Latest Jmol

(Portage version: 2.1.10.3/cvs/Linux x86_64)

2 files changed, 409 insertions, 0 deletions

diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
new file mode 100644
index 000000000000..3b43c219d94f
--- /dev/null
+++ b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
@@ -0,0 +1,96 @@
+diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
+--- jmol-11.0.3-orig/manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet0.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,6 @@
++Main-Class: JmolApplet

++Sealed: true

++

++Name: org/jmol/api/

++Sealed: false

++

+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
+--- jmol-11.0.3-orig/manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet1.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,6 @@
++Name: org/jmol/api/

++Sealed: false

++

++Name: org/jmol/applet/

++Sealed: true

++

+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
+--- jmol-11.0.3-orig/manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet2.txt	2007-05-16 01:56:19.000000000 -0500
+@@ -0,0 +1,3 @@
++Name: javax/vecmath/
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
+--- jmol-11.0.3-orig/manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet3.txt	2007-05-16 01:56:47.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/g3d/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
+--- jmol-11.0.3-orig/manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet4.txt	2007-05-16 01:57:05.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/adapter/smarter/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
+--- jmol-11.0.3-orig/manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet5.txt	2007-05-16 01:57:23.000000000 -0500
+@@ -0,0 +1,4 @@
++Name: org/openscience/jmol/ui/
++Sealed: true
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
+--- jmol-11.0.3-orig/manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet6.txt	2007-05-16 01:57:46.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/viewer/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
+--- jmol-11.0.3-orig/manifest/appletMain.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/appletMain.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,5 @@
++Manifest-Version: 1.0

++Sealed: true

++

++Name: org/jmol/api/

++Sealed: false

+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
+--- jmol-11.0.3-orig/manifest/appletMonolithic.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/appletMonolithic.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,7 @@
++Main-Class: JmolApplet

++Sealed: true

++

++Name: org/jmol/api/

++Sealed: false

++

++

+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
+--- jmol-11.0.3-orig/manifest/applet.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,2 @@
++Manifest-Version: 1.0

++Sealed: true

+\ No newline at end of file
+diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
+--- jmol-11.0.3-orig/manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/application.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1 @@
++Main-Class: org.openscience.jmol.app.Jmol

+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
+--- jmol-11.0.3-orig/manifest/jvxl.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/jvxl.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1 @@
++Main-Class: org.openscience.jvxl.Jvxl

diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
new file mode 100644
index 000000000000..c1b22e83c615
--- /dev/null
+++ b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
@@ -0,0 +1,313 @@
+--- build.xml	2011-02-25 12:59:43.000000000 -0600
++++ build.xml.new	2011-02-27 12:16:02.398959959 -0600
+@@ -110,10 +110,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -123,14 +119,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />

+-        </uptodate>

+       </and>

+     </condition>

+     

+@@ -140,14 +128,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolDevelopersGuide.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolDevelopersGuide_fr.docbook.xml"/>

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolDevelopersGuide_de.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -157,14 +137,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolAppletGuide_de.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -385,17 +357,12 @@
+   </target>

+ 

+   <target name="jar" id="jar"

+-          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">

++          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">

+     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >

+       <fileset dir="build/doc/JmolUserGuide">

+         <include name="**/*.html" />

+       </fileset>

+     </copy>

+-    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >

+-      <fileset dir="build/doc/JmolUserGuide_fr">

+-        <include name="**/*.html" />

+-      </fileset>

+-    </copy>

+     <copy todir="${classes.dir}/org/openscience/jmol/Data" >

+       <fileset dir="build/doc/JmolHistory">

+         <include name="**/*.html" />

+@@ -587,18 +554,6 @@
+       <fileset dir="${appletjars.dir}" includes="**/*"/>

+     </jar>

+ 

+-    <for list="${all.JmolApplet.languages}" delimiter=","

+-         param="current.Jmol.language">

+-      <sequential>

+-        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

+-             manifest="manifest/applet_i18n.txt" >

+-          <fileset dir="${applet.classes.dir}">

+-            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />

+-          </fileset>

+-        </jar>

+-      </sequential>

+-    </for>

+-

+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

+       <fileset dir="${applet.classes.dir}">

+         <include name="org/jmol/minimize/**" />

+@@ -712,7 +667,6 @@
+         <include name="org/jmol/bspt/**" />

+         <include name="org/jmol/g3d/**" />

+         <include name="org/jmol/geodesic/**" />

+-        <include name="org/jmol/i18n/**" />

+         <include name="org/jmol/modelset/**" />

+         <include name="org/jmol/script/**" />

+         <include name="org/jmol/shape/**" />

+@@ -738,7 +692,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />

+       </indexjars>

+     </jar>

+     <!-- changes to this must be replicated below for the signed applet -->

+@@ -851,16 +804,6 @@
+              keystore="selfSignedCertificate/selfSignedCertificate.store"

+              storepass="selfSignedCertificate" alias="selfSignedCertificate" />

+ 

+-    <for list="${all.JmolApplet.languages}" delimiter=","

+-         param="current.Jmol.language">

+-      <sequential>

+-      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

+-                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"

+-                 keystore="selfSignedCertificate/selfSignedCertificate.store"

