From: <eg...@us...> - 2008-02-24 17:00:39
|
Revision: 10228 http://cdk.svn.sourceforge.net/cdk/?rev=10228&view=rev Author: egonw Date: 2008-02-24 09:00:30 -0800 (Sun, 24 Feb 2008) Log Message: ----------- Removed some weka traces Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2008-02-24 16:54:26 UTC (rev 10227) +++ trunk/cdk/build.xml 2008-02-24 17:00:30 UTC (rev 10228) @@ -472,7 +472,6 @@ <antcall target="compile-module"><param name="module" value="qsarmolecular"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="qsarprotein"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="qsar-cml"/><param name="source" value="${src}/main"/></antcall> - <antcall target="compile-module"><param name="module" value="qsarweka"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="forcefield"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="builder3d"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="builder3dtools"/><param name="source" value="${src}/main"/></antcall> @@ -508,7 +507,6 @@ <antcall target="compile-module"><param name="module" value="test-qsarbond"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsarmolecular"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsarprotein"/><param name="source" value="${src}/test"/></antcall> - <antcall target="compile-module"><param name="module" value="test-qsarweka"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-pdb"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-inchi"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-libiomd"/><param name="source" value="${src}/test"/></antcall> @@ -539,7 +537,6 @@ <includesfile name="${metainf}/io-jmol.libdepends"/> <includesfile name="${metainf}/io.libdepends"/> <includesfile name="${metainf}/libiocml.libdepends"/> - <includesfile name="${metainf}/libioweka.libdepends"/> <includesfile name="${metainf}/nonotify.libdepends"/> <includesfile name="${metainf}/pdb-cml.libdepends"/> <includesfile name="${metainf}/pdb.libdepends"/> @@ -549,7 +546,6 @@ <includesfile name="${metainf}/qsarmolecular.libdepends"/> <includesfile name="${metainf}/qsarprotein.libdepends"/> <includesfile name="${metainf}/qsar-cml.libdepends"/> - <includesfile name="${metainf}/qsarweka.libdepends"/> <includesfile name="${metainf}/reaction.libdepends"/> <includesfile name="${metainf}/render.libdepends"/> <includesfile name="${metainf}/standard.libdepends"/> @@ -578,7 +574,6 @@ <include name="cdk-io.jar"/> <include name="cdk-io-jmol.jar"/> <include name="cdk-libiocml.jar"/> - <include name="cdk-libioweka.jar"/> <include name="cdk-libiomd.jar"/> <include name="cdk-nonotify.jar"/> <include name="cdk-pdb-cml.jar"/> @@ -589,7 +584,6 @@ <include name="cdk-qsarmolecular.jar"/> <include name="cdk-qsarprotein.jar"/> <include name="cdk-qsar-cml.jar"/> - <include name="cdk-qsarweka.jar"/> <include name="cdk-reaction.jar"/> <include name="cdk-render.jar"/> <include name="cdk-standard.jar"/> @@ -646,7 +640,6 @@ <include name="cdk-io.jar"/> <include name="cdk-io-jmol.jar"/> <include name="cdk-libiocml.jar"/> - <include name="cdk-libioweka.jar"/> <include name="cdk-libiomd.jar"/> <include name="cdk-nonotify.jar"/> <include name="cdk-pdb-cml.jar"/> @@ -657,7 +650,6 @@ <include name="cdk-qsarmolecular.jar"/> <include name="cdk-qsarprotein.jar"/> <include name="cdk-qsar-cml.jar"/> - <include name="cdk-qsarweka.jar"/> <include name="cdk-reaction.jar"/> <include name="cdk-render.jar"/> <include name="cdk-standard.jar"/> @@ -723,7 +715,6 @@ <includesfile name="${metainf}/test-structgen.libdepends"/> <includesfile name="${metainf}/test-valencycheck.libdepends"/> <includesfile name="${metainf}/test-charges.libdepends"/> - <includesfile name="${metainf}/test-weka.libdepends"/> <includesfile name="${metainf}/test-libiomd.libdepends"/> <includesfile name="${metainf}/test-pcore.libdepends"/> <includesfile name="${metainf}/test-formula.libdepends"/> @@ -752,7 +743,6 @@ <include name="cdk-test-structgen.jar"/> <include name="cdk-test-valencycheck.jar"/> <include name="cdk-test-charges.jar"/> - <include name="cdk-test-weka.jar"/> <include name="cdk-test-libiomd.jar"/> <include name="cdk-test-pcore.jar"/> <include name="cdk-test-formula.jar"/> @@ -991,7 +981,6 @@ <antcall target="test-module"><param name="module" value="qsarbond"/></antcall> <antcall target="test-module"><param name="module" value="qsarmolecular"/></antcall> <antcall target="test-module"><param name="module" value="qsarprotein"/></antcall> - <antcall target="test-module"><param name="module" value="weka"/></antcall> <antcall target="test-module"><param name="module" value="pdb"/></antcall> <antcall target="test-module"><param name="module" value="pcore"/></antcall> <antcall target="test-module"><param name="module" value="inchi"/></antcall> Modified: trunk/cdk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java =================================================================== --- trunk/cdk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java 2008-02-24 16:54:26 UTC (rev 10227) +++ trunk/cdk/src/test/org/openscience/cdk/modulesuites/MqsarTests.java 2008-02-24 17:00:30 UTC (rev 10228) @@ -28,7 +28,6 @@ import junit.framework.TestSuite; import org.openscience.cdk.test.qsar.model.R2.RJavaEnvironmentTest; -import org.openscience.cdk.test.qsar.model.weka.QSARWekaModelTests; /** * TestSuite that runs all the sample tests. @@ -59,8 +58,6 @@ // from cdk.test.qsar.model.R2 - suite.addTest(QSARWekaModelTests.suite()); - return suite; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-02-25 11:02:12
|
Revision: 10231 http://cdk.svn.sourceforge.net/cdk/?rev=10231&view=rev Author: egonw Date: 2008-02-25 02:31:08 -0800 (Mon, 25 Feb 2008) Log Message: ----------- The build.xml fix in r10230 uncovered many missing dependencies. This commit fixes those for the 'dist-all' target. Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/META-INF/applications.cdkdepends trunk/cdk/src/META-INF/atomtype.cdkdepends trunk/cdk/src/META-INF/builder3d.cdkdepends trunk/cdk/src/META-INF/builder3dtools.cdkdepends trunk/cdk/src/META-INF/control.cdkdepends trunk/cdk/src/META-INF/experimental.cdkdepends trunk/cdk/src/META-INF/extra.cdkdepends trunk/cdk/src/META-INF/forcefield.cdkdepends trunk/cdk/src/META-INF/formula.cdkdepends trunk/cdk/src/META-INF/io.cdkdepends trunk/cdk/src/META-INF/libiomd.cdkdepends trunk/cdk/src/META-INF/pcore.cdkdepends trunk/cdk/src/META-INF/qsaratomic.cdkdepends trunk/cdk/src/META-INF/qsarbond.cdkdepends trunk/cdk/src/META-INF/qsarmolecular.cdkdepends trunk/cdk/src/META-INF/qsarprotein.cdkdepends trunk/cdk/src/META-INF/reaction.cdkdepends trunk/cdk/src/META-INF/sdg.cdkdepends trunk/cdk/src/META-INF/smarts.cdkdepends trunk/cdk/src/META-INF/smiles.cdkdepends trunk/cdk/src/META-INF/standard.cdkdepends trunk/cdk/src/META-INF/structgen.cdkdepends trunk/cdk/src/META-INF/valencycheck.cdkdepends trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DHub.java trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleAddAtom.java trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleChangeFormalC.java trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleHighlight.java trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleMove.java trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleRemove.java trunk/cdk/src/main/org/openscience/cdk/controller/ExampleController2DModule.java trunk/cdk/src/main/org/openscience/cdk/controller/IChemModelRelay.java trunk/cdk/src/main/org/openscience/cdk/controller/IController2DModule.java trunk/cdk/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/GeometryToolsInternalCoordinates.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/IJava2DRenderer.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/JCPActionChangeMode.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/Java2DRenderer.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/SomeToolBar.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestEditor.java trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestRenderer.java trunk/cdk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java Added Paths: ----------- trunk/cdk/src/META-INF/progzjcp.cdkdepends trunk/cdk/src/META-INF/progzjcp.libdepends trunk/cdk/src/META-INF/test.cdkdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/build.xml 2008-02-25 10:31:08 UTC (rev 10231) @@ -481,7 +481,8 @@ <antcall target="compile-module"><param name="module" value="experimental"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="pcore"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="applications"/><param name="source" value="${src}/main"/></antcall> - <antcall target="compile-module"><param name="module" value="inchi"/><param name="source" value="${src}/main"/></antcall> + <antcall target="compile-module"><param name="module" value="inchi"/><param name="source" value="${src}/main"/></antcall> + <antcall target="compile-module"><param name="module" value="progzjcp"/><param name="source" value="${src}/main"/></antcall> </target> <target id="test-dist-all" name="test-dist-all" description="test-dist-all"> Modified: trunk/cdk/src/META-INF/applications.