diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
| commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
| tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-chemistry/jmol | |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-chemistry/jmol')
| -rw-r--r-- | sci-chemistry/jmol/Manifest | 15 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch | 96 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/caffeine.xyz | 26 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/index.html | 14 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch | 96 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch | 266 | ||||
| -rw-r--r-- | sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch | 330 | ||||
| -rw-r--r-- | sci-chemistry/jmol/jmol-12.0.45-r1.ebuild | 100 | ||||
| -rw-r--r-- | sci-chemistry/jmol/jmol-12.2.27-r1.ebuild | 98 | ||||
| -rw-r--r-- | sci-chemistry/jmol/metadata.xml | 15 |
11 files changed, 1369 insertions, 0 deletions
diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest new file mode 100644 index 000000000000..b47b85f09a7c --- /dev/null +++ b/sci-chemistry/jmol/Manifest @@ -0,0 +1,15 @@ +AUX 12.0.45/jmol-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112 WHIRLPOOL abb250bc77d15a5f3e0a441dd0ffd8809642d8959f896c1ae394b85695b74bd4578013ad99b38abca822ad5db514562b121ad6b2f0265090653d7e359ee85a2f +AUX 12.0.45/jmol-nointl.patch 13315 SHA256 6bbf13c59bc3633dc089346c1133ad2b3d0614463abdf364f5ec2e2ccd658df0 SHA512 deb54c7f94e3fd4b43a701d58c992edbc80f650397feea97594a8f00cdc14463a19e2314fa616fb3a0ca42af8b70770c0426b8eacfe1d81a30b53c566e6342c0 WHIRLPOOL 570e359517e1011ba76447161e6c03925db0e6533d262f11f13d9553f75989faa27a0ae5f39352dad19ec53e804e8e39e76bbc79f1b44b495fe948e7b8633472 +AUX caffeine.xyz 1116 SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f SHA512 863ee4a327b2d765ed042cf24055c708d3970a20c3c3b2ee45b46096390be11a7c02915faedb30ee6cb69101faa5942fcfb19fe2b530afb93460a2cd167c3688 WHIRLPOOL 18df972f5cbafc35be4bf20de29ad8049e7c6f921a668f0c80cd9aff2c3ede32b9b30e830f2629be2136923c554c3711b809915d45ea1bd1da854d8768d6e254 +AUX index.html 328 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451 SHA512 e89c62ba91ecebb38d6f9c88cc1f257600bd7d6005df97713f2715036d3308dee53f7b838ca749c1acc810cc4701c384525f2763b96ac2f1d6802e639cd1961b WHIRLPOOL 0b407f950f4f2523d21c03b6e4f20f9ef4009e54d666ad3a222b87b0e49576816f3940e4fe076e55e9fda9832170c54f17ed543420333fe489f45f4d7296ee79 +AUX jmol-11.0.3-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112 WHIRLPOOL abb250bc77d15a5f3e0a441dd0ffd8809642d8959f896c1ae394b85695b74bd4578013ad99b38abca822ad5db514562b121ad6b2f0265090653d7e359ee85a2f +AUX jmol-11.0.3-nointl.patch 11109 SHA256 56ad460779a0ecfb90ad61cf4cfae2fad9b017f9f78581a720241e4ea208b49a SHA512 0fe07fb53d989298f7395be39c6ee75f56ab59fc096e956d8481c38581706b17f799e745fcd5b6652c4f1115d4425e7ff9ebef454b606d8de7829e07e26b27e2 WHIRLPOOL daf992208b99fec51f5f0b26ca22d520ebd820a22d439c7baa2b84f2b4b3829ac7139d7d3c48076dd4681af1296fd5e61badd91332efa03cc97e58027b21697a +AUX jmol-12.2.27-nointl.patch 13821 SHA256 330a911405f00552d37a9c241c4a18b9d3e6812ce858933dbc4574df8248e345 SHA512 6ad196dfd6d38a086fad461f8170340f8ef3beb7ae69916e0285d8e30ce8a40efc278e461a3d0ae0da71611529f4a0e58c9a73336319764b1fef62d75336a8dc WHIRLPOOL 94be437d33ec73ed53c8461e78a7799c2aa34c9b606e309554da191ff74a465fe2243f4953a615aca790d3558e2b69b7edd122526f900475f5b05bb20d98d0fe +DIST Jmol-12.0.45-full.tar.gz 26501382 SHA256 f9a3fe242841f9b56a718f8da2efe4130e497afe2c12d77f2e68344c62d7f70e SHA512 b0e999335c039e5bde5e261c076f3eb75dd0c33a351445d5c086995d32b3fd03795b3a11dc57a06bf8ac39e74945f3c9f4547ecfbf18b56d827b9a42f5208c11 WHIRLPOOL d0bbae1fc5c96ddfb4dd29f6e09701e496a333a2f44ba266e2a24c60de2d36d73c2184bd9b8f6054b0955535d49856154d6101644ef0297b825c4f6745cfe3bb +DIST Jmol-12.2.27-full.tar.gz 29493780 SHA256 f2ca3b810ea16a488f6f57003d2a407c8ac040d610479a7ae6d95631157db801 SHA512 a8608e64dc06b6d3b0cb7e911f0a224456a65bdc15c51d6b420ee6abf8d82cdcec9f54f6b1a51cfe032e2e074f173f50a88bcff783311de19ce9b95ad990ebca WHIRLPOOL