Latest Jmol for testing

svn path=/; revision=335

5 files changed, 352 insertions, 381 deletions

diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest
index 4ad5c1a..58e36de 100644
--- a/sci-chemistry/jmol/Manifest
+++ b/sci-chemistry/jmol/Manifest
@@ -2,6 +2,8 @@ AUX caffeine.xyz 1116 RMD160 92b432c6584cd927fa1bfb155ea41011ab7a82d8 SHA1 d0f35
 AUX index.html 328 RMD160 60d2a573c228e018a864fd7d9cfc7554264ccd6b SHA1 7ab256d768d3a4da43b5e497dfb1c3a53a8068a9 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451
 AUX jmol-11.0.3-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd
 AUX jmol-11.4.6-nointl.patch 10695 RMD160 3d10af3e3c8debeb6680ab37e3e7fbf0cb871d4d SHA1 39f48d30de57e92f6399178a0605059eefda6373 SHA256 d34440c05b251e9392d9e4c85eceaeab9aaddac35be04e71781d95541252dc6f
+AUX jmol-12.2.27-nointl.patch 13821 RMD160 4d6a6a598f4b550b6c2e3665c01b4f915d39c563 SHA1 2bc04f7a5e781f8628622a69f12d1f4a33b26140 SHA256 330a911405f00552d37a9c241c4a18b9d3e6812ce858933dbc4574df8248e345
 AUX selfSignedCertificate.store 1516 RMD160 583b7bab5578e1e32f649388b7009dc654df1199 SHA1 88d9123bdc1a376ba00e00c8abef4751adefe3a5 SHA256 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5
-DIST jmol-11.4.6-full.tar.gz 16022367 RMD160 281fc0886df82763545fde94c040f3011ad0e672 SHA1 b83df223bc6c1ecb64c9d3de0e6baca2882f07fa SHA256 c5c4dd6d28adf15c25f4a5f795578d3f25f245b40b3a2bb5dc09b3e2f30b048b
-EBUILD jmol-11.4.6.ebuild 3191 RMD160 f7a2d94379fa69d38053ee0ee0edc70398e83012 SHA1 93a0d72fe9f0e26edc0e6ea36fd6c1abd297b51a SHA256 767d3036f6e3ca0d1d37c3a08a2bee09f8fd938557dbecb438c15d9e4ebebd16
+DIST Jmol-12.2.27-full.tar.gz 29493780 RMD160 e0f530e92ed079b1debf9fbd5c720ad19ba71977 SHA1 663a3a83a1fff373cea624d4cec4fdd71efcd505 SHA256 f2ca3b810ea16a488f6f57003d2a407c8ac040d610479a7ae6d95631157db801
+DIST jmol-selfSignedCertificate.store.tar 10240 RMD160 a6d4df5f108a2c13074190569b95d3310439ea57 SHA1 218fff84df0c542b634ba08ed2e82d3d3280a481 SHA256 416744934991ef4f1fa298c0afc8e855d43771de2f2278ed3fbc60f707ea46b2
+EBUILD jmol-12.2.27.ebuild 3120 RMD160 6789d7bb9340d2674c4d101f7465baf22344bbbf SHA1 59d700dffcef83f8c96b98d2bc7a79ee7927d6a7 SHA256 8d998f8cc358528019b33b1a705bab31c23e0c79e37bd73e0b1cfd76dd776ea4
diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch
deleted file mode 100644
index 3b43c21..0000000
--- a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-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/jmol-11.4.6-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
index 252e236..0a43faa 100644
--- a/sci-chemistry/jmol/files/jmol-11.4.6-nointl.patch
+++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
@@ -1,267 +1,330 @@
---- jmol-11.4.6/build.xml.orig	2008-09-16 15:27:28.388008850 -0500
-+++ jmol-11.4.6/build.xml	2008-09-16 15:38:57.637384713 -0500
-@@ -104,10 +104,6 @@
-           <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>
- 
-@@ -117,14 +113,6 @@
-           <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>
-     
-@@ -134,14 +122,6 @@
-           <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>
- 
-@@ -151,14 +131,6 @@
-           <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>
- 
-@@ -350,17 +322,12 @@
-   </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="${classes.dir}/org/openscience/jmol/Data" >
-       <fileset dir="build/doc/JmolHistory">
-         <include name="**/*.html" />
-@@ -506,7 +473,6 @@
- 	        <!-- note that this class is included in JmolApplet0.jar -->
- 	        <exclude name="org/jmol/api/JmolAppletInterface.class" />