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/applications.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/applications.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -10,7 +10,9 @@ cdk-libio.jar cdk-libiocml.jar cdk-qsar.jar +cdk-qsarmolecular.jar cdk-render.jar cdk-standard.jar cdk-svg.jar cdk-smiles.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/atomtype.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/atomtype.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/atomtype.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,2 +1,2 @@ cdk-interfaces.jar - +cdk-core.jar Modified: trunk/cdk/src/META-INF/builder3d.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/builder3d.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/builder3d.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,5 +1,6 @@ cdk-core.jar cdk-data.jar +cdk-nonotify.jar cdk-extra.jar cdk-interfaces.jar cdk-io.jar Modified: trunk/cdk/src/META-INF/builder3dtools.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/builder3dtools.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/builder3dtools.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,5 +1,6 @@ cdk-core.jar cdk-data.jar +cdk-nonotify.jar cdk-extra.jar cdk-interfaces.jar cdk-io.jar Modified: trunk/cdk/src/META-INF/control.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/control.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/control.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -5,3 +5,5 @@ cdk-io.jar cdk-valencycheck.jar cdk-sdg.jar +cdk-atomtype.jar + Modified: trunk/cdk/src/META-INF/experimental.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/experimental.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/experimental.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -9,3 +9,5 @@ cdk-smiles.jar cdk-reaction.jar cdk-sdg.jar +cdk-atomtype.jar +cdk-smarts.jar Modified: trunk/cdk/src/META-INF/extra.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/extra.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/extra.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -6,3 +6,5 @@ cdk-render.jar cdk-standard.jar cdk-valencycheck.jar +cdk-atomtype.jar +cdk-formula.jar Modified: trunk/cdk/src/META-INF/forcefield.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/forcefield.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/forcefield.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -6,3 +6,5 @@ cdk-io.jar cdk-standard.jar cdk-charges.jar +cdk-extra.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/formula.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/formula.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/formula.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,4 +1,6 @@ cdk-core.jar cdk-extra.jar cdk-interfaces.jar -cdk-standard.jar \ No newline at end of file +cdk-standard.jar +cdk-data.jar + Modified: trunk/cdk/src/META-INF/io.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/io.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/io.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,3 +1,4 @@ cdk-interfaces.jar cdk-core.jar cdk-standard.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/libiomd.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/libiomd.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/libiomd.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,4 +1,6 @@ cdk-core.jar cdk-interfaces.jar +cdk-standard.jar cdk-data.jar cdk-libiocml.jar +cdk-io.jar Modified: trunk/cdk/src/META-INF/pcore.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/pcore.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/pcore.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -7,3 +7,4 @@ cdk-standard.jar cdk-valencycheck.jar cdk-smarts.jar +cdk-extra.jar Added: trunk/cdk/src/META-INF/progzjcp.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/progzjcp.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/progzjcp.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -0,0 +1,12 @@ +cdk-interfaces.jar +cdk-core.jar +cdk-standard.jar +cdk-render.jar +cdk-io.jar +cdk-valencycheck.jar +cdk-sdg.jar +cdk-atomtype.jar +cdk-data.jar +cdk-extra.jar +cdk-control.jar +cdk-render.jar Added: trunk/cdk/src/META-INF/progzjcp.libdepends =================================================================== --- trunk/cdk/src/META-INF/progzjcp.libdepends (rev 0) +++ trunk/cdk/src/META-INF/progzjcp.libdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -0,0 +1,2 @@ +vecmath1.2-1.14.jar + Modified: trunk/cdk/src/META-INF/qsaratomic.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsaratomic.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/qsaratomic.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -8,3 +8,4 @@ cdk-reaction.jar cdk-charges.jar cdk-qsar.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/qsarbond.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsarbond.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/qsarbond.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -8,3 +8,4 @@ cdk-reaction.jar cdk-charges.jar cdk-qsar.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/qsarmolecular.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsarmolecular.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/qsarmolecular.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -9,3 +9,6 @@ cdk-charges.jar cdk-qsar.jar cdk-qsaratomic.jar +cdk-atomtype.jar +cdk-smiles.jar +cdk-formula.jar Modified: trunk/cdk/src/META-INF/qsarprotein.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsarprotein.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/qsarprotein.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -8,3 +8,4 @@ cdk-reaction.jar cdk-charges.jar cdk-qsar.jar +cdk-pdb.jar Modified: trunk/cdk/src/META-INF/reaction.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/reaction.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/reaction.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,8 +1,10 @@ cdk-interfaces.jar cdk-data.jar +cdk-nonotify.jar cdk-core.jar cdk-standard.jar cdk-extra.jar cdk-libiocml.jar cdk-valencycheck.jar cdk-sdg.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/sdg.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/sdg.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/sdg.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -4,3 +4,5 @@ cdk-render.jar cdk-io.jar cdk-valencycheck.jar +cdk-atomtype.jar + Modified: trunk/cdk/src/META-INF/smarts.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/smarts.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/smarts.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -6,3 +6,4 @@ cdk-render.jar cdk-standard.jar cdk-valencycheck.jar +cdk-extra.jar Modified: trunk/cdk/src/META-INF/smiles.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/smiles.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/smiles.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,4 +1,5 @@ cdk-data.jar +cdk-nonotify.jar cdk-core.jar cdk-interfaces.jar cdk-io.jar @@ -6,3 +7,4 @@ cdk-standard.jar cdk-valencycheck.jar cdk-extra.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/standard.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/standard.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/standard.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -1,2 +1,3 @@ cdk-interfaces.jar cdk-core.jar +cdk-atomtype.jar Modified: trunk/cdk/src/META-INF/structgen.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/structgen.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/structgen.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -3,3 +3,5 @@ cdk-standard.jar cdk-nonotify.jar cdk-formula.jar +cdk-atomtype.jar +cdk-valencycheck.jar Added: trunk/cdk/src/META-INF/test.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/test.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -0,0 +1 @@ +cdk-interfaces.jar Modified: trunk/cdk/src/META-INF/valencycheck.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/valencycheck.cdkdepends 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/META-INF/valencycheck.cdkdepends 2008-02-25 10:31:08 UTC (rev 10231) @@ -2,3 +2,4 @@ cdk-core.jar cdk-io.jar cdk-standard.jar +cdk-atomtype.jar Modified: trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DHub.