8 jdk -->
<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+ <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"/>
+ -->
<!-- the classpath for building the 1.1 applet -->
<path id="jalviewlite.deps">
<fileset dir="${java118.home}">
<include name="lib/classes.zip"/>
</fileset>
- <pathelement location="lib/jmol.jar"/>
+ <pathelement location="lib/${jmolJar}"/>
</path>
</target>
target="1.1"
srcdir="${sourceDir}"
destdir="${outputDir}"
- classpath="lib/JmolApplet.jar"
+ classpath="lib/${jmolJar}"
includes="jalview/appletgui/**"
excludes="ext/**,MCview/**,org/**,vamsas/**"
/>
</target>
<target name="obfuscate" depends="packageApplet">
+ <path id="obfuscateDeps.path">
+ <pathelement location="${applet.jre.tools}"/>
+ <pathelement location="lib/${jmolJar}"/>
+ </path>
<taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
<proguard>
- -libraryjars "${java.home}/lib/rt.jar";lib/JmolApplet.jar
+ <injar file="in.jar"/>
+ <outjar file="jalviewApplet.jar"/>
+ <libraryjar refid="obfuscateDeps.path"/>
+ <keep access="public" type="class"
+ name="jalview.bin.JalviewLite">
+ <field access="public"/>
+ <method access="public"/>
+ <constructor access="public"/>
+ </keep>
+<!-- -libraryjars "${obfuscateDeps}"
-injars in.jar
-outjars jalviewApplet.jar
-keep public class jalview.bin.JalviewLite
{ public * ; }
+ -->
</proguard>
<delete file="in.jar"/>
</target>
-#Thu May 24 16:17:26 BST 2007\r
+#Sun Jun 17 14:17:08 BST 2007\r
jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor\r
jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor\r
jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor\r
jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor\r
jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor\r
-jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor\r
jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor\r
+jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor\r
jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor\r
-jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor\r
+jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor\r
jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor\r
-jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor\r
-jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor\r
-jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor\r
+jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
+jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor\r
jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor\r
+jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor\r
jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor\r
jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor\r
jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- if (_identity == null) {\r
- return super.getIdentity();\r
- }\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
+import jalview.schemabinding.version2.Colour;\r
import jalview.schemabinding.version2.JalviewUserColours;\r
-import jalview.schemabinding.version2.Colour; // Added Manually\r
+\r
/**\r
* Class JalviewUserColoursDescriptor.\r
* \r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- if (_identity == null) {\r
- return super.getIdentity();\r
- }\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- if (_identity == null) {\r
- return super.getIdentity();\r
- }\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- if (_identity == null) {\r
- return super.getIdentity();\r
- }\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- if (_identity == null) {\r
- return super.getIdentity();\r
- }\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r
*/\r
private java.lang.String _xmlName;\r
\r
- /**\r
- * Field _identity.\r
- */\r
- private org.exolab.castor.xml.XMLFieldDescriptor _identity;\r
-\r
\r
//----------------/\r
//- Constructors -/\r
*/\r
public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
) {\r
- return _identity;\r
+ return super.getIdentity();\r
}\r
\r
/**\r