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Viewing all changes in revision 9.

Committer: Bazaar Package Importer
Author(s): Shaun Jackman
Date: 2011-03-21 16:34:04 UTC
mfrom: (1.2.3 upstream)
Revision ID: james.westby@ubuntu.com-20110321163404-l83x81gqlhr53l1q

Tags: 1.5.60-1

* New upstream release.
* Remove libjhdf5-java from the dependencies.

files added:
src/org/broad/igv/tools/parsers/GCTtoIGVConverter.java

src/org/broad/igv/tools/parsers/GeneToLocusHelper.java

files removed:
src/edu/mit/broad/picard/util/StringUtil.java

src/org/broad/igv/h5/H5Constants.java

src/org/broad/igv/h5/HDF5EntityCache.java

src/org/broad/igv/h5/HDF5LocalReader.java

src/org/broad/igv/h5/TestH5String.java

files modified:
.pc/01-build.xml/build.xml

build.xml

debian/changelog

debian/control

debian/patches/01-build.xml

igv_linux-64.sh

igv_linux.sh

igv_mac-intel.command

igv_mac-powerpc.sh

igv_win.bat

src/edu/mit/broad/picard/util/ArrayUtil.java

src/edu/mit/broad/picard/util/SequenceUtil.java

src/log4j.properties

src/org/broad/igv/IGVPreferences.java

src/org/broad/igv/PreferenceManager.java

src/org/broad/igv/das/DASFeatureSource.java

src/org/broad/igv/data/AbstractDataSource.java

src/org/broad/igv/data/ChromosomeData.java

src/org/broad/igv/data/HDFDataManager.java

src/org/broad/igv/data/IGVDataset.java

src/org/broad/igv/data/IGVDatasetParser.java

src/org/broad/igv/data/seg/SegmentedDataWriter.java

src/org/broad/igv/exceptions/DataLoadException.java

src/org/broad/igv/exceptions/ProbeMappingException.java

src/org/broad/igv/feature/AbstractFeature.java

src/org/broad/igv/feature/BasicFeature.java

src/org/broad/igv/feature/CytoBandFileParser.java

src/org/broad/igv/feature/Exon.java

src/org/broad/igv/feature/FeatureDB.java

src/org/broad/igv/feature/GFFParser.java

src/org/broad/igv/feature/GeneManager.java

src/org/broad/igv/feature/Genome.java

src/org/broad/igv/feature/GenomeImporter.java

src/org/broad/igv/feature/GenomeManager.java

src/org/broad/igv/feature/Locus.java

src/org/broad/igv/feature/dranger/DRangerFeature.java

src/org/broad/igv/h5/HDF5ReaderFactory.java

src/org/broad/igv/maf/MAFManager.java

src/org/broad/igv/maf/MAFRemoteReader.java

src/org/broad/igv/maf/conservation/OmegaDataSource.java

src/org/broad/igv/main/BatchRunner.java

src/org/broad/igv/main/CommandExecutor.java

src/org/broad/igv/renderer/BasicFeatureRenderer.java

src/org/broad/igv/sam/AbstractAlignment.java

src/org/broad/igv/sam/Alignment.java

src/org/broad/igv/sam/AlignmentDataManager.java

src/org/broad/igv/sam/AlignmentInterval.java

src/org/broad/igv/sam/AlignmentLoader.java

src/org/broad/igv/sam/AlignmentRenderer.java

src/org/broad/igv/sam/AlignmentTrack.java

src/org/broad/igv/sam/CoverageTrack.java

src/org/broad/igv/sam/DotAlignedAlignment.java

src/org/broad/igv/sam/EWigTrack.java

src/org/broad/igv/sam/FeatureWrappedAlignment.java

src/org/broad/igv/sam/ReadMate.java

src/org/broad/igv/sam/SamAlignment.java

src/org/broad/igv/sam/reader/BAMHttpQueryReader.java

src/org/broad/igv/sam/reader/CachingQueryReader.java

src/org/broad/igv/sam/reader/FeatureIndex.java

src/org/broad/igv/sam/reader/GeraldParser.java

src/org/broad/igv/sam/reader/GeraldQueryReader.java

src/org/broad/igv/sam/reader/SamQueryReaderFactory.java

src/org/broad/igv/sam/reader/SamQueryTextReader.java

src/org/broad/igv/sam/reader/SamUtils.java

src/org/broad/igv/session/Session.java