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DHub.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DHub.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -47,9 +47,10 @@ * * <p>FIXME: will replace the old Controller2D class. * - * @author egonw * @cdk.svnrev $Revision: 9162 $ - * @auther Niels Out + * @cdk.module progzjcp + * @author Niels Out + * @author egonw */ public class Controller2DHub implements IMouseEventRelay, IChemModelRelay { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleAddAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleAddAtom.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleAddAtom.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -47,9 +47,9 @@ /** * Adds an atom on the given location on mouseclick * - * @author Niels Out + * @author Niels Out * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp */ public class Controller2DModuleAddAtom implements IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleChangeFormalC.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleChangeFormalC.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleChangeFormalC.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -46,9 +46,9 @@ /** * Changes (Increases or Decreases) Formal Charge of an atom * - * @author Niels Out + * @author Niels Out * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp */ public class Controller2DModuleChangeFormalC implements IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleHighlight.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleHighlight.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleHighlight.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -34,7 +34,7 @@ * * @author Niels Out * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp */ public class Controller2DModuleHighlight implements IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleMove.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleMove.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleMove.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -49,7 +49,7 @@ * * @author Niels Out * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp */ public class Controller2DModuleMove implements IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleRemove.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleRemove.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/Controller2DModuleRemove.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -46,7 +46,7 @@ * * @author Niels Out * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp */ public class Controller2DModuleRemove implements IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/ExampleController2DModule.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/ExampleController2DModule.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/ExampleController2DModule.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -48,7 +48,7 @@ * * @author Niels Out * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp */ public class ExampleController2DModule implements IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/controller/IChemModelRelay.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/IChemModelRelay.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/IChemModelRelay.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -31,6 +31,9 @@ import org.openscience.cdk.renderer.progz.IJava2DRenderer; import org.openscience.cdk.interfaces.IChemModel; +/** + * @cdk.module progzjcp + */ public interface IChemModelRelay { public abstract IAtom getClosestAtom(Point2d worldCoord); Modified: trunk/cdk/src/main/org/openscience/cdk/controller/IController2DModule.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/controller/IController2DModule.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/controller/IController2DModule.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -35,7 +35,8 @@ * * @author egonw * @cdk.svnrev $Revision: 9162 $ - * + * @cdk.module progzjcp + * * @see Controller2DModel */ public interface IController2DModule { Modified: trunk/cdk/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/io/iterator/IteratingMDLConformerReader.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -39,7 +39,7 @@ * <p/> * </pre> * - * @cdk.module io + * @cdk.module extra * @cdk.svnrev $Revision: 9162 $ * @author Rajarshi Guha * @see org.openscience.cdk.ConformerContainer Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/GeometryToolsInternalCoordinates.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/GeometryToolsInternalCoordinates.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/GeometryToolsInternalCoordinates.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -54,8 +54,8 @@ * @author Ludovic Petain * @author Christian Hoppe * - * @cdk.module standard - * @cdk.svnrev $Revision: 9162 $ + * @cdk.module progzjcp + * @cdk.svnrev $Revision: 9162 $ */ public class GeometryToolsInternalCoordinates { Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/IJava2DRenderer.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/IJava2DRenderer.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/IJava2DRenderer.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -28,6 +28,9 @@ import org.openscience.cdk.renderer.ISimpleRenderer2D; +/** + * @cdk.module progzjcp + */ public interface IJava2DRenderer extends ISimpleRenderer2D { /** Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/JCPActionChangeMode.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/JCPActionChangeMode.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/JCPActionChangeMode.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -41,9 +41,9 @@ /** * JChemPaint menu actions * - * @author nielsout - * @cdk.module jchempaint - * @cdk.svnrev $Revision: 9162 $ + * @author nielsout + * @cdk.module jchempaint + * @cdk.svnrev $Revision: 9162 $ */ public class JCPActionChangeMode extends AbstractAction { Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/Java2DRenderer.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/Java2DRenderer.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/Java2DRenderer.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -68,8 +68,9 @@ /** * A Java2D based 2D renderer for IChemObjects. * - * @author nielsout - * @cdk.svnrev $Revision: 9162 $ + * @author nielsout + * @cdk.svnrev $Revision: 9162 $ + * @cdk.module progzjcp */ public class Java2DRenderer implements IJava2DRenderer { Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/SomeToolBar.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/SomeToolBar.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/SomeToolBar.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -56,9 +56,9 @@ * This class makes the JCPToolBar * *@author steinbeck - *@author nielsout (changes for java2D version) + *@author nielsout (changes for java2D version) * @cdk.module jchempaint - * @cdk.svnrev $Revision: 9162 $ + * @cdk.svnrev $Revision: 9162 $ */ public class SomeToolBar { Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestEditor.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestEditor.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestEditor.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -58,10 +58,10 @@ /** * Test class for testing the new Java2DRenderer and Controller2DHub. * - * @author nielsout - * @author egonw - * @cdk.module jchempaint - * @cdk.svnrev $Revision: 9162 $ + * @author nielsout + * @author egonw + * @cdk.module jchempaint + * @cdk.svnrev $Revision: 9162 $ */ public class TestEditor extends JPanel { Modified: trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestRenderer.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestRenderer.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/main/org/openscience/cdk/renderer/progz/TestRenderer.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -51,8 +51,9 @@ /** * Test class for testing the new Java2DRenderer. * - * @author nielsout + * @author nielsout * @cdk.svnrev $Revision: 9162 $ + * @cdk.module progzjcp */ public class TestRenderer extends JPanel { Modified: trunk/cdk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java =================================================================== --- trunk/cdk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java 2008-02-25 07:55:17 UTC (rev 10230) +++ trunk/cdk/src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java 2008-02-25 10:31:08 UTC (rev 10231) @@ -40,7 +40,7 @@ * It keeps track of the atom types which have been tested, to ensure * that all atom types are tested. * - * @cdk.module test + * @cdk.module test-atomtype */ abstract public class AbstractAtomTypeTest extends NewCDKTestCase { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-02-25 13:59:11