ae0826eab7eb364acb4f30eb77850450b871a24d8940eaabaf8fe9f3770efc39deb604e3c5f875a695c0d33b516ad47d523982c7a6460f2421f961f50a7680bf +DIST jmol-selfSignedCertificate.store.tar 10240 SHA256 416744934991ef4f1fa298c0afc8e855d43771de2f2278ed3fbc60f707ea46b2 SHA512 2c3e9d1183a0b174273346d0fba0729caa415ef53fe01629a4c47daa2393c9e18ca3f57984911e6340197429cf0ee581c64bb9b6072db902102976030d9f2c23 WHIRLPOOL 79dc2b2c95b304569f44bb986af3aa25150b0c5f8a9fc9b1698a979647800e60d0f20a7a4abbc89533a21f3d7f4b93a430840eed71bbe04b1cc0bdbcfae7fe63 +EBUILD jmol-12.0.45-r1.ebuild 2923 SHA256 6fb9b443fcfbe680b0e120d0233b0531116351a91bee3bf8d398a921480cfad9 SHA512 6336b5293150abcf0f8349ebd80088b26b4b6da3633f00ac53a9396569e65f1736f2fa14cd69f65ea16838e3507d0050734c71c23734311cefe41dc1bd3d0974 WHIRLPOOL c7890e2d7a8b8ebbf082d2fb65b18923ffad36c0f9ebc95bf00039f6f7b70cbe32bb3773b0e09c1f88146e8d1c19cb9c7099ccb97482c8e43b9f437571a5b07e +EBUILD jmol-12.2.27-r1.ebuild 2783 SHA256 41f0fbe61872ec8763ff3887f3f574bf9e3ed12751cd44fa7355968c78fea2fc SHA512 dd81a4edccc022a8f7aab66a8a8005feb68eec7e2e3a1a2278f9565c8b3bec364b5dcb0f994c1202a3fb97491ca31b11941ed41501e0a485d9238f233d9e0940 WHIRLPOOL 93d2ea57d5fec5229770ecc2f3e1df317ede5cb97eb4036e81bddd390311fa4df4e587254ae4627094eb323013626cf9a5084a9c884dc4e2ca8e16b50093894e +MISC ChangeLog 2878 SHA256 18b594c9d1d7ef41e2292dd65768c5847c18ed35c3bc4c65b83fef7f8326b075 SHA512 918cc2877676a207b037b56c1b2400b6b700c8bc367e2399fd4bf4f367ae81dddeaa7cfbbc3d9b73b1d3771ecff22b19e1031753e1ae579f2aeb3cba72c51a66 WHIRLPOOL cf0834fc982455bac386a8b1d9c8e05f2204a8a448579bc09f376a2eb14302c0d7bbc5864a47c8699e06d3b459c56273afb22feb7e96cf9ebe2bcfedd7b38ddb +MISC ChangeLog-2015 2982 SHA256 bf3153e33aa2d74e25570ecf4fec84e9bee42ad661c18791e1aacdb1e17e1f1a SHA512 fed110fe8de1074909ef53be8d8eb9f576946987e98cccb44540cedd990c37dd85dac54c2af67ba3c460b3a0c083582c883b621d8fe8c8a21b464eb3f3cdff10 WHIRLPOOL 6f7dc08ffcf2644bd452668f256f93f3fad41908fe5ae65cdc3230175fdaab984b82a25103e3181afa427a50ced58f278b2642439dbe3f894c6bbf268008e332 +MISC metadata.xml 458 SHA256 d1ff80e0cb82997846dd7daa0fb55428e4c29dd60645273cb29bd148c625d3e7 SHA512 2808cc38baa2aefa5fb873cab1f2f96d52125c41f969d37cf9405b19c16883aa0bec82895fc40001acc1eb9b7b02ceb5fb03b9a517b887e56ea13d3889dd9012 WHIRLPOOL a9e37b078f979bd05d2c86fa3d5b33b16ebb5f6c853001e95f3c3e26fb460427e20750241194b17709706263ccffbe8d85d5c8b3df793475a64cd43792942571 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>
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz new file mode 100644 index 000000000000..f0325b049f3c --- /dev/null +++ b/sci-chemistry/jmol/files/caffeine.xyz @@ -0,0 +1,26 @@ +24 +Caffeine +H -3.3804130 -1.1272367 0.5733036 +N 0.9668296 -1.0737425 -0.8198227 +C 0.0567293 0.8527195 0.3923156 +N -1.3751742 -1.0212243 -0.0570552 +C -1.2615018 0.2590713 0.5234135 +C -0.3068337 -1.6836331 -0.7169344 +C 1.1394235 0.1874122 -0.2700900 +N 0.5602627 2.0839095 0.8251589 +O -0.4926797 -2.8180554 -1.2094732 +C -2.6328073 -1.7303959 -0.0060953 +O -2.2301338 0.7988624 1.0899730 +H 2.5496990 2.9734977 0.6229590 +C 2.0527432 -1.7360887 -1.4931279 +H -2.4807715 -2.7269528 0.4882631 +H -3.0089039 -1.9025254 -1.0498023 +H 2.9176101 -1.8481516 -0.7857866 +H 2.3787863 -1.1211917 -2.3743655 +H 1.7189877 -2.7489920 -1.8439205 +C -0.1518450 3.0970046 1.5348347 +C 1.8934096 2.1181245 0.4193193 +N 2.2861252 0.9968439 -0.2440298 +H -0.1687028 4.0436553 0.9301094 +H 0.3535322 3.2979060 2.5177747 +H -1.2074498 2.7537592 1.7203047 diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html new file mode 100644 index 000000000000..35a5d49217e2 --- /dev/null +++ b/sci-chemistry/jmol/files/index.html @@ -0,0 +1,14 @@ +<html> + <head> + <title>Jmol Test Page</title> + <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br> + <script src="./Jmol.js"></script> + </head> + <body> + <script> + jmolInitialize("./"); // REQUIRED + jmolApplet(400, "load ./caffeine.xyz"); + </script></div> + </body> +</html> + diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch new file mode 100644 index 000000000000..3b43c219d94f --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-11.0.3-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/jmol-11.0.3-nointl.patch b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch new file mode 100644 index 000000000000..25fd17e36c68 --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch @@ -0,0 +1,266 @@ +--- jmol-11.0.3-orig/build.xml 2007-05-17 09:35:04.000000000 -0500 ++++ jmol-11.0.3/build.xml 2007-05-17 09:40:21.000000000 -0500 +@@ -100,10 +100,6 @@ + <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>
