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Added bursi and cpdb endpoints to DS.

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1 parent a5a33d6 commit 333fcf343b10f12458dc7e1c99a68c63dcda17d6 @olas committed Apr 22, 2010
Showing with 204,008 additions and 0 deletions.
  1. +14 −0 features/net.bioclipse.ds_feature/feature.xml
  2. BIN plugins/net.bioclipse.ds.bursi.signatures/.DS_Store
  3. +8 −0 plugins/net.bioclipse.ds.bursi.signatures/.classpath
  4. +28 −0 plugins/net.bioclipse.ds.bursi.signatures/.project
  5. +27 −0 plugins/net.bioclipse.ds.bursi.signatures/META-INF/MANIFEST.MF
  6. +12 −0 plugins/net.bioclipse.ds.bursi.signatures/build.properties
  7. +2,275 −0 plugins/net.bioclipse.ds.bursi.signatures/data/bursiSign_1.train.model
  8. +4,340 −0 plugins/net.bioclipse.ds.bursi.signatures/data/bursiSignsXYZ_1.tab
  9. +2,055 −0 plugins/net.bioclipse.ds.bursi.signatures/data/bursiSignsXYZ_1.txt.model
  10. +199 −0 plugins/net.bioclipse.ds.bursi.signatures/data/bursiSignsXYZ_1.txt.range
  11. BIN plugins/net.bioclipse.ds.bursi.signatures/icons/form.gif
  12. BIN plugins/net.bioclipse.ds.bursi.signatures/jars/libsvm.jar
  13. +1 −0 plugins/net.bioclipse.ds.bursi.signatures/permissions.properties
  14. +52 −0 plugins/net.bioclipse.ds.bursi.signatures/plugin.xml
  15. +69 −0 plugins/net.bioclipse.ds.bursi.signatures/src/net/bioclipse/ds/bursi/signatures/Activator.java
  16. +46 −0 plugins/net.bioclipse.ds.bursi.signatures/src/net/bioclipse/ds/bursi/signatures/DSTestsProperty.java
  17. +427 −0 plugins/net.bioclipse.ds.bursi.signatures/src/net/bioclipse/ds/bursi/signatures/SignSIgRunner.java
  18. +33 −0 ...ioclipse.ds.bursi.signatures/src/net/bioclipse/ds/bursi/signatures/SignSigPropertyCalculator.java
  19. +66 −0 ...ins/net.bioclipse.ds.bursi.signatures/src/net/bioclipse/ds/bursi/signatures/SignSigTestmodel.java
  20. BIN plugins/net.bioclipse.ds.cpdb.signatures/.DS_Store
  21. +8 −0 plugins/net.bioclipse.ds.cpdb.signatures/.classpath
  22. +28 −0 plugins/net.bioclipse.ds.cpdb.signatures/.project
  23. +23 −0 plugins/net.bioclipse.ds.cpdb.signatures/META-INF/MANIFEST.MF
  24. +9 −0 plugins/net.bioclipse.ds.cpdb.signatures/build.properties
  25. BIN plugins/net.bioclipse.ds.cpdb.signatures/data/.DS_Store
  26. +419 −0 plugins/net.bioclipse.ds.cpdb.signatures/data/cpdbasRatMmol_Sign1.train.scale.model
  27. BIN plugins/net.bioclipse.ds.cpdb.signatures/jars/libsvm.jar
  28. +28 −0 plugins/net.bioclipse.ds.cpdb.signatures/plugin.xml
  29. BIN plugins/net.bioclipse.ds.cpdb.signatures/src/.DS_Store
  30. BIN plugins/net.bioclipse.ds.cpdb.signatures/src/net/.DS_Store
  31. BIN plugins/net.bioclipse.ds.cpdb.signatures/src/net/bioclipse/.DS_Store
  32. BIN plugins/net.bioclipse.ds.cpdb.signatures/src/net/bioclipse/ds/.DS_Store
  33. BIN plugins/net.bioclipse.ds.cpdb.signatures/src/net/bioclipse/ds/cpdb/.DS_Store
  34. +52 −0 plugins/net.bioclipse.ds.cpdb.signatures/src/net/bioclipse/ds/cpdb/signatures/Activator.java
  35. +444 −0 plugins/net.bioclipse.ds.cpdb.signatures/src/net/bioclipse/ds/cpdb/signatures/CPDBSignSigRunner.java
  36. +44 −0 plugins/net.bioclipse.ds.cpdb.signatures/src/net/bioclipse/ds/cpdb/signatures/RGBMatch.java
  37. +7 −0 plugins/net.bioclipse.ds.cpdb/.classpath
  38. +28 −0 plugins/net.bioclipse.ds.cpdb/.project
  39. +18 −0 plugins/net.bioclipse.ds.cpdb/META-INF/MANIFEST.MF
  40. +4 −0 plugins/net.bioclipse.ds.cpdb/build.properties
  41. +150,090 −0 plugins/net.bioclipse.ds.cpdb/data/CPDBAS_CleanMMX-1.sdf
  42. +41,669 −0 plugins/net.bioclipse.ds.cpdb/data/cpdb-processed.sdf
  43. +21 −0 plugins/net.bioclipse.ds.cpdb/html/carcinogenicity.html
  44. BIN plugins/net.bioclipse.ds.cpdb/icons/db.gif
  45. BIN plugins/net.bioclipse.ds.cpdb/icons/form.gif
