[phenotips/ontologizer] ac3b54: - updated dependencies

GitHub noreply at github.com
Fri Jan 19 16:19:57 EST 2018


  Branch: refs/heads/master
  Home:   https://github.com/phenotips/ontologizer
  Commit: ac3b543f62021d7e1c2572fb19937d2ccd81eb23
      https://github.com/phenotips/ontologizer/commit/ac3b543f62021d7e1c2572fb19937d2ccd81eb23
  Author: Sergiu Dumitriu <sergiu at phenotips.org>
  Date:   2018-01-19 (Fri, 19 Jan 2018)

  Changed paths:
    M cmdline/pom.xml
    M cmdline/src/main/java/ontologizer/OntologizerCMD.java
    M cmdline/src/main/java/ontologizer/OntologizerMethodCompareCMD.java
    M cmdline/src/main/java/ontologizer/playground/AffyParseTest.java
    M cmdline/src/main/java/ontologizer/playground/GeneLister.java
    M cmdline/src/main/java/ontologizer/playground/HTTPTest.java
    M cmdline/src/main/java/ontologizer/playground/OverlapLister.java
    M cmdline/src/main/java/ontologizer/playground/SteffenExec.java
    M cmdline/src/main/java/ontologizer/playground/SubTermLister.java
    M cmdline/src/main/java/ontologizer/playground/SuperTermLister.java
    M cmdline/src/main/java/ontologizer/playground/affy/AffyParse.java
    M cmdline/src/main/java/ontologizer/sampling/SetConstructor.java
    M core/pom.xml
    M core/src/main/java/ontologizer/calculation/util/Gamma.java
    M core/src/main/java/ontologizer/enumeration/GOTermCounter.java
    M core/src/main/java/ontologizer/go/OBOParser.java
    M core/src/main/java/ontologizer/util/BareBonesBrowserLaunch.java
    M core/src/main/java/ontologizer/worksets/WorkSetLoadThread.java
    M core/src/main/java/sonumina/math/graph/DirectedGraph.java
    M gui/pom.xml
    M gui/src/main/java/ontologizer/gui/swt/AboutWindow.java
    M gui/src/main/java/ontologizer/gui/swt/ApplicationWindow.java
    M gui/src/main/java/ontologizer/gui/swt/FileCacheWindow.java
    M gui/src/main/java/ontologizer/gui/swt/GeneEditor.java
    M gui/src/main/java/ontologizer/gui/swt/GraphWindow.java
    M gui/src/main/java/ontologizer/gui/swt/HelpWindow.java
    M gui/src/main/java/ontologizer/gui/swt/ISimpleAction.java
    M gui/src/main/java/ontologizer/gui/swt/LogWindow.java
    M gui/src/main/java/ontologizer/gui/swt/MainWindow.java
    M gui/src/main/java/ontologizer/gui/swt/NewProjectWizard.java
    M gui/src/main/java/ontologizer/gui/swt/Ontologizer.java
    M gui/src/main/java/ontologizer/gui/swt/PreferencesWindow.java
    M gui/src/main/java/ontologizer/gui/swt/ProjectSettingsComposite.java
    M gui/src/main/java/ontologizer/gui/swt/ResultWindow.java
    M gui/src/main/java/ontologizer/gui/swt/WizardWindow.java
    M gui/src/main/java/ontologizer/gui/swt/WorkSetWindow.java
    M gui/src/main/java/ontologizer/gui/swt/cocao/CocoaUIEnhancer.java
    M gui/src/main/java/ontologizer/gui/swt/images/Images.java
    M gui/src/main/java/ontologizer/gui/swt/result/AbstractGOGraphGenerationThread.java
    M gui/src/main/java/ontologizer/gui/swt/result/AbstractResultComposite.java
    M gui/src/main/java/ontologizer/gui/swt/result/EnrichedGOTermsComposite.java
    M gui/src/main/java/ontologizer/gui/swt/result/EnrichedGOTermsResultHTMLWriter.java
    M gui/src/main/java/ontologizer/gui/swt/result/EnrichedGOTermsResultLatexWriter.java
    M gui/src/main/java/ontologizer/gui/swt/result/EnrichedGraphGenerationThread.java
    M gui/src/main/java/ontologizer/gui/swt/result/GraphGenerationThread.java
    M gui/src/main/java/ontologizer/gui/swt/result/IGraphAction.java
    M gui/src/main/java/ontologizer/gui/swt/result/ITableAction.java
    M gui/src/main/java/ontologizer/gui/swt/result/PValuesSVDGOTermsComposite.java
    M gui/src/main/java/ontologizer/gui/swt/result/ResultControls.java
    M gui/src/main/java/ontologizer/gui/swt/result/SVDGOTermsComposite.java
    M gui/src/main/java/ontologizer/gui/swt/result/SemanticSimilarityComposite.java
    M gui/src/main/java/ontologizer/gui/swt/result/SemanticSimilarityNatModel.java
    M gui/src/main/java/ontologizer/gui/swt/result/TermFilterSelectionComposite.java
    M gui/src/main/java/ontologizer/gui/swt/support/Chart.java
    M gui/src/main/java/ontologizer/gui/swt/support/FileGridCompositeWidgets.java