src/org/broad/igv/session/SessionReader.java

src/org/broad/igv/session/SessionWriter.java

src/org/broad/igv/session/ViewContext.java

src/org/broad/igv/tdf/TDFDataSource.java

src/org/broad/igv/tdf/TDFDataset.java

src/org/broad/igv/tdf/TDFReader.java

src/org/broad/igv/tools/IgvTools.java

src/org/broad/igv/tools/IgvToolsGui.java

src/org/broad/igv/track/AttributeManager.java

src/org/broad/igv/track/FeatureDirSource.java

src/org/broad/igv/track/FeatureTrack.java

src/org/broad/igv/track/IndexedBEDFeatureSource.java

src/org/broad/igv/track/TrackLoader.java

src/org/broad/igv/track/TrackManager.java

src/org/broad/igv/track/TrackMenuUtils.java

src/org/broad/igv/track/tribble/CachingFeatureReader.java

src/org/broad/igv/track/tribble/CodecFactory.java

src/org/broad/igv/track/tribble/TribbleFeatureSource.java

src/org/broad/igv/ui/IGVCommandBar.java

src/org/broad/igv/ui/IGVMainFrame.java

src/org/broad/igv/ui/PreferencesEditor.java

src/org/broad/igv/ui/PreferencesEditor.jfd

src/org/broad/igv/ui/ShutdownThread.java

src/org/broad/igv/ui/UIConstants.java

src/org/broad/igv/ui/action/FitDataToWindowMenuAction.java

src/org/broad/igv/ui/action/LoadFromServerAction.java

src/org/broad/igv/ui/action/LoadFromURLMenuAction.java

src/org/broad/igv/ui/action/OpenSessionMenuAction.java

src/org/broad/igv/ui/action/RegionsBaseMenuAction.java

src/org/broad/igv/ui/action/RemoveUserDefinedGenomeMenuAction.java

src/org/broad/igv/ui/action/SearchCommand.java

src/org/broad/igv/ui/util/FileChooserDialog.java

src/org/broad/igv/ui/util/GenericUtilities.java

src/org/broad/igv/util/FileUtils.java

src/org/broad/igv/util/LRUCache.java

src/org/broad/igv/util/MacroSnapshotAction.java

src/org/broad/igv/util/ParsingUtils.java

src/org/broad/igv/util/SeekableFileStream.java

src/org/broad/tribble/readers/BasicFeatureReader.java

src/resources/about.properties

Show diffs side-by-side

added added

removed removed

.pc/01-build.xml/build.xml

debian/changelog

debian/patches/01-build.xml

igv_linux-64.sh

igv_mac-intel.command

igv_mac-powerpc.sh

src/edu/mit/broad/picard/util/ArrayUtil.java

src/edu/mit/broad/picard/util/SequenceUtil.java

src/edu/mit/broad/picard/util/StringUtil.java

src/log4j.properties

src/org/broad/igv/IGVPreferences.java

src/org/broad/igv/PreferenceManager.java

src/org/broad/igv/das/DASFeatureSource.java

src/org/broad/igv/data/AbstractDataSource.java

src/org/broad/igv/data/ChromosomeData.java

src/org/broad/igv/data/HDFDataManager.java

src/org/broad/igv/data/IGVDataset.java

src/org/broad/igv/data/IGVDatasetParser.java

src/org/broad/igv/data/seg/SegmentedDataWriter.java

src/org/broad/igv/exceptions/DataLoadException.java

src/org/broad/igv/exceptions/ProbeMappingException.java

src/org/broad/igv/feature/AbstractFeature.java

src/org/broad/igv/feature/BasicFeature.java

src/org/broad/igv/feature/CytoBandFileParser.java

src/org/broad/igv/feature/Exon.java

src/org/broad/igv/feature/FeatureDB.java

src/org/broad/igv/feature/GFFParser.java

src/org/broad/igv/feature/GeneManager.java

src/org/broad/igv/feature/Genome.java

src/org/broad/igv/feature/GenomeImporter.java

src/org/broad/igv/feature/GenomeManager.java

src/org/broad/igv/feature/Locus.java

src/org/broad/igv/feature/dranger/DRangerFeature.java

src/org/broad/igv/h5/H5Constants.java

src/org/broad/igv/h5/HDF5EntityCache.java

src/org/broad/igv/h5/HDF5LocalReader.java