  46. BIN plugins/net.bioclipse.ds.cpdb/icons/poison.gif
  47. BIN plugins/net.bioclipse.ds.cpdb/icons/poll.gif
  48. +262 −0 plugins/net.bioclipse.ds.cpdb/plugin.xml
  49. +50 −0 plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/Activator.java
  50. +29 −0 plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/calc/CarcinogenicityConsensusCalculator.java
  51. +33 −0 plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/calc/ExactMatchCalculator.java
  52. +33 −0 plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/calc/NearestMatchCalculator.java
  53. +34 −0 plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/calc/SignaturesMatchCalculator.java
  54. +155 −0 plugins/net.bioclipse.ds.cpdb/src/net/bioclipse/ds/cpdb/impl/SignMatchImpl.java
  55. +7 −0 plugins/net.bioclipse.ds.cpdb/toc.xml
  56. +7 −0 plugins/net.bioclipse.ds.signatures.tests/.classpath
  57. +28 −0 plugins/net.bioclipse.ds.signatures.tests/.project
  58. +22 −0 plugins/net.bioclipse.ds.signatures.tests/META-INF/MANIFEST.MF
  59. +5 −0 plugins/net.bioclipse.ds.signatures.tests/build.properties
  60. +13 −0 plugins/net.bioclipse.ds.signatures.tests/plugin.xml
  61. +37 −0 plugins/net.bioclipse.ds.signatures.tests/src/net/bioclipse/ds/signatures/tests/APITest.java
  62. +51 −0 ...s.signatures.tests/src/net/bioclipse/ds/signatures/tests/AbstractSignaturesManagerPluginTest.java
  63. +40 −0 plugins/net.bioclipse.ds.signatures.tests/src/net/bioclipse/ds/signatures/tests/Activator.java
  64. +24 −0 ...se.ds.signatures.tests/src/net/bioclipse/ds/signatures/tests/AllSignaturesManagerPluginTests.java
  65. +24 −0 ...ioclipse.ds.signatures.tests/src/net/bioclipse/ds/signatures/tests/AllSignaturesManagerTests.java
  66. +35 −0 plugins/net.bioclipse.ds.signatures.tests/src/net/bioclipse/ds/signatures/tests/CoverageTest.java
  67. +23 −0 ...signatures.tests/src/net/bioclipse/ds/signatures/tests/JavaScriptSignaturesManagerPluginTest.java
  68. +23 −0 ...se.ds.signatures.tests/src/net/bioclipse/ds/signatures/tests/JavaSignaturesManagerPluginTest.java
  69. BIN plugins/net.bioclipse.ds.signatures/.DS_Store
  70. +8 −0 plugins/net.bioclipse.ds.signatures/.classpath
  71. +28 −0 plugins/net.bioclipse.ds.signatures/.project
  72. +21 −0 plugins/net.bioclipse.ds.signatures/META-INF/MANIFEST.MF
  73. +68 −0 plugins/net.bioclipse.ds.signatures/META-INF/spring/context.xml
  74. +6 −0 plugins/net.bioclipse.ds.signatures/build.properties
  75. BIN plugins/net.bioclipse.ds.signatures/jars/signatures-1.0-SNAPSHOT.jar
  76. +13 −0 plugins/net.bioclipse.ds.signatures/plugin.xml
  77. BIN plugins/net.bioclipse.ds.signatures/src/.DS_Store
  78. BIN plugins/net.bioclipse.ds.signatures/src/net/.DS_Store
  79. BIN plugins/net.bioclipse.ds.signatures/src/net/bioclipse/.DS_Store
  80. BIN plugins/net.bioclipse.ds.signatures/src/net/bioclipse/ds/.DS_Store
  81. BIN plugins/net.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/.DS_Store
  82. +105 −0 plugins/net.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/Activator.java
  83. +18 −0 ...ioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/IJavaScriptSignaturesManager.java
  84. +15 −0 .../net.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/IJavaSignaturesManager.java
  85. +82 −0 plugins/net.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/ISignaturesManager.java
  86. +116 −0 plugins/net.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/SignaturesManager.java
  87. +49 −0 ...et.bioclipse.ds.signatures/src/net/bioclipse/ds/signatures/business/SignaturesManagerFactory.java
@@ -58,4 +58,18 @@ The Eclipse Public License accompanies this distribution, and is available at ht
version="0.0.0"
unpack="false"/>
+ <plugin
+ id="net.bioclipse.ds.signatures"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