- 	        <include name="org/jmol/applet/**" />
--	        <include name="org/jmol/i18n/**" />
- 	      </fileset>
- 	    </jar>
- 
-@@ -602,12 +568,6 @@
- 	      </fileset>
- 	    </jar>
- 
--	  <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" manifest="manifest/applet_i18n.txt" >
--      <fileset dir="${applet.classes.dir}">
--        <include name="org/jmol/translation/**" />
--      </fileset>
--    </jar>
--
- 
-     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
-     <!-- changes to this must be replicated below for the signed applet -->
-@@ -636,7 +596,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSpecial.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Viewer.jar" />
--        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" />
-       </indexjars>
-     </jar>
-     <!-- changes to this must be replicated below for the signed applet -->
-@@ -728,11 +687,6 @@
-     	
-     	
-   	
--  	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n.jar"
--             signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar"
--             keystore="selfSignedCertificate/selfSignedCertificate.store"
--             storepass="selfSignedCertificate" alias="selfSignedCertificate" />
--
-     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
-     <!-- this one must be treated specially because of jar indexing
-          we cannot simply rename the jar file, because the index has
-@@ -762,7 +716,6 @@
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSpecial.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
-         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Viewer.jar" />
--        <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar" />
-       </indexjars>
-     </jar>
-     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
-@@ -772,7 +725,7 @@
-   </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}"/>
-@@ -829,7 +782,6 @@
-       <fileset dir=".">
-         <include name="applet.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -908,7 +860,6 @@
-       <fileset dir=".">
-         <include name="apisio.classes" />
-         <include name="build.xml" />
--        <include name="build-i18n.xml" />
-       </fileset>
-     </copy>
- 
-@@ -1000,7 +951,7 @@
-   <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="${javadoc.dir}"/>
-     <delete dir="packaging/rpm/dist"/>
-@@ -1063,16 +1014,6 @@
-       <arg value="../../../doc/source/JmolGuide.docbook.xml" />
-       <arg value="../../${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"
-@@ -1087,26 +1028,6 @@
-       <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"
-@@ -1120,24 +1041,6 @@
-       <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="../${docbook-xsl}/html/docbook.xsl" />
--    </java>
-   </target>
- 
-   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
-@@ -1151,24 +1054,6 @@
-       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
-       <arg value="../${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">
-@@ -1200,12 +1085,4 @@
-     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
-   </target>
- 
--  <!-- i18n stuff -->
--  <target name="main-i18n" depends="classes">
--    <ant antfile="build-i18n.xml" target="main-i18n"/>
--  </target>
--  <target name="spotless-i18n">
--    <ant antfile="build-i18n.xml" target="spotless-i18n"/>
--  </target>
--
- </project>
+--- orig-build.xml	2012-05-31 13:42:43.943062427 -0500
++++ build.xml	2012-05-31 14:01:01.691982062 -0500
+@@ -52,8 +52,6 @@
+ 