+
+@@ -113,14 +109,6 @@ + <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>
+
+@@ -130,14 +118,6 @@ + <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>
+
+@@ -147,14 +127,6 @@ + <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>
+
+@@ -332,17 +304,12 @@ + </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="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -462,7 +429,6 @@ + <!-- note that this class is included in JmolApplet0.jar -->
+ <exclude name="org/jmol/api/JmolAppletInterface.class" />
+ <include name="org/jmol/applet/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/popup/**" />
+ </fileset>
+ </jar>
+@@ -502,12 +468,6 @@ + </fileset>
+ </jar>
+
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet_i18n.jar" manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/**" />
+- </fileset>
+- </jar>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- changes to this must be replicated below for the signed applet -->
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0.jar"
+@@ -527,7 +487,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolApplet4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolApplet_i18n.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -564,10 +523,6 @@ + signedjar="${jmol.applet.build.dir}/JmolAppletSigned6.jar"
+ keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet_i18n.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+@@ -589,7 +544,6 @@ + <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -599,7 +553,7 @@ + </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}"/>
+@@ -655,7 +609,6 @@ + <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -744,7 +697,6 @@ + <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -839,7 +791,7 @@ + <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="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -900,16 +852,6 @@ + <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${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"
+@@ -924,26 +866,6 @@ + <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"
+@@ -957,24 +879,6 @@ + <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="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -988,24 +892,6 @@ + <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${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">
+@@ -1036,12 +922,4 @@ + <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>
diff --git a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch new file mode 100644 index 000000000000..0a43faaf653d --- /dev/null +++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch @@ -0,0 +1,330 @@ +--- 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/jmol-12.0.45-r1.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild new file mode 100644 index 000000000000..589cc469b42f --- /dev/null +++ b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild @@ -0,0 +1,100 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 +WEBAPP_OPTIONAL="yes" + +inherit eutils webapp java-pkg-2 java-ant-2 + +MY_P=Jmol + +DESCRIPTION="Java molecular viever for 3-D chemical structures" +HOMEPAGE="http://jmol.