|
Revision: 10237 http://cdk.svn.sourceforge.net/cdk/?rev=10237&view=rev Author: egonw Date: 2008-02-25 05:58:06 -0800 (Mon, 25 Feb 2008) Log Message: ----------- Fixed last few dependency problems Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/META-INF/test-experimental.cdkdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2008-02-25 13:38:54 UTC (rev 10236) +++ trunk/cdk/build.xml 2008-02-25 13:58:06 UTC (rev 10237) @@ -503,11 +503,11 @@ <antcall target="compile-module"><param name="module" value="test-forcefield"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-valencycheck"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-charges"/><param name="source" value="${src}/test"/></antcall> - <antcall target="compile-module"><param name="module" value="test-experimental"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsar"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsaratomic"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsarbond"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsarmolecular"/><param name="source" value="${src}/test"/></antcall> + <antcall target="compile-module"><param name="module" value="test-experimental"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-qsarprotein"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-pdb"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-inchi"/><param name="source" value="${src}/test"/></antcall> Modified: trunk/cdk/src/META-INF/test-experimental.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-experimental.cdkdepends 2008-02-25 13:38:54 UTC (rev 10236) +++ trunk/cdk/src/META-INF/test-experimental.cdkdepends 2008-02-25 13:58:06 UTC (rev 10237) @@ -20,3 +20,5 @@ cdk-test.jar cdk-test-core.jar cdk-test-atomtype.jar +cdk-test-qsar.jar +cdk-test-qsarmolecular.jar This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-03-04 22:00:56
|
Revision: 10299 http://cdk.svn.sourceforge.net/cdk/?rev=10299&view=rev Author: egonw Date: 2008-03-04 14:00:17 -0800 (Tue, 04 Mar 2008) Log Message: ----------- Set up a new module to get this code well tested Modified Paths: -------------- trunk/cdk/build.xml trunk/cdk/src/META-INF/builder3d.cdkdepends trunk/cdk/src/META-INF/builder3dtools.cdkdepends trunk/cdk/src/META-INF/experimental.cdkdepends trunk/cdk/src/META-INF/extra.cdkdepends trunk/cdk/src/META-INF/pcore.cdkdepends trunk/cdk/src/META-INF/qsarmolecular.cdkdepends trunk/cdk/src/META-INF/reaction.cdkdepends trunk/cdk/src/META-INF/smarts.cdkdepends trunk/cdk/src/META-INF/test-extra.cdkdepends trunk/cdk/src/META-INF/test-pcore.cdkdepends trunk/cdk/src/META-INF/test-reaction.cdkdepends trunk/cdk/src/META-INF/test-smarts.cdkdepends trunk/cdk/src/META-INF/test-standard.cdkdepends trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java Added Paths: ----------- trunk/cdk/src/META-INF/isomorphism.cdkdepends trunk/cdk/src/META-INF/isomorphism.libdepends Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/build.xml 2008-03-04 22:00:17 UTC (rev 10299) @@ -459,6 +459,7 @@ <antcall target="compile-module"><param name="module" value="formula"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="structgen"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="pdb"/><param name="source" value="${src}/main"/></antcall> + <antcall target="compile-module"><param name="module" value="isomorphism"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="extra"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="smiles"/><param name="source" value="${src}/main"/></antcall> <antcall target="compile-module"><param name="module" value="libiocml"/><param name="source" value="${src}/main"/></antcall> Modified: trunk/cdk/src/META-INF/builder3d.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/builder3d.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/builder3d.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -10,3 +10,4 @@ cdk-forcefield.jar cdk-valencycheck.jar cdk-sdg.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/builder3dtools.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/builder3dtools.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/builder3dtools.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -11,3 +11,4 @@ cdk-valencycheck.jar cdk-sdg.jar cdk-smiles.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/experimental.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/experimental.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/experimental.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -12,3 +12,4 @@ cdk-atomtype.jar cdk-smarts.jar cdk-qsar.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/extra.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/extra.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/extra.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -8,3 +8,4 @@ cdk-valencycheck.jar cdk-atomtype.jar cdk-formula.jar +cdk-isomorphism.jar Added: trunk/cdk/src/META-INF/isomorphism.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/isomorphism.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/isomorphism.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -0,0 +1,4 @@ +cdk-interfaces.jar +cdk-core.jar +cdk-atomtype.jar +cdk-data.jar Added: trunk/cdk/src/META-INF/isomorphism.libdepends =================================================================== --- trunk/cdk/src/META-INF/isomorphism.libdepends (rev 0) +++ trunk/cdk/src/META-INF/isomorphism.libdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -0,0 +1,3 @@ +vecmath1.2-1.14.jar +log4j.jar +jgrapht-0.6.0.jar Modified: trunk/cdk/src/META-INF/pcore.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/pcore.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/pcore.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -8,3 +8,4 @@ cdk-valencycheck.jar cdk-smarts.jar cdk-extra.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/qsarmolecular.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/qsarmolecular.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/qsarmolecular.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -12,3 +12,4 @@ cdk-atomtype.jar cdk-smiles.jar cdk-formula.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/reaction.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/reaction.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/reaction.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -8,3 +8,4 @@ cdk-valencycheck.jar cdk-sdg.jar cdk-atomtype.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/smarts.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/smarts.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/smarts.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -7,3 +7,4 @@ cdk-standard.jar cdk-valencycheck.jar cdk-extra.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/test-extra.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-extra.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/test-extra.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -22,3 +22,4 @@ cdk-charges.jar cdk-test.jar cdk-formula.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/test-pcore.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-pcore.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/test-pcore.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -10,3 +10,4 @@ cdk-test.jar cdk-smarts.jar cdk-pcore.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/test-reaction.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-reaction.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/test-reaction.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -10,3 +10,4 @@ cdk-valencycheck.jar cdk-smiles.jar cdk-test.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/test-smarts.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-smarts.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/test-smarts.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -9,3 +9,4 @@ cdk-valencycheck.jar cdk-test.jar cdk-smarts.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/META-INF/test-standard.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-standard.cdkdepends 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/META-INF/test-standard.cdkdepends 2008-03-04 22:00:17 UTC (rev 10299) @@ -10,3 +10,4 @@ cdk-smiles.jar cdk-test.jar cdk-applications.jar +cdk-isomorphism.jar Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/IQueryAtomContainer.