src/org/broad/igv/h5/HDF5ReaderFactory.java

src/org/broad/igv/h5/TestH5String.java

src/org/broad/igv/maf/MAFManager.java

src/org/broad/igv/maf/MAFRemoteReader.java

src/org/broad/igv/maf/conservation/OmegaDataSource.java

src/org/broad/igv/main/BatchRunner.java

src/org/broad/igv/main/CommandExecutor.java

src/org/broad/igv/renderer/BasicFeatureRenderer.java

src/org/broad/igv/sam/AbstractAlignment.java

src/org/broad/igv/sam/Alignment.java

src/org/broad/igv/sam/AlignmentDataManager.java

src/org/broad/igv/sam/AlignmentInterval.java

src/org/broad/igv/sam/AlignmentLoader.java

src/org/broad/igv/sam/AlignmentRenderer.java

src/org/broad/igv/sam/AlignmentTrack.java

src/org/broad/igv/sam/CoverageTrack.java

src/org/broad/igv/sam/DotAlignedAlignment.java

src/org/broad/igv/sam/EWigTrack.java

src/org/broad/igv/sam/FeatureWrappedAlignment.java

src/org/broad/igv/sam/ReadMate.java

src/org/broad/igv/sam/SamAlignment.java

src/org/broad/igv/sam/reader/BAMHttpQueryReader.java

src/org/broad/igv/sam/reader/CachingQueryReader.java

src/org/broad/igv/sam/reader/FeatureIndex.java

src/org/broad/igv/sam/reader/GeraldParser.java

src/org/broad/igv/sam/reader/GeraldQueryReader.java

src/org/broad/igv/sam/reader/SamQueryReaderFactory.java

src/org/broad/igv/sam/reader/SamQueryTextReader.java

src/org/broad/igv/sam/reader/SamUtils.java

src/org/broad/igv/session/Session.java

src/org/broad/igv/session/SessionReader.java

src/org/broad/igv/session/SessionWriter.java

src/org/broad/igv/session/ViewContext.java

src/org/broad/igv/tdf/TDFDataSource.java

src/org/broad/igv/tdf/TDFDataset.java

src/org/broad/igv/tdf/TDFReader.java

src/org/broad/igv/tools/IgvTools.java

src/org/broad/igv/tools/IgvToolsGui.java

src/org/broad/igv/tools/parsers/GCTtoIGVConverter.java

src/org/broad/igv/tools/parsers/GeneToLocusHelper.java

src/org/broad/igv/track/AttributeManager.java

src/org/broad/igv/track/FeatureDirSource.java

src/org/broad/igv/track/FeatureTrack.java

src/org/broad/igv/track/IndexedBEDFeatureSource.java

src/org/broad/igv/track/TrackLoader.java

src/org/broad/igv/track/TrackManager.java

src/org/broad/igv/track/TrackMenuUtils.java

src/org/broad/igv/track/tribble/CachingFeatureReader.java

src/org/broad/igv/track/tribble/CodecFactory.java

src/org/broad/igv/track/tribble/TribbleFeatureSource.java

src/org/broad/igv/ui/IGVCommandBar.java

src/org/broad/igv/ui/IGVMainFrame.java

src/org/broad/igv/ui/PreferencesEditor.java

src/org/broad/igv/ui/PreferencesEditor.jfd

src/org/broad/igv/ui/ShutdownThread.java

src/org/broad/igv/ui/UIConstants.java

src/org/broad/igv/ui/action/FitDataToWindowMenuAction.java

src/org/broad/igv/ui/action/LoadFromServerAction.java

src/org/broad/igv/ui/action/LoadFromURLMenuAction.java

src/org/broad/igv/ui/action/OpenSessionMenuAction.java

src/org/broad/igv/ui/action/RegionsBaseMenuAction.java

src/org/broad/igv/ui/action/RemoveUserDefinedGenomeMenuAction.java

src/org/broad/igv/ui/action/SearchCommand.java

src/org/broad/igv/ui/util/FileChooserDialog.java

src/org/broad/igv/ui/util/GenericUtilities.java

src/org/broad/igv/util/FileUtils.java

src/org/broad/igv/util/LRUCache.java

src/org/broad/igv/util/MacroSnapshotAction.java

src/org/broad/igv/util/ParsingUtils.java

src/org/broad/igv/util/SeekableFileStream.java

src/org/broad/tribble/readers/BasicFeatureReader.java

src/resources/about.properties

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