+ <plugin
+ id="net.bioclipse.ds.cpdb"
+ download-size="0"
+ install-size="0"
+ version="0.0.0"
+ unpack="false"/>
+
</feature>
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@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
+ <classpathentry kind="con" path="org.eclipse.pde.core.requiredPlugins"/>
+ <classpathentry kind="src" path="src"/>
+ <classpathentry exported="true" kind="lib" path="jars/libsvm.jar" sourcepath="net.bioclipse.ds.signsig.bursisrc.zip"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>net.bioclipse.ds.bursi.signatures</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.ManifestBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.pde.SchemaBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.pde.PluginNature</nature>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
@@ -0,0 +1,27 @@
+Manifest-Version: 1.0
+Bundle-ManifestVersion: 2
+Bundle-Name: Bursi Signature Significance
+Bundle-SymbolicName: net.bioclipse.ds.bursi.signatures;singleton:=true
+Bundle-Version: 2.2.0.RC3
+Bundle-Activator: net.bioclipse.ds.bursi.signatures.Activator
+Bundle-Vendor: The Bioclipse Team
+Require-Bundle: org.eclipse.ui,
+ org.eclipse.core.runtime,
+ net.bioclipse.ds;bundle-version="0.1.1",
+ net.bioclipse.core;bundle-version="2.0.0",
+ net.bioclipse.ui;bundle-version="2.0.0",
+ net.bioclipse.ui.business;bundle-version="2.0.0",
+ net.bioclipse.scripting;bundle-version="2.0.0",
+ net.bioclipse.scripting.ui;bundle-version="2.0.0",
+ net.bioclipse.cdk.smartsmatching;bundle-version="2.0.0",
+ net.bioclipse.cdk.business;bundle-version="2.0.0",
+ org.openscience.cdk.interfaces;bundle-version="1.2.2",
+ org.openscience.cdk.smarts;bundle-version="1.2.2",
+ org.openscience.cdk.core;bundle-version="1.2.2",
+ net.bioclipse.cdk.ui.sdfeditor;bundle-version="2.0.0",
+ net.bioclipse.ds.signatures;bundle-version="1.0.0"
+Bundle-RequiredExecutionEnvironment: J2SE-1.5
+Bundle-ActivationPolicy: lazy
+Import-Package: org.apache.log4j;version="1.2.15"
+Bundle-ClassPath: .,
+ jars/libsvm.jar
@@ -0,0 +1,12 @@
+source.. = src/
+output.. = bin/
+bin.includes = META-INF/,\
+ .,\
+ plugin.xml,\
+ jars/,\
+ jars/libsvm.jar,\
+ data/,\
+ exec/,\
+ icons/,\
+ permissions.properties
+source.. = src/
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@@ -0,0 +1 @@
+permissions.executable = exec/signatures-linux,exec/signatures-macosx
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<?eclipse version="3.4"?>
+<plugin>
+ <extension
+ point="net.bioclipse.decisionsupport">
+ <test
+ id="bursi.signatures"
+ name="Bursi Signature Significance"
+ class="net.bioclipse.ds.bursi.signatures.SignSIgRunner"
+ endpoint="net.bioclipse.ds.mutagenicity"
+ propertycalculator="Bursi Signature Significance"
+ reportmodel="net.bioclipse.ds.bursi.signatures.SignSigTestmodel">
+ </test>
+ </extension>
+
+
+ <extension
+ point="net.bioclipse.cdk.propertyCalculator">
+ <Calculator
+ class="net.bioclipse.ds.bursi.signatures.SignSigPropertyCalculator"
+ id="Bursi Signature Significance">
+ </Calculator>
+ </extension>
+
+ <extension
+ point="org.eclipse.ui.menus">
+ <menuContribution
+ locationURI="popup:net.bioclipse.ds.context?after=single">
+ <command
+ commandId="net.bioclipse.cdk.ui.sdfeditor.addProperty"
+ label="Bursi Signature Significance"
+ icon="icons/form.gif"
+ style="push">
+ <parameter
+ name="net.bioclipse.cdk.ui.sdfeditor.calculatorId"
+ value="Signature Significance">
+ </parameter>
+ <visibleWhen
+ checkEnabled="false">
+ <with
+ variable="activeEditor">
+ <instanceof
+ value="net.bioclipse.cdk.ui.sdfeditor.editor.MultiPageMoleculesEditorPart">
+ </instanceof>
+ </with>
+ </visibleWhen>
+ </command>
+ </menuContribution>
+ </extension>
+
+
+</plugin>
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