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -26,10 +26,10 @@ * General concept of a IAtomContainer aimed at doing molecular subgraph * queries using the UniversalIsomorphismTester. * - * @author egonw - * @cdk.module standard + * @author egonw + * @cdk.module interfaces * @cdk.svnrev $Revision: 9162 $ - * @see UniversalIsomorphismTester + * @see UniversalIsomorphismTester */ public interface IQueryAtomContainer extends IAtomContainer { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/InverseSymbolSetQueryAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -38,7 +38,7 @@ * @cdk.svnrev $Revision$ *@cdk.created 2004-09-16 *@see SymbolSetQueryAtom - *@cdk.module extra + *@cdk.module isomorphism */ public class InverseSymbolSetQueryAtom extends org.openscience.cdk.PseudoAtom implements IQueryAtom { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/OrderQueryBond.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -28,8 +28,8 @@ import org.openscience.cdk.CDKConstants; /** - * @cdk.module extra - * @cdk.svnrev $Revision$ + * @cdk.module isomorphism + * @cdk.svnrev $Revision$ */ public class OrderQueryBond extends org.openscience.cdk.Bond implements IQueryBond { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/QueryAtomContainer.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -28,7 +28,7 @@ import org.openscience.cdk.interfaces.IBond; /** - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ */ public class QueryAtomContainer extends org.openscience.cdk.AtomContainer implements IQueryAtomContainer { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolAndChargeQueryAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -26,7 +26,7 @@ import org.openscience.cdk.interfaces.IAtom; /** - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ */ public class SymbolAndChargeQueryAtom extends org.openscience.cdk.Atom implements IQueryAtom { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -26,7 +26,7 @@ import org.openscience.cdk.interfaces.IAtom; /** - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision: 9162 $ */ public class SymbolChargeIDQueryAtom extends org.openscience.cdk.Atom implements IQueryAtom { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -26,7 +26,7 @@ import org.openscience.cdk.interfaces.IAtom; /** - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ */ public class SymbolQueryAtom extends org.openscience.cdk.Atom implements IQueryAtom { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/SymbolSetQueryAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -38,7 +38,7 @@ * @cdk.svnrev $Revision$ *@cdk.created 2004-09-16 *@see InverseSymbolSetQueryAtom - *@cdk.module extra + *@cdk.module isomorphism */ public class SymbolSetQueryAtom extends org.openscience.cdk.PseudoAtom implements IQueryAtom { Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -28,7 +28,7 @@ /** * This matcher any Atom. * - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ * @cdk.keyword SMARTS */ Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -29,7 +29,7 @@ /** * This matches a bond of any order * - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ * @cdk.keyword SMARTS */ Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -30,7 +30,7 @@ * This matcher any aromatic atom. This assumes that aromaticity in the molecule * has been perceived. * - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ * @cdk.keyword SMARTS */ Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -30,7 +30,7 @@ /** * This matches an aromatic bond * - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ * @cdk.keyword SMARTS */ Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -29,7 +29,7 @@ /** * Abstract smarts atom * - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ * @cdk.keyword SMARTS */ Modified: trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java 2008-03-04 21:58:47 UTC (rev 10298) +++ trunk/cdk/src/main/org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java 2008-03-04 22:00:17 UTC (rev 10299) @@ -30,7 +30,7 @@ /** * Abstarct smarts bond * - * @cdk.module extra + * @cdk.module isomorphism * @cdk.svnrev $Revision$ * @cdk.keyword SMARTS */ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-03-04 22:01:54
|
Revision: 10300 http://cdk.svn.sourceforge.net/cdk/?rev=10300&view=rev Author: egonw Date: 2008-03-04 14:01:19 -0800 (Tue, 04 Mar 2008) Log Message: ----------- Set up a test module for 'isomorphism' Modified Paths: -------------- trunk/cdk/build.xml Added Paths: ----------- trunk/cdk/src/META-INF/test-isomorphism.cdkdepends trunk/cdk/src/META-INF/test-isomorphism.devellibdepends trunk/cdk/src/META-INF/test-isomorphism.libdepends trunk/cdk/src/test/org/openscience/cdk/IsomorphismCoverageTest.java trunk/cdk/src/test/org/openscience/cdk/modulesuites/MisomorphismTests.java Modified: trunk/cdk/build.xml =================================================================== --- trunk/cdk/build.xml 2008-03-04 22:00:17 UTC (rev 10299) +++ trunk/cdk/build.xml 2008-03-04 22:01:19 UTC (rev 10300) @@ -497,6 +497,7 @@ <antcall target="compile-module"><param name="module" value="test-nonotify"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-io"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-structgen"/><param name="source" value="${src}/test"/></antcall> + <antcall target="compile-module"><param name="module" value="test-isomorphism"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-extra"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-smiles"/><param name="source" value="${src}/test"/></antcall> <antcall target="compile-module"><param name="module" value="test-reaction"/><param name="source" value="${src}/test"/></antcall> Added: trunk/cdk/src/META-INF/test-isomorphism.cdkdepends =================================================================== --- trunk/cdk/src/META-INF/test-isomorphism.cdkdepends (rev 0) +++ trunk/cdk/src/META-INF/test-isomorphism.cdkdepends 2008-03-04 22:01:19 UTC (rev 10300) @@ -0,0 +1,6 @@ +cdk-interfaces.jar +cdk-core.jar +cdk-atomtype.jar +cdk-data.jar +cdk-test.jar +cdk-isomorphism.jar Added: trunk/cdk/src/META-INF/test-isomorphism.devellibdepends =================================================================== --- trunk/cdk/src/META-INF/test-isomorphism.devellibdepends (rev 0) +++ trunk/cdk/src/META-INF/test-isomorphism.devellibdepends 2008-03-04 22:01:19 UTC (rev 10300) @@ -0,0 +1,2 @@ +junit-4.3.1.jar + Added: trunk/cdk/src/META-INF/test-isomorphism.libdepends =================================================================== --- trunk/cdk/src/META-INF/test-isomorphism.libdepends (rev 0) +++ trunk/cdk/src/META-INF/test-isomorphism.libdepends 2008-03-04 22:01:19 UTC (rev 10300) @@ -0,0 +1,3 @@ +vecmath1.2-1.14.jar +log4j.jar +jgrapht-0.6.0.jar Added: trunk/cdk/src/test/org/openscience/cdk/IsomorphismCoverageTest.java =================================================================== --- trunk/cdk/src/test/org/openscience/cdk/IsomorphismCoverageTest.java (rev 0) +++ trunk/cdk/src/test/org/openscience/cdk/IsomorphismCoverageTest.java 2008-03-04 22:01:19 UTC (rev 10300) @@ -0,0 +1,56 @@ +/* $Revision: 7921 $ $Author: egonw $ $Date: 2007-02-09 00:35:55 +0100 (Fri, 09 Feb 2007) $ + * + * Copyright (C) 2004-2007 Egon Willighagen <eg...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk; + +import junit.framework.Test; +import junit.framework.TestSuite; + +/** + * TestSuite that uses tests whether all public methods in the core + * module are tested. Unlike Emma, it does not test that all code is + * tested, just all methods. + * + * @cdk.module test-isomorphism + */ +public class IsomorphismCoverageTest extends CoverageTest { + + private final static String CLASS_LIST = "isomorphism.javafiles"; + + public IsomorphismCoverageTest(String name) { + super(name); + } + + protected void setUp() throws Exception { + super.setUp(); + super.loadClassList(CLASS_LIST); + } + + public static Test suite() { + TestSuite suite = new TestSuite(); + suite.addTestSuite(IsomorphismCoverageTest.class); + return suite; + } + + public void testCoverage() { + assertTrue(super.runCoverageTest()); + } + +} Added: trunk/cdk/src/test/org/openscience/cdk/modulesuites/MisomorphismTests.java =================================================================== --- trunk/cdk/src/test/org/openscience/cdk/modulesuites/MisomorphismTests.java (rev 0) +++ trunk/cdk/src/test/org/openscience/cdk/modulesuites/MisomorphismTests.java 2008-03-04 22:01:19 UTC (rev 10300) @@ -0,0 +1,45 @@ +/* $Revision: 5867 $ $Author: egonw $ $Date: 2006-03-30 02:18:21 +0200 (Thu, 30 Mar 2006) $ + * + * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU Lesser General Public License + * as published by the Free Software Foundation; either version 2.1 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU Lesser General Public License for more details. + * + * You should have received a copy of the GNU Lesser General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.modulesuites; + +import junit.framework.JUnit4TestAdapter; +import junit.framework.Test; +import junit.framework.TestSuite; +import org.openscience.cdk.IsomorphismCoverageTest; + +/** + * TestSuite that runs all the tests for the CDK core module. + * + * @cdk.module test-isomorphism + * @cdk.depends log4j.jar + * @cdk.depends junit.jar + */ +public class MisomorphismTests { + + public static Test suite() { + TestSuite suite= new TestSuite("CDK isomorphism Tests"); + + suite.addTest(new JUnit4TestAdapter(IsomorphismCoverageTest.class)); + + return suite; + } + +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-03-11 13:55:06