    M gui/src/main/java/ontologizer/gui/swt/support/FolderComposite.java
    M gui/src/main/java/ontologizer/gui/swt/support/GLCanvasExample.java
    M gui/src/main/java/ontologizer/gui/swt/support/GLGraphCanvas.java
    M gui/src/main/java/ontologizer/gui/swt/support/GraphCanvas.java
    M gui/src/main/java/ontologizer/gui/swt/support/GraphCanvasExample.java
    M gui/src/main/java/ontologizer/gui/swt/support/GraphPaint.java
    M gui/src/main/java/ontologizer/gui/swt/support/IGraphCanvas.java
    M gui/src/main/java/ontologizer/gui/swt/support/IGraphGenerationFinished.java
    M gui/src/main/java/ontologizer/gui/swt/support/IGraphGenerationSupport.java
    M gui/src/main/java/ontologizer/gui/swt/support/IMinimizedAdapter.java
    M gui/src/main/java/ontologizer/gui/swt/support/IRestoredAdapter.java
    M gui/src/main/java/ontologizer/gui/swt/support/NewGraphGenerationThread.java
    M gui/src/main/java/ontologizer/gui/swt/support/PGraphCanvas.java
    M gui/src/main/java/ontologizer/gui/swt/support/SWTUtil.java
    M gui/src/main/java/ontologizer/gui/swt/support/ScatterPlot.java
    M gui/src/main/java/ontologizer/gui/swt/support/SeparatorLine.java
    M gui/src/main/java/ontologizer/gui/swt/threads/AbortCalculationException.java
    M gui/src/main/java/ontologizer/gui/swt/threads/AbstractOntologizerThread.java
    M gui/src/main/java/ontologizer/gui/swt/threads/AnalyseThread.java
    M gui/src/main/java/ontologizer/gui/swt/threads/SimilarityThread.java
    M gui/src/main/java/tools/Sleak.java
    M tests/pom.xml
    M tests/src/test/java/att/grappa/TestGradient.java
    M tests/src/test/java/ontologizer/SmithWatermanTest.java
    M tests/src/test/java/ontologizer/association/AbstractByteLineScannerTest.java
    M tests/src/test/java/ontologizer/association/AssociationParserTest.java
    M tests/src/test/java/ontologizer/association/AssociationParserTest2.java
    M tests/src/test/java/ontologizer/association/AssociationTest.java
    M tests/src/test/java/ontologizer/calculation/Bayes2GOCalculationTest.java
    M tests/src/test/java/ontologizer/calculation/FixedAlphaBetaScoreTest.java
    M tests/src/test/java/ontologizer/calculation/ProbabilisticCalculationTest.java
    M tests/src/test/java/ontologizer/dotwriter/GODOTWriterTest.java
    M tests/src/test/java/ontologizer/go/DescriptionParserTest.java
    M tests/src/test/java/ontologizer/go/OBOParserTest.java
    M tests/src/test/java/ontologizer/go/OntologyTest.java
    M tests/src/test/java/ontologizer/go/ParsedContainerTest.java
    M tests/src/test/java/ontologizer/go/PrefixPoolTest.java
    M tests/src/test/java/ontologizer/go/TermContainerTest.java
    M tests/src/test/java/ontologizer/go/TermIDTest.java
    M tests/src/test/java/ontologizer/go/TermTest.java
    M tests/src/test/java/ontologizer/internal/InternalOntology.java
    M tests/src/test/java/ontologizer/sampling/KSubsetSamplerTest.java
    M tests/src/test/java/ontologizer/sampling/StudySetSamplerTest.java
    M tests/src/test/java/ontologizer/sampling/WeightedUrnTest.java
    M tests/src/test/java/ontologizer/sets/tests/StudySetTest.java
    M tests/src/test/java/ontologizer/statistics/tests/HypergeometricTest.java
    M tests/src/test/java/ontologizer/tests/PValueSetStoreSecondVersionTest.java
    M tests/src/test/java/ontologizer/tests/PValueSetStoreTest.java
    M tests/src/test/java/ontologizer/tests/StudySetTest.java
    M tests/src/test/java/ontologizer/types/tests/ByteStringTest.java
    M tests/src/test/java/sonumina/collections/FullStringIndexTest.java
    M tests/src/test/java/sonumina/collections/ReferencePoolTest.java
    M tests/src/test/java/sonumina/math/combinatorics/MultisetEnumeratorTest.java
    M tests/src/test/java/sonumina/math/combinatorics/SubsetGeneratorTest.java
    M tests/src/test/java/sonumina/math/graph/DirectedGraphLayoutTest.java
    M tests/src/test/java/sonumina/math/graph/DirectedGraphTest.java

  Log Message:
  -----------
  - updated dependencies
- applied codestyle
- updated deprecated code
- removed some dead code
- fixed resource leaks
- fixed other codestyle issues




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