+   <property file="proxy.properties" />

+ 

+-  <import file="tools/build-i18n.xml"/>

+-

+   <path id="project.class.path">

+     <fileset dir="${lib.dir}">

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

+@@ -111,10 +109,6 @@
+           <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>

+ 

+@@ -124,14 +118,6 @@
+           <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>

+     

+@@ -141,14 +127,6 @@
+           <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>

+ 

+@@ -158,14 +136,6 @@
+           <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>

+ 

+@@ -388,17 +358,12 @@
+   </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" />

+@@ -603,18 +568,6 @@
+       <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/**" />

+@@ -729,7 +682,6 @@
+         <include name="org/jmol/constant/**" />

+         <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/**" />

+@@ -755,7 +707,6 @@
+         <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 -->

+@@ -868,16 +819,6 @@
+              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

+@@ -905,7 +846,6 @@
+ 		<include name="org/jmol/shape/**" />

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

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

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

+       </fileset>    	

+       <indexjars>

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Console.jar" />

+@@ -924,7 +864,6 @@
+         <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"

+@@ -963,18 +902,6 @@
+       </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/**" />

+@@ -1088,7 +1015,6 @@
+         <include name="org/jmol/constant/**" />

+         <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/**" />

+@@ -1114,7 +1040,6 @@
+         <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 -->

+@@ -1123,7 +1048,7 @@
+   </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}"/>

+@@ -1183,7 +1108,6 @@
+       <fileset dir=".">

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

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

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

+       </fileset>

+     </copy>

+ 

+@@ -1278,7 +1202,6 @@
+       <fileset dir=".">

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

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

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

+       </fileset>

+     </copy>

+ 

+@@ -1374,7 +1297,7 @@
+   <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"/>

+@@ -1438,16 +1361,6 @@
+       <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"

+@@ -1462,26 +1375,6 @@
+       <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"

+@@ -1495,24 +1388,6 @@
+       <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"

+@@ -1526,24 +1401,6 @@
+       <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">

+@@ -1575,12 +1432,4 @@
+     <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>

diff --git a/sci-chemistry/jmol/files/selfSignedCertificate.store b/sci-chemistry/jmol/files/selfSignedCertificate.store
deleted file mode 100644
index a7b0ccb..0000000
--- a/sci-chemistry/jmol/files/selfSignedCertificate.store
+++ /dev/null
diff --git a/sci-chemistry/jmol/jmol-11.4.6.ebuild b/sci-chemistry/jmol/jmol-12.2.27.ebuild
index 4d988b2..c8a4095 100644
--- a/sci-chemistry/jmol/jmol-11.4.6.ebuild
+++ b/sci-chemistry/jmol/jmol-12.2.27.ebuild
@@ -1,13 +1,19 @@
-# Copyright 1999-2008 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
+EAPI=1
 WEBAPP_OPTIONAL="yes"
 
 inherit eutils webapp java-pkg-2 java-ant-2
 
+MY_P="Jmol"
+
 DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures."
-SRC_URI="mirror://sourceforge/${PN}/${P}-full.tar.gz"
+SRC_URI="
+	mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz
+	http://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar"
+
 HOMEPAGE="http://jmol.sourceforge.net/"
 KEYWORDS="~x86 ~amd64"
 LICENSE="LGPL-2.1"
@@ -20,33 +26,27 @@ SLOT="0"
 COMMON_DEP="dev-java/commons-cli
 	dev-java/itext
 	sci-libs/jmol-acme
-	sci-libs/vecmath-objectclub"
-
-RDEPEND=">=virtual/jre-1.4
+	sci-libs/vecmath-objectclub
+	sci-libs/naga"
+RDEPEND=">=virtual/jre-1.5
 	${COMMON_DEP}"
-DEPEND=">=virtual/jdk-1.4
+DEPEND=">=virtual/jdk-1.5
+	dev-java/saxon:6.5
 	!client-only? ( ${WEBAPP_DEPEND} )
 	${COMMON_DEP}"
 
 pkg_setup() {
 
-	if ! use client-only ; then
-		webapp_pkg_setup || die "Failed to setup webapp"
-	fi
-
+	use client-only || webapp_pkg_setup
 	java-pkg-2_pkg_setup
-
 }
 
 src_unpack() {
 
 	unpack ${A}
-	epatch "${FILESDIR}"/${P}-nointl.patch
-#	epatch "${FILESDIR}"/${P}-manifest.patch
+	cd "${S}"
 
-	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
-	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
-		|| die "Failed to install Cert file."
+	epatch "${FILESDIR}"/${P}-nointl.patch
 
 	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
 	cd "${S}/jars"
@@ -62,6 +62,8 @@ src_unpack() {
 	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
 	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
 	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
+	java-pkg_jar-from naga
+	java-pkg_jar-from saxon-6.5 saxon.jar
 
 	mkdir -p "${S}/build/appjars" || die
 }