|
Revision: 10352 http://cdk.svn.sourceforge.net/cdk/?rev=10352&view=rev Author: egonw Date: 2008-03-11 06:53:52 -0700 (Tue, 11 Mar 2008) Log Message: ----------- Moved weka to the right project Added Paths: ----------- trunk/cdk-gpl/jar/weka.jar Removed Paths: ------------- trunk/cdk/jar/weka.jar Deleted: trunk/cdk/jar/weka.jar =================================================================== (Binary files differ) Copied: trunk/cdk-gpl/jar/weka.jar (from rev 10351, trunk/cdk/jar/weka.jar) =================================================================== (Binary files differ) This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <eg...@us...> - 2008-03-11 14:28:56
|
Revision: 10354 http://cdk.svn.sourceforge.net/cdk/?rev=10354&view=rev Author: egonw Date: 2008-03-11 07:28:47 -0700 (Tue, 11 Mar 2008) Log Message: ----------- Moved another weka file Added Paths: ----------- trunk/cdk-gpl/src/main/org/openscience/cdk/libio/weka/Weka.java Removed Paths: ------------- trunk/cdk/src/main/org/openscience/cdk/libio/weka/Weka.java Deleted: trunk/cdk/src/main/org/openscience/cdk/libio/weka/Weka.java =================================================================== --- trunk/cdk/src/main/org/openscience/cdk/libio/weka/Weka.java 2008-03-11 14:27:00 UTC (rev 10353) +++ trunk/cdk/src/main/org/openscience/cdk/libio/weka/Weka.java 2008-03-11 14:28:47 UTC (rev 10354) @@ -1,366 +0,0 @@ -/* $Revision: 6228 $ $Author: egonw $ $Date: 2006-05-11 18:34:42 +0200 (Thu, 11 May 2006) $ - * - * Copyright (C) 2006-2007 Miguel Rojas-Cherto <mig...@us...> - * - * Contact: cdk...@li... - * - * This program is free software; you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation; either version 2 of the License, or - * (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along - * with this program; if not, write to the Free Software Foundation, Inc., - * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. - */ -package org.openscience.cdk.libio.weka; - -import weka.classifiers.Classifier; -import weka.core.Instance; -import weka.core.Instances; - -import java.io.*; -import java.util.Vector; - - -/** - * <p>Weka class is a library which use the program WEKA: a Machine Learning Project.</p> - * To inizalizate weka class is typically done like: <pre> - * Classifier lr = new LinearRegression(); - * weka.setDataset("/some/where/dataTraining.arff", lr); - * String testARFF = "/some/where/dataTest.arff"; - * double[] result = weka.getPrediction(testARFF); - * </pre> - * You have also the possibility to introduce directly values, done like: - * <pre> - * Classifier lr = new LinearRegression(); - * String[] attrib = {"X1","X2","X3","Y" }; - * int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC, }; - * weka.setDataset(attrib, typAttrib, y, x, lr); - * double[] resultY = weka.getPrediction(testX); - * </pre> - * - * @author Miguel Rojas - * @cdk.created 2006-05-23 - * @cdk.license GPL - * @cdk.module qsarweka - * @cdk.svnrev $Revision: 9162 $ - * @cdk.keyword weka, machine learning - * @cdk.depends weka.jar - */ -public class Weka { - - public static final int NUMERIC = 0; - public static final int NOMINAL = 1; - public static final int REGULAR = 2; - public static final int DATA = 3; - public static final int STRING = 4; - - /** type of classifier*/ - private Classifier classifier = null; - /** Class for handling an ordered set of weighted instances*/ - private Instances instances; - /**String with the attribut class*/ - private String[] classAttrib = null; - /** - * Constructor of the Weka - */ - public Weka() { - } - /** - * Set the file format arff to analize which contains the dataset and the type of classifier. - * The file is found into the src. - * - * @param pathTable Path of the dataset file format arff to train - * @param classifier Type of Classifier - * @return The Instances value - * @throws Exception - */ - public Instances setDatasetCDK(String pathTable, Object object) throws Exception{ - if (object instanceof Classifier) this.classifier = (Classifier) object; - InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathTable); - BufferedReader insr = new BufferedReader(new InputStreamReader(ins)); - this.classAttrib = extractClass(insr); - - ins = this.getClass().getClassLoader().getResourceAsStream(pathTable); - insr = new BufferedReader(new InputStreamReader(ins)); - return createInstance(insr); - - } - /** - * Set the file format arff to analize which contains the dataset and the type of classifier. - * - * - * @param pathTable Path of the dataset file format arff to train - * @param classifier Type of Classifier - * @return The Instances value - * @throws Exception - */ - public Instances setDataset(String pathTable, Object object) throws Exception{ - if (object instanceof Classifier) this.classifier = (Classifier) object; - BufferedReader insr = new BufferedReader(new FileReader(pathTable)); - this.classAttrib = extractClass(insr); - - insr = new BufferedReader(new FileReader(pathTable)); - return createInstance(insr); - - } - private Instances createInstance(BufferedReader insr) throws Exception{ - instances = new Instances(insr); - instances.setClassIndex(instances.numAttributes() - 1); - if (classifier != null) classifier.buildClassifier(instances); - return instances; - } - /** - * Extract the class name attribute manually from the file - * - * @param input The BufferedReader - * @return Array with the class attributes - */ - private String[] extractClass(BufferedReader input) { - Vector attribV = new Vector(); - String[] classAttrib = null; - String line; - try { - while ((line = input.readLine()) != null) { - if(line.startsWith("@attribute class {")){ - int strlen = line.length(); - String line_ = null; - out: - for (int i = 0; i < strlen; i++){ - switch(line.charAt(i)){ - case '{': - line_ = line.substring(i); - break out; - } - } - StringBuffer edited = new StringBuffer(); - strlen = line_.length(); - edited = new StringBuffer(); - for (int i = 0; i < strlen; i++){ - switch(line_.charAt(i)){ - case '"': - break; - case ',': - attribV.add(edited.toString()); - edited = new StringBuffer(); - break; - case '{': - break; - case '}': - attribV.add(edited.toString()); - break; - default: - edited.append(line_.charAt(i)); - } - } - - } - } - if(attribV.size() > 0){ - classAttrib = new String[attribV.size()]; - attribV.copyInto(classAttrib); - } - } catch (IOException e) { - e.printStackTrace(); - } - return classAttrib; - } - /** - * - * Set the array which contains the dataset and the type of classifier. This method - * will be used for classifier which work with numerical values. - * - * @param attrib String with the attribut names - * @param typAttrib Attribute type: NUMERICAL or NOMINAL. - * @param y An array containing the dependent variable. It is possible numeric or string. - * @param x An array of independent variables. The observations should be in the rows - * and the variables should be in the columns - * @param classifier Type of Classifier - * @return The Instances value - * @throws Exception - */ - public Instances setDataset(String[] attrib, int[] typAttrib, Object[]y, Object[][] x, Classifier classifier) throws Exception{ - return setDataset(attrib, typAttrib ,null,y,x,classifier); - } - /** - * - * Set the array which contains the dataset and the type of classifier.This method - * will be used for classifier which work with String values. - * - * @param attrib String with the attribut names. - * @param typAttrib Attribute type: NUMERICAL or NOMINAL. - * @param classAttrib String with the attribut class. - * @param