+-                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />

+-      </sequential>

+-    </for>

+-

+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

+     <!-- this one must be treated specially because of jar indexing

+          we cannot simply rename the jar file, because the index has

+@@ -906,7 +849,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />

+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />

+       </indexjars>

+     </jar>

+     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"

+@@ -944,18 +886,6 @@
+ 	      </fileset>

+ 	    </jar>

+ 

+-	    <for list="${all.JmolApplet.languages}" delimiter=","

+-	         param="current.Jmol.language">

+-	      <sequential>

+-	        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"

+-	             manifest="manifest/applet_i18n.txt" >

+-	          <fileset dir="${applet.classes.dir}">

+-	            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />

+-	          </fileset>

+-	        </jar>

+-	      </sequential>

+-	    </for>

+-

+ 	    <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

+ 	      <fileset dir="${applet.classes.dir}">

+ 	        <include name="org/jmol/minimize/**" />

+@@ -1069,7 +999,6 @@
+ 	        <include name="org/jmol/bspt/**" />

+ 	        <include name="org/jmol/g3d/**" />

+ 	        <include name="org/jmol/geodesic/**" />

+-	        <include name="org/jmol/i18n/**" />

+ 	        <include name="org/jmol/modelset/**" />

+ 	        <include name="org/jmol/script/**" />

+ 	        <include name="org/jmol/shape/**" />

+@@ -1095,7 +1024,6 @@
+ 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

+ 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

+ 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

+-	        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />

+ 	      </indexjars>

+ 	    </jar>

+ 	    <!-- changes to this must be replicated below for the signed applet -->

+@@ -1104,7 +1032,7 @@
+ 	  </target>

+ 

+ 	<target name="dist" id="dist"

+-          depends="doc,main-i18n,main,signed-applet">

++          depends="doc,main,signed-applet">

+     <!-- first build binary distribution -->

+     <delete dir="build/dist/jmol-${version}"/>

+     <mkdir dir="build/dist/jmol-${version}"/>

+@@ -1163,7 +1091,6 @@
+       <fileset dir=".">

+         <include name="applet.classes" />

+         <include name="build.xml" />

+-        <include name="build-i18n.xml" />

+       </fileset>

+     </copy>

+ 

+@@ -1246,7 +1173,6 @@
+       <fileset dir=".">

+         <include name="apisio.classes" />

+         <include name="build.xml" />

+-        <include name="build-i18n.xml" />

+       </fileset>

+     </copy>

+ 

+@@ -1342,7 +1268,7 @@
+   <target name="xclean" id="xclean">

+   </target>

+ 

+-  <target name="spotless" id="spotless" depends="clean,spotless-i18n">

++  <target name="spotless" id="spotless" depends="clean">

+     <delete dir="build"/>

+     <delete dir="${javadoc.dir}"/>

+     <delete dir="packaging/rpm/dist"/>

+@@ -1406,16 +1332,6 @@
+       <arg value="../../../doc/source/JmolGuide.docbook.xml" />

+       <arg value="../../${docbook-xsl}/html/chunk.xsl" />

+     </java>

+-    <echo message="Generating user's guide (fr)" />

+-    <mkdir dir="build/doc/JmolUserGuide_fr" />

+-    <java fork="true" dir="build/doc/JmolUserGuide_fr"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <jvmarg value="${proxyHost}" />

+-      <jvmarg value="${proxyPort}" />

+-      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />

+-      <arg value="../../${docbook-xsl}/html/chunk.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolHistory" id="jmolHistory"

+@@ -1430,26 +1346,6 @@
+       <arg value="../../../doc/source/JmolHistory.xml" />

+       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+     </java>

+-    <echo message="Generating history of changes (fr)" />

+-    <java fork="true" dir="build/doc/JmolHistory"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="ChangeLog_fr.html" />

+-      <arg value="../../../doc/source/JmolHistory_fr.xml" />

+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+-      <arg value="lang=fr" />

+-    </java>

+-    <echo message="Generating history of changes (nl)" />

+-    <java fork="true" dir="build/doc/JmolHistory"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="ChangeLog_nl.html" />

+-      <arg value="../../../doc/source/JmolHistory_nl.xml" />

+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+-      <arg value="lang=nl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"

+@@ -1463,24 +1359,6 @@
+       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />

+       <arg value="../${docbook-xsl}/html/docbook.xsl" />

+     </java>

+-    <echo message="Generating developer's guide (fr)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolDevelopersGuide_fr.html" />

+-      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+-    <echo message="Generating developer's guide (de)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolDevelopersGuide_de.html" />

+-      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"

+@@ -1494,24 +1372,6 @@
+       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />

+       <arg value="../${docbook-xsl}/html/docbook.xsl" />

+     </java>

+-    <echo message="Generating applet guide (fr)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolAppletGuide_fr.html" />

+-      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+-    <echo message="Generating applet guide (de)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolAppletGuide_de.html" />

+-      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="test" id="test" depends="main,compile-tests">

+@@ -1543,12 +1403,4 @@
+     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />

+   </target>

+ 

+-  <!-- i18n stuff -->

+-  <target name="main-i18n" depends="classes">

+-    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>

+-  </target>

+-  <target name="spotless-i18n">

+-    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>

+-  </target>

+-

+ </project>