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar" + +WEBAPP_MANUAL_SLOT="yes" +SLOT="0" +KEYWORDS="~amd64 ~x86" +LICENSE="LGPL-2.1" +IUSE="client-only vhosts" + +COMMON_DEP=" + dev-java/commons-cli:1 + dev-java/itext:0 + sci-libs/jmol-acme:0 + sci-libs/vecmath-objectclub:0" + +RDEPEND=">=virtual/jre-1.4 + ${COMMON_DEP}" +DEPEND=">=virtual/jdk-1.4 + !client-only? ( ${WEBAPP_DEPEND} ) + ${COMMON_DEP}" + +pkg_setup() { + use client-only || webapp_pkg_setup + java-pkg-2_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/${PV}/${PN}-nointl.patch \ + "${FILESDIR}"/${PV}/${PN}-manifest.patch + + mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory." + cp "${WORKDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \ + || die "Failed to install Cert file." + + rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die + cd "${S}/jars" + +# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. + if use amd64; then + mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." + rm -v *.jar *.tar.gz || die "Failed to remove jars." + mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." + fi + + java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar + java-pkg_jar-from itext iText.jar itext-1.4.5.jar + java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar + java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar + + mkdir -p "${S}/build/appjars" || die +} + +src_compile() { + # prevent absorbing dep's classes + eant -Dlibjars.uptodate=true main +} + +src_install() { + java-pkg_dojar build/Jmol.jar + dohtml -r build/doc/* || die "Failed to install html docs." + dodoc *.txt doc/*license* || die "Failed to install licenses." + + java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ + --java_args "-Xmx512m" + + if ! use client-only ; then + webapp_src_preinst + cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + + webapp_src_install + fi +} + +pkg_postinst() { + use client-only || webapp_pkg_postinst +} + +pkg_prerm() { + use client-only || webapp_pkg_prerm +} diff --git a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild new file mode 100644 index 000000000000..2b78a243a22d --- /dev/null +++ b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild @@ -0,0 +1,98 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=5 +WEBAPP_OPTIONAL="yes" + +inherit eutils webapp java-pkg-2 java-ant-2 + +MY_P=Jmol + +DESCRIPTION="Java molecular viever for 3-D chemical structures" +HOMEPAGE="http://jmol.sourceforge.net/" +SRC_URI=" + mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz + https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar" + +LICENSE="LGPL-2.1" +KEYWORDS="~x86 ~amd64" +IUSE="+client-only vhosts" + +WEBAPP_MANUAL_SLOT="yes" +SLOT="0" + +COMMON_DEP=" + dev-java/commons-cli:1 + dev-java/itext:0 + sci-libs/jmol-acme:0 + sci-libs/vecmath-objectclub:0 + sci-libs/naga" +RDEPEND=">=virtual/jre-1.5 + ${COMMON_DEP}" +DEPEND=">=virtual/jdk-1.5 + dev-java/saxon:6.5 + !client-only? ( ${WEBAPP_DEPEND} ) + ${COMMON_DEP}" + +pkg_setup() { + use client-only || webapp_pkg_setup + java-pkg-2_pkg_setup +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-nointl.patch + + rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die + cd "${S}/jars" + +# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along. + if use amd64; then + mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar." + rm -v *.jar *.tar.gz || die "Failed to remove jars." + mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar." + fi + + java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar + 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 --build-only saxon-6.5 saxon.jar + + mkdir -p "${S}/build/appjars" || die +} + +src_compile() { + # prevent absorbing dep's classes + eant -Dlibjars.uptodate=true main +} + +src_install() { + java-pkg_dojar build/Jmol.jar + dohtml -r build/doc/* || die "Failed to install html docs." + dodoc *.txt doc/*license* || die "Failed to install licenses." + + java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \ + --java_args "-Xmx512m" + + if ! use client-only ; then + webapp_src_preinst + cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed." + + webapp_src_install + fi +} + +pkg_postinst() { + use client-only || webapp_pkg_postinst +} + +pkg_prerm() { + use client-only || webapp_pkg_prerm +} diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml new file mode 100644 index 000000000000..888f06b55ce5 --- /dev/null +++ b/sci-chemistry/jmol/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> + <use> + <flag name="client-only">Install the viewer only, no applet files for httpd + </flag> + </use> + <upstream> + <remote-id type="sourceforge">jmol</remote-id> + </upstream> +</pkgmetadata> |