y An array containing the dependent variable. It is possible numeric or string. - * @param x An array of independent variables. The observations should be in the rows - * and the variables should be in the columns - * @param classifier Type of classifier - * @return The Instances value - * @throws Exception - */ - public Instances setDataset(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, Object[][] x, Object object) throws Exception{ - if (object instanceof Classifier) this.classifier = (Classifier) object; - this.classAttrib = classAttrib; - Reader reader = createAttributes(attrib,typAttrib,classAttrib,y,x); - instances = new Instances(reader); - instances.setClassIndex(instances.numAttributes() - 1); - if (object instanceof Classifier) classifier.buildClassifier(instances); - return instances; - } - /** - * Return of the predicted value - * - * @param value An array of independent variables which contians the values with whose to test - * @return Result of the prediction - * @throws Exception - */ - public Object[] getPrediction(Object[][] value) throws Exception{ - Object[] object = new Object[value.length]; - for(int j = 0 ; j < value.length ; j++){ - Instance instance = new Instance(instances.numAttributes()); - instance.setDataset(instances); - for(int i = 0 ; i < value[0].length ; i++){ - if(instance.attribute(i).isNumeric()) - instance.setValue(i, ((Double)value[j][i]).doubleValue()); - else if(instance.attribute(i).isString()) - instance.setValue(i, ""+value[j][i]); - } - instance.setValue(value[0].length, 0.0); - double result = classifier.classifyInstance(instance); - if(classAttrib != null){ - object[j] = classAttrib[(new Double(result)).intValue()]; - } - else - object[j] = new Double(result); - } - return object; - } - /** - * Return of the predicted value. The file is found into src. - * - * @param pathARFF path of the file format arff which contians the values with whose to test. - * @return Result of the prediction. - * @throws Exception - */ - public Object[] getPredictionCDK(String pathARFF) throws Exception{ - InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathARFF); - Reader insr = new InputStreamReader(ins); - return createObjects(new BufferedReader(insr)); - } - - /** - * Return of the predicted value. - * - * @param pathARFF path of the file format arff which contians the values with whose to test. - * @return Result of the prediction. - * @throws Exception - */ - public Object[] getPrediction(String pathARFF) throws Exception{ - BufferedReader br = new BufferedReader(new FileReader(pathARFF)); - - return createObjects(br); - } - /** - * iniziate the object. - * - * @param br The BufferedReader - * @return An Array of objects: classAttrib and Double - * @throws Exception - */ - private Object[] createObjects(BufferedReader br) throws Exception{ - Instances test = new Instances(br); - Object[] object = new Object[test.numInstances()]; - for(int i = 0 ; i < test.numInstances(); i++){ - double result = classifier.classifyInstance(test.instance(i)); - if(classAttrib != null) - object[i] = classAttrib[(new Double(result)).intValue()]; - else - object[i] = new Double(result); - } - return object; - } - /** - * create a Reader with necessary attributes to iniziate a Instances for weka. - * - * @param attrib String with the attribut class - * @param typAttrib Attribute type: NOMINAL or NUMERIC. - * @param y An array containing the independent variable. - * @param x An array of dependent variables. - * @return The Reader containing the attributes - * @throws IOException - */ - private Reader createAttributes(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, Object[][] x) throws IOException{ - String string ="@relation table1 \n"; - for(int i = 0; i < attrib.length ; i++){ - string += ("@attribute "+attrib[i]); - if(typAttrib[i] == NUMERIC) - string += " numeric \n"; - else if(typAttrib[i] == NOMINAL) - string += " string \n"; - else if(typAttrib[i] == DATA) - string += " data \n"; - else if(typAttrib[i] == REGULAR) - string += " regular \n"; - else if(typAttrib[i] == STRING) - string += " string \n"; - } - - if(classAttrib != null){ - string += "@attribute class "; - string += "{"; - for(int i = 0; i < classAttrib.length ; i++){ - string += (classAttrib[i]); - if(i != classAttrib.length -1) - string += ","; - } - string += "}\n"; - } - - string += ("@data "); - if(x != null && y != null){ - for(int j = 0 ; j < x.length; j++){ - for(int i = 0 ; i < x[0].length ; i++){ - if (x[j][i] instanceof Double) { - if (((Double)x[j][i]).isNaN()) { - string += "?,"; - continue; - } - } - string += x[j][i]+","; - } - string += y[j]+ ", \n"; - } - } - if(x != null && y == null){ - for(int j = 0 ; j < x.length; j++){ - for(int i = 0 ; i < x[0].length ; i++){ - if (x[j][i] instanceof Double) { - if (((Double)x[j][i]).isNaN()) { - string += "?,"; - continue; - } - } - string += x[j][i]+","; - } - string += "\n"; - } - } - return (Reader)new StringReader(string); - } - - /** - * get the value which belongs this position in the classification - * @param result Position in the classification - * @return Real value - */ - /*private double[] getValue(double[] result) { - Instance instance = instances.instance(0); - instance.numClasses(); - return null; - }*/ -} Copied: trunk/cdk-gpl/src/main/org/openscience/cdk/libio/weka/Weka.java (from rev 10351, trunk/cdk/src/main/org/openscience/cdk/libio/weka/Weka.java) =================================================================== --- trunk/cdk-gpl/src/main/org/openscience/cdk/libio/weka/Weka.java (rev 0) +++ trunk/cdk-gpl/src/main/org/openscience/cdk/libio/weka/Weka.java 2008-03-11 14:28:47 UTC (rev 10354) @@ -0,0 +1,366 @@ +/* $Revision: 6228 $ $Author: egonw $ $Date: 2006-05-11 18:34:42 +0200 (Thu, 11 May 2006) $ + * + * Copyright (C) 2006-2007 Miguel Rojas-Cherto <mig...@us...> + * + * Contact: cdk...@li... + * + * This program is free software; you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation; either version 2 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along + * with this program; if not, write to the Free Software Foundation, Inc., + * 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + */ +package org.openscience.cdk.libio.weka; + +import weka.classifiers.Classifier; +import weka.core.Instance; +import weka.core.Instances; + +import java.io.*; +import java.util.Vector; + + +/** + * <p>Weka class is a library which use the program WEKA: a Machine Learning Project.</p> + * To inizalizate weka class is typically done like: <pre> + * Classifier lr = new LinearRegression(); + * weka.setDataset("/some/where/dataTraining.arff", lr); + * String testARFF = "/some/where/dataTest.arff"; + * double[] result = weka.getPrediction(testARFF); + * </pre> + * You have also the possibility to introduce directly values, done like: + * <pre> + * Classifier lr = new LinearRegression(); + * String[] attrib = {"X1","X2","X3","Y" }; + * int[] typAttrib = {Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC,Weka.NUMERIC, }; + * weka.setDataset(attrib, typAttrib, y, x, lr); + * double[] resultY = weka.getPrediction(testX); + * </pre> + * + * @author Miguel Rojas + * @cdk.created 2006-05-23 + * @cdk.license GPL + * @cdk.module qsarweka + * @cdk.svnrev $Revision: 9162 $ + * @cdk.keyword weka, machine learning + * @cdk.depends weka.jar + */ +public class Weka { + + public static final int NUMERIC = 0; + public static final int NOMINAL = 1; + public static final int REGULAR = 2; + public static final int DATA = 3; + public static final int STRING = 4; + + /** type of classifier*/ + private Classifier classifier = null; + /** Class for handling an ordered set of weighted instances*/ + private Instances instances; + /**String with the attribut class*/ + private String[] classAttrib = null; + /** + * Constructor of the Weka + */ + public Weka() { + } + /** + * Set the file format arff to analize which contains the dataset and the type of classifier. + * The file is found into the src. + * + * @param pathTable Path of the dataset file format arff to train + * @param classifier Type of Classifier + * @return The Instances value + * @throws Exception + */ + public Instances setDatasetCDK(String pathTable, Object object) throws Exception{ + if (object instanceof Classifier) this.classifier = (Classifier) object; + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathTable); + BufferedReader insr = new BufferedReader(new InputStreamReader(ins)); + this.classAttrib = extractClass(insr); + + ins = this.getClass().getClassLoader().getResourceAsStream(pathTable); + insr = new BufferedReader(new InputStreamReader(ins)); + return createInstance(insr); + + } + /** + * Set the file format arff to analize which contains the dataset and the type of classifier. + * + * + * @param pathTable Path of the dataset file format arff to train + * @param classifier Type of Classifier + * @return The Instances value + * @throws Exception + */ + public Instances setDataset(String pathTable, Object object) throws Exception{ + if (object instanceof Classifier) this.classifier = (Classifier) object; + BufferedReader insr = new BufferedReader(new FileReader(pathTable)); + this.classAttrib = extractClass(insr); + + insr = new BufferedReader(new FileReader(pathTable)); + return createInstance(insr); + + } + private Instances createInstance(BufferedReader insr) throws Exception{ + instances = new Instances(insr); + instances.setClassIndex(instances.numAttributes() - 1); + if (classifier != null) classifier.buildClassifier(instances); + return instances; + } + /** + * Extract the class name attribute manually from the file + * + * @param input The BufferedReader + * @return Array with the class attributes + */ + private String[] extractClass(BufferedReader input) { + Vector attribV = new Vector(); + String[] classAttrib = null; + String line; + try { + while ((line = input.readLine()) != null) { + if(line.startsWith("@attribute class {")){ + int strlen = line.length(); + String line_ = null; + out: + for (int i = 0; i < strlen; i++){ + switch(line.charAt(i)){ + case '{': + line_ = line.substring(i); + break out; + } + } + StringBuffer edited = new StringBuffer(); + strlen = line_.length(); + edited = new StringBuffer(); + for (int i = 0; i < strlen; i++){ + switch(line_.charAt(i)){ + case '"': + break; + case ',': + attribV.add(edited.toString()); + edited = new StringBuffer(); + break; + case '{': + break; + case '}': + attribV.add(edited.toString()); + break; + default: + edited.append(line_.charAt(i)); + } + } + + } + } + if(attribV.size() > 0){ + classAttrib = new String[attribV.size()]; + attribV.copyInto(classAttrib); + } + } catch (IOException e) { + e.printStackTrace(); + } + return classAttrib; + } + /** + * + * Set the array which contains the dataset and the type of classifier. This method + * will be used for classifier which work with numerical values. + * + * @param attrib String with the attribut names + * @param typAttrib Attribute type: NUMERICAL or NOMINAL. + * @param y An array containing the dependent variable. It is possible numeric or string. + * @param x An array of independent variables. The observations should be in the rows + * and the variables should be in the columns + * @param classifier Type of Classifier + * @return The Instances value + * @throws Exception + */ + public Instances setDataset(String[] attrib, int[] typAttrib, Object[]y, Object[][] x, Classifier classifier) throws Exception{ + return setDataset(attrib, typAttrib ,null,y,x,classifier); + } + /** + * + * Set the array which contains the dataset and the type of classifier.This method + * will be used for classifier which work with String values. + * + * @param attrib String with the attribut names. + * @param typAttrib Attribute type: NUMERICAL or NOMINAL. + * @param classAttrib String with the attribut class. + * @param y An array containing the dependent variable. It is possible numeric or string. + * @param x An array of independent variables. The observations should be in the rows + * and the variables should be in the columns + * @param classifier Type of classifier + * @return The Instances value + * @throws Exception + */ + public Instances setDataset(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, Object[][] x, Object object) throws Exception{ + if (object instanceof Classifier) this.classifier = (Classifier) object; + this.classAttrib = classAttrib; + Reader reader = createAttributes(attrib,typAttrib,classAttrib,y,x); + instances = new Instances(reader); + instances.setClassIndex(instances.numAttributes() - 1); + if (object instanceof Classifier) classifier.buildClassifier(instances); + return instances; + } + /** + * Return of the predicted value + * + * @param value An array of independent variables which contians the values with whose to test + * @return Result of the prediction + * @throws Exception + */ + public Object[] getPrediction(Object[][] value) throws Exception{ + Object[] object = new Object[value.length]; + for(int j = 0 ; j < value.length ; j++){ + Instance instance = new Instance(instances.numAttributes()); + instance.setDataset(instances); + for(int i = 0 ; i < value[0].length ; i++){ + if(instance.attribute(i).isNumeric()) + instance.setValue(i, ((Double)value[j][i]).doubleValue()); + else if(instance.attribute(i).isString()) + instance.setValue(i, ""+value[j][i]); + } + instance.setValue(value[0].length, 0.0); + double result = classifier.classifyInstance(instance); + if(classAttrib != null){ + object[j] = classAttrib[(new Double(result)).intValue()]; + } + else + object[j] = new Double(result); + } + return object; + } + /** + * Return of the predicted value. The file is found into src. + * + * @param pathARFF path of the file format arff which contians the values with whose to test. + * @return Result of the prediction. + * @throws Exception + */ + public Object[] getPredictionCDK(String pathARFF) throws Exception{ + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(pathARFF); + Reader insr = new InputStreamReader(ins); + return createObjects(new BufferedReader(insr)); + } + + /** + * Return of the predicted value. + * + * @param pathARFF path of the file format arff which contians the values with whose to test. + * @return Result of the prediction. + * @throws Exception + */ + public Object[] getPrediction(String pathARFF) throws Exception{ + BufferedReader br = new BufferedReader(new FileReader(pathARFF)); + + return createObjects(br); + } + /** + * iniziate the object. + * + * @param br The BufferedReader + * @return An Array of objects: classAttrib and Double + * @throws Exception + */ + private Object[] createObjects(BufferedReader br) throws Exception{ + Instances test = new Instances(br); + Object[] object = new Object[test.numInstances()]; + for(int i = 0 ; i < test.numInstances(); i++){ + double result = classifier.classifyInstance(test.instance(i)); + if(classAttrib != null) + object[i] = classAttrib[(new Double(result)).intValue()]; + else + object[i] = new Double(result); + } + return object; + } + /** + * create a Reader with necessary attributes to iniziate a Instances for weka. + * + * @param attrib String with the attribut class + * @param typAttrib Attribute type: NOMINAL or NUMERIC. + * @param y An array containing the independent variable. + * @param x An array of dependent variables. + * @return The Reader containing the attributes + * @throws IOException + */ + private Reader createAttributes(String[] attrib, int[] typAttrib, String[] classAttrib, Object[]y, Object[][] x) throws IOException{ + String string ="@relation table1 \n"; + for(int i = 0; i < attrib.length ; i++){ + string += ("@attribute "+attrib[i]); + if(typAttrib[i] == NUMERIC) + string += " numeric \n"; + else if(typAttrib[i] == NOMINAL) + string += " string \n"; + else if(typAttrib[i] == DATA) + string += " data \n"; + else if(typAttrib[i] == REGULAR) + string += " regular \n"; + else if(typAttrib[i] == STRING) + string += " string \n"; + } + + if(classAttrib != null){ + string += "@attribute class "; + string += "{"; + for(int i = 0; i < classAttrib.length ; i++){ + string += (classAttrib[i]); + if(i != classAttrib.length -1) + string += ","; + } + string += "}\n"; + } + + string += ("@data "); + if(x != null && y != null){ + for(int j = 0 ; j < x.length; j++){ + for(int i = 0 ; i < x[0].length ; i++){ + if (x[j][i] instanceof Double) { + if (((Double)x[j][i]).isNaN()) { + string += "?,"; + continue; + } + } + string += x[j][i]+","; + } + string += y[j]+ ", \n"; + } + } + if(x != null && y == null){ + for(int j = 0 ; j < x.length; j++){ + for(int i = 0 ; i < x[0].length ; i++){ + if (x[j][i] instanceof Double) { + if (((Double)x[j][i]).isNaN()) { + string += "?,"; + continue; + } + } + string += x[j][i]+","; + } + string += "\n"; + } + } + return (Reader)new StringReader(string); + } + + /** + * get the value which belongs this position in the classification + * @param result Position in the classification + * @return Real value + */ + /*private double[] getValue(double[] result) { + Instance instance = instances.instance(0); + instance.numClasses(); + return null; + }*/ +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |