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Viewing all changes in revision 12.

Committer: Package Import Robot
Author(s): Shaun Jackman
Date: 2011-12-22 16:59:30 UTC
mfrom: (1.2.6)
Revision ID: package-import@ubuntu.com-20111222165930-4b3xz53pj44oqizf

Tags: 2.0.30-1

New upstream release.

files added:
lib/mysql-connector-java-3.1.14-bin.jar

src/org/broad/igv/data/db

src/org/broad/igv/data/db/SampleInfoSQLReader.java

src/org/broad/igv/data/db/SegmentedSQLReader.java

src/org/broad/igv/data/expression/ProbeToLocusMap.java

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

src/org/broad/igv/feature/genome/FastaSequence.java

src/org/broad/igv/feature/genome/FastaSequenceIndex.java

src/org/broad/igv/feature/genome/GenomeListItem.java

src/org/broad/igv/feature/genome/IGVSequence.java

src/org/broad/igv/feature/genome/Sequence.java

src/org/broad/igv/feature/genome/SequenceHelper.java

src/org/broad/igv/feature/genome/SequenceServletWrapper.java

src/org/broad/igv/feature/genome/ServletSequence.java

src/org/broad/igv/feature/tribble/VCFExample.java

src/org/broad/igv/feature/tribble/VCFWrapperCodec.java

src/org/broad/igv/gs/GSOpenSessionMenuAction.java

src/org/broad/igv/gs/GSSaveSessionMenuAction.java

src/org/broad/igv/gs/atm

src/org/broad/igv/gs/atm/ATMUtils.java

src/org/broad/igv/gs/atm/FileParameter.java

src/org/broad/igv/gs/atm/GSDataFormat.java

src/org/broad/igv/gs/atm/SubToolDescriptor.java

src/org/broad/igv/gs/atm/WebToolDescriptor.java

src/org/broad/igv/gs/dm

src/org/broad/igv/gs/dm/DMUtils.java

src/org/broad/igv/gs/dm/GSDataFormat.java

src/org/broad/igv/gs/dm/GSDirectoryListing.java

src/org/broad/igv/gs/dm/GSFileMetadata.java

src/org/broad/igv/hic

src/org/broad/igv/hic/ColorScale.java

src/org/broad/igv/hic/ColorScalePanel.java

src/org/broad/igv/hic/Context.java

src/org/broad/igv/hic/HeatmapPanel.java

src/org/broad/igv/hic/HeatmapRenderer.java

src/org/broad/igv/hic/HiCRulerPanel.java

src/org/broad/igv/hic/MainWindow.java

src/org/broad/igv/hic/MainWindow.jfd

src/org/broad/igv/hic/ThumbnailPanel.java

src/org/broad/igv/hic/data

src/org/broad/igv/hic/data/Block.java

src/org/broad/igv/hic/data/Chromosome.java

src/org/broad/igv/hic/data/ContactRecord.java

src/org/broad/igv/hic/data/ContactRecordCodec.java

src/org/broad/igv/hic/data/Dataset.java

src/org/broad/igv/hic/data/DatasetReader.java

src/org/broad/igv/hic/data/Matrix.java

src/org/broad/igv/hic/data/MatrixZoomData.java

src/org/broad/igv/hic/data/binary_file_layout.txt

src/org/broad/igv/hic/tools

src/org/broad/igv/hic/tools/AlignmentPair.java

src/org/broad/igv/hic/tools/AlignmentsSorter.java

src/org/broad/igv/hic/tools/AsciiPairIterator.java

src/org/broad/igv/hic/tools/BAMPairIterator.java

src/org/broad/igv/hic/tools/HiCTools.java

src/org/broad/igv/hic/tools/PairIterator.java

src/org/broad/igv/hic/tools/Preprocessor.java

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

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

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

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

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

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

src/org/broad/igv/util/converters

src/org/broad/igv/util/converters/DensitiesToBedGraph.java

src/org/broad/igv/util/converters/TarjeiToBedgraph.java

src/org/broad/igv/util/stream/IGVUrlHelper.java

src/org/broad/igv/variant

src/org/broad/igv/variant/Allele.java

src/org/broad/igv/variant/Genotype.java

src/org/broad/igv/variant/Variant.java

src/org/broad/igv/variant/VariantMenu.java

src/org/broad/igv/variant/VariantRenderer.java

src/org/broad/igv/variant/VariantTrack.java

src/org/broad/igv/variant/util

src/org/broad/igv/variant/util/AutismUtils.java

src/org/broad/igv/variant/util/PedigreeUtils.java

src/org/broad/igv/variant/util/VCFtoBed.java

src/org/broad/igv/variant/vcf

src/org/broad/igv/variant/vcf/VCFAllele.java

src/org/broad/igv/variant/vcf/VCFGenotype.java

src/org/broad/igv/variant/vcf/VCFVariant.java

src/org/broad/tribble/dbsnp/OldDbSNPCodec.java

src/org/broad/tribble/dbsnp/OldDbSNPFeature.java

src/org/broad/tribble/example/ProfileIndexReading.java

src/org/broad/tribble/source/PerformanceLoggingFeatureSource.java

files removed:
src/org/broad/igv/data/HDFDataManager.java

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

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

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

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

src/org/broad/igv/h5

src/org/broad/igv/h5/DataAccessException.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/HDF5Reader.java

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

src/org/broad/igv/h5/HDF5RemoteReader.java

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

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

src/org/broad/igv/remote

src/org/broad/igv/remote/HTTPConnectionTests.java

src/org/broad/igv/remote/SequenceServletWrapper.java

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

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

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

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

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

src/org/broad/igv/util/ftp

src/org/broad/igv/util/ftp/FTPClient.java

src/org/broad/igv/util/ftp/FTPReply.java

src/org/broad/igv/util/ftp/FTPStream.java

src/org/broad/igv/util/ftp/FTPUtils.java

src/org/broad/igv/util/stream/ApacheURLHelper.java

src/org/broad/igv/vcf

src/org/broad/igv/vcf/AutismUtils.java

src/org/broad/igv/vcf/PedigreeUtils.java

src/org/broad/igv/vcf/TrackMenu.java

src/org/broad/igv/vcf/VCFMenu.java

src/org/broad/igv/vcf/VCFRenderer.java

src/org/broad/igv/vcf/VCFTools.java

src/org/broad/igv/vcf/VCFTrack.java

src/org/broad/igv/vcf/VCFtoBed.java

src/org/broad/igv/vcf/Variant.java

src/org/broad/igv/vcf/VariantInfoDialog.form

src/org/broad/igv/vcf/VariantInfoDialog.java

src/org/broad/tribble/dbsnp/DbSNPCodec.java

src/org/broad/tribble/dbsnp/DbSNPFeature.java

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

debian/changelog

debian/patches/01-build.xml

lib/vcf.jar

src/org/broad/igv/Globals.java

src/org/broad/igv/IGVPreferences.java

src/org/broad/igv/PreferenceManager.java

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

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

src/org/broad/igv/batch/CommandListener.java

src/org/broad/igv/batch/TestClient.java

src/org/broad/igv/bbfile/BBFileReader.java

src/org/broad/igv/bbfile/BPTree.java

src/org/broad/igv/bbfile/BPTreeLeafNodeItem.java

src/org/broad/igv/bbfile/BedFeature.java

src/org/broad/igv/bbfile/BigBedIterator.java

src/org/broad/igv/bbfile/RPTreeLeafNode.java

src/org/broad/igv/bigwig/BigWigDataSource.java

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

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

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

src/org/broad/igv/data/rnai/RNAIGCTDatasetParser.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/genome/GenomeDescriptor.java

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

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

src/org/broad/igv/feature/genome/GenomeZipDescriptor.java

src/org/broad/igv/feature/tribble/BEDCodec.java

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

src/org/broad/igv/feature/tribble/GFFCodec.java

src/org/broad/igv/feature/tribble/PSLCodec.java

src/org/broad/igv/feature/tribble/REPMaskCodec.java

src/org/broad/igv/feature/tribble/SAMCodec.java

src/org/broad/igv/goby/GobyAlignment.java

src/org/broad/igv/gs/GSFileBrowser.java

src/org/broad/igv/gs/GSFileBrowser.jfd

src/org/broad/igv/gs/GSUtils.java

src/org/broad/igv/lists/GeneListManagerUI.java

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

src/org/broad/igv/peaks/BedToPeaks.java

src/org/broad/igv/peaks/PeakCodec.java

src/org/broad/igv/peaks/PeakCommandBar.java

src/org/broad/igv/peaks/PeakCommandBar.jfd

src/org/broad/igv/peaks/PeakParser.java

src/org/broad/igv/peaks/PeakRenderer.java

src/org/broad/igv/peaks/PeakTrack.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/session/Persistable.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/tdf/Accumulator.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/track/TrackGroup.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/TrackProperties.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/event/GlobalKeyDispatcher.java

src/org/broad/igv/ui/panel/AttributeHeaderPanel.java

src/org/broad/igv/ui/panel/AttributePanel.java

src/org/broad/igv/ui/panel/DataPanel.java

src/org/broad/igv/ui/panel/DataPanelContainer.java

src/org/broad/igv/ui/panel/DataPanelLayout.java

src/org/broad/igv/ui/panel/DataPanelPainter.java

src/org/broad/igv/ui/panel/MainPanel.java

src/org/broad/igv/ui/panel/RegionNavigatorDialog.java

src/org/broad/igv/ui/panel/RegionOfInterestPanel.java

src/org/broad/igv/ui/panel/RulerPanel.java

src/org/broad/igv/ui/panel/TrackNamePanel.java

src/org/broad/igv/ui/panel/TrackPanel.java

src/org/broad/igv/ui/panel/TrackPanelComponent.java

src/org/broad/igv/ui/panel/TrackPanelScrollPane.java

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

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

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

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

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

src/org/broad/igv/util/LoginDialog.jfd

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

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

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

src/org/broad/igv/util/TestS3Access.java

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

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

src/org/broad/igv/util/stream/IGVSeekableStreamFactory.java

src/org/broad/igv/util/stream/SeekableFTPStreamHelper.java

src/org/broad/igv/util/stream/SeekablePicardHTTPStream.java

src/org/broad/igv/util/stream/SeekableServiceStream.java

src/org/broad/igv/util/stream/SeekableSplitStream.java

src/org/broad/tribble/AbstractFeatureCodec.java

src/org/broad/tribble/Feature.java

src/org/broad/tribble/FeatureCodec.java

src/org/broad/tribble/bed/BEDCodec.java

src/org/broad/tribble/example/CountRecords.java

src/org/broad/tribble/example/IndexToTable.java

src/org/broad/tribble/gelitext/GeliTextCodec.java

src/org/broad/tribble/index/AbstractIndex.java

src/org/broad/tribble/index/Index.java

src/org/broad/tribble/index/IndexFactory.java

src/org/broad/tribble/index/interval/IntervalTreeIndex.java

src/org/broad/tribble/index/linear/LinearIndex.java

src/org/broad/tribble/index/linear/LinearIndexCreator.java

src/org/broad/tribble/source/BasicFeatureSource.java

src/org/broad/tribble/source/query/AsciiQuerySource.java

src/org/broad/tribble/source/query/IndexFreeAsciiQuerySource.java

src/org/broad/tribble/source/tabix/TabixReader.java

src/org/broad/tribble/util/LittleEndianInputStream.java

src/org/broad/tribble/util/LittleEndianOutputStream.java

src/org/broad/tribble/util/SeekableBufferedStream.java

src/org/broad/tribble/util/SeekableFTPStreamHelper.java

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

src/org/broad/tribble/util/SeekableHTTPStream.java

src/org/broad/tribble/util/ftp/FTPClient.java

src/org/broad/tribble/util/ftp/FTPReply.java

src/org/broad/tribble/util/ftp/FTPUtils.java

src/resources/about.properties

src/resources/codonTable.txt

Show diffs side-by-side

added added

removed removed

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

debian/changelog

debian/patches/01-build.xml

lib/mysql-connector-java-3.1.14-bin.jar

src/org/broad/igv/Globals.java

src/org/broad/igv/IGVPreferences.java

src/org/broad/igv/PreferenceManager.java

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

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

src/org/broad/igv/batch/CommandListener.java

src/org/broad/igv/batch/TestClient.java

src/org/broad/igv/bbfile/BBFileReader.java

src/org/broad/igv/bbfile/BPTree.java

src/org/broad/igv/bbfile/BPTreeLeafNodeItem.java

src/org/broad/igv/bbfile/BedFeature.java

src/org/broad/igv/bbfile/BigBedIterator.java

src/org/broad/igv/bbfile/RPTreeLeafNode.java

src/org/broad/igv/bigwig/BigWigDataSource.java

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

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

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

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

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

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

src/org/broad/igv/data/db/

src/org/broad/igv/data/db/SampleInfoSQLReader.java

src/org/broad/igv/data/db/SegmentedSQLReader.java

src/org/broad/igv/data/expression/ProbeToLocusMap.java

src/org/broad/igv/data/rnai/RNAIGCTDatasetParser.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/genome/FastaSequence.java

src/org/broad/igv/feature/genome/FastaSequenceIndex.java

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

src/org/broad/igv/feature/genome/GenomeDescriptor.java

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

src/org/broad/igv/feature/genome/GenomeListItem.java

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

src/org/broad/igv/feature/genome/GenomeZipDescriptor.java

src/org/broad/igv/feature/genome/IGVSequence.java

src/org/broad/igv/feature/genome/Sequence.java

src/org/broad/igv/feature/genome/SequenceHelper.java

src/org/broad/igv/feature/genome/SequenceServletWrapper.java

src/org/broad/igv/feature/genome/ServletSequence.java

src/org/broad/igv/feature/tribble/BEDCodec.java

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

src/org/broad/igv/feature/tribble/GFFCodec.java

src/org/broad/igv/feature/tribble/PSLCodec.java

src/org/broad/igv/feature/tribble/REPMaskCodec.java

src/org/broad/igv/feature/tribble/SAMCodec.java

src/org/broad/igv/feature/tribble/VCFExample.java

src/org/broad/igv/feature/tribble/VCFWrapperCodec.java

src/org/broad/igv/goby/GobyAlignment.java

src/org/broad/igv/gs/GSFileBrowser.java

src/org/broad/igv/gs/GSFileBrowser.jfd

src/org/broad/igv/gs/GSOpenSessionMenuAction.java

src/org/broad/igv/gs/GSSaveSessionMenuAction.java

src/org/broad/igv/gs/GSUtils.java

src/org/broad/igv/gs/atm/

src/org/broad/igv/gs/atm/ATMUtils.java

src/org/broad/igv/gs/atm/FileParameter.java

src/org/broad/igv/gs/atm/GSDataFormat.java

src/org/broad/igv/gs/atm/SubToolDescriptor.java

src/org/broad/igv/gs/atm/WebToolDescriptor.java

src/org/broad/igv/gs/dm/

src/org/broad/igv/gs/dm/DMUtils.java

src/org/broad/igv/gs/dm/GSDataFormat.java

src/org/broad/igv/gs/dm/GSDirectoryListing.java

src/org/broad/igv/gs/dm/GSFileMetadata.java

src/org/broad/igv/h5/

src/org/broad/igv/h5/DataAccessException.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/HDF5Reader.java

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

src/org/broad/igv/h5/HDF5RemoteReader.java

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

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

src/org/broad/igv/hic/

src/org/broad/igv/hic/ColorScale.java

src/org/broad/igv/hic/ColorScalePanel.java

src/org/broad/igv/hic/Context.java

src/org/broad/igv/hic/HeatmapPanel.java

src/org/broad/igv/hic/HeatmapRenderer.java

src/org/broad/igv/hic/HiCRulerPanel.java

src/org/broad/igv/hic/MainWindow.java

src/org/broad/igv/hic/MainWindow.jfd

src/org/broad/igv/hic/ThumbnailPanel.java

src/org/broad/igv/hic/data/

src/org/broad/igv/hic/data/Block.java

src/org/broad/igv/hic/data/Chromosome.java

src/org/broad/igv/hic/data/ContactRecord.java

src/org/broad/igv/hic/data/ContactRecordCodec.java

src/org/broad/igv/hic/data/Dataset.java

src/org/broad/igv/hic/data/DatasetReader.java

src/org/broad/igv/hic/data/Matrix.java

src/org/broad/igv/hic/data/MatrixZoomData.java

src/org/broad/igv/hic/data/binary_file_layout.txt

src/org/broad/igv/hic/tools/

src/org/broad/igv/hic/tools/AlignmentPair.java

src/org/broad/igv/hic/tools/AlignmentsSorter.java

src/org/broad/igv/hic/tools/AsciiPairIterator.java

src/org/broad/igv/hic/tools/BAMPairIterator.java

src/org/broad/igv/hic/tools/HiCTools.java

src/org/broad/igv/hic/tools/PairIterator.java

src/org/broad/igv/hic/tools/Preprocessor.java

src/org/broad/igv/lists/GeneListManagerUI.java

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

src/org/broad/igv/peaks/BedToPeaks.java

src/org/broad/igv/peaks/PeakCodec.java

src/org/broad/igv/peaks/PeakCommandBar.java

src/org/broad/igv/peaks/PeakCommandBar.jfd

src/org/broad/igv/peaks/PeakParser.java

src/org/broad/igv/peaks/PeakRenderer.java

src/org/broad/igv/peaks/PeakTrack.java

src/org/broad/igv/remote/

src/org/broad/igv/remote/HTTPConnectionTests.java

src/org/broad/igv/remote/SequenceServletWrapper.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/session/Persistable.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/tdf/Accumulator.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/track/TrackGroup.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/TrackProperties.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/event/GlobalKeyDispatcher.java

src/org/broad/igv/ui/panel/AttributeHeaderPanel.java

src/org/broad/igv/ui/panel/AttributePanel.java

src/org/broad/igv/ui/panel/DataPanel.java

src/org/broad/igv/ui/panel/DataPanelContainer.java

src/org/broad/igv/ui/panel/DataPanelLayout.java

src/org/broad/igv/ui/panel/DataPanelPainter.java

src/org/broad/igv/ui/panel/MainPanel.java

src/org/broad/igv/ui/panel/RegionNavigatorDialog.java

src/org/broad/igv/ui/panel/RegionOfInterestPanel.java

src/org/broad/igv/ui/panel/RulerPanel.java

src/org/broad/igv/ui/panel/TrackNamePanel.java

src/org/broad/igv/ui/panel/TrackPanel.java

src/org/broad/igv/ui/panel/TrackPanelComponent.java

src/org/broad/igv/ui/panel/TrackPanelScrollPane.java

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

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

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

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

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

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

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

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

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

src/org/broad/igv/util/LoginDialog.jfd

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

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

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

src/org/broad/igv/util/TestS3Access.java

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

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

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

src/org/broad/igv/util/converters/

src/org/broad/igv/util/converters/DensitiesToBedGraph.java

src/org/broad/igv/util/converters/TarjeiToBedgraph.java

src/org/broad/igv/util/ftp/

src/org/broad/igv/util/ftp/FTPClient.java

src/org/broad/igv/util/ftp/FTPReply.java

src/org/broad/igv/util/ftp/FTPStream.java

src/org/broad/igv/util/ftp/FTPUtils.java

src/org/broad/igv/util/stream/ApacheURLHelper.java

src/org/broad/igv/util/stream/IGVSeekableStreamFactory.java

src/org/broad/igv/util/stream/IGVUrlHelper.java

src/org/broad/igv/util/stream/SeekableFTPStreamHelper.java

src/org/broad/igv/util/stream/SeekablePicardHTTPStream.java

src/org/broad/igv/util/stream/SeekableServiceStream.java

src/org/broad/igv/util/stream/SeekableSplitStream.java

src/org/broad/igv/variant/

src/org/broad/igv/variant/Allele.java

src/org/broad/igv/variant/Genotype.java

src/org/broad/igv/variant/Variant.java

src/org/broad/igv/variant/VariantMenu.java

src/org/broad/igv/variant/VariantRenderer.java

src/org/broad/igv/variant/VariantTrack.java

src/org/broad/igv/variant/util/

src/org/broad/igv/variant/util/AutismUtils.java

src/org/broad/igv/variant/util/PedigreeUtils.java

src/org/broad/igv/variant/util/VCFtoBed.java

src/org/broad/igv/variant/vcf/

src/org/broad/igv/variant/vcf/VCFAllele.java

src/org/broad/igv/variant/vcf/VCFGenotype.java

src/org/broad/igv/variant/vcf/VCFVariant.java

src/org/broad/igv/vcf/

src/org/broad/igv/vcf/AutismUtils.java

src/org/broad/igv/vcf/PedigreeUtils.java

src/org/broad/igv/vcf/TrackMenu.java

src/org/broad/igv/vcf/VCFMenu.java

src/org/broad/igv/vcf/VCFRenderer.java

src/org/broad/igv/vcf/VCFTools.java

src/org/broad/igv/vcf/VCFTrack.java

src/org/broad/igv/vcf/VCFtoBed.java

src/org/broad/igv/vcf/Variant.java

src/org/broad/igv/vcf/VariantInfoDialog.form

src/org/broad/igv/vcf/VariantInfoDialog.java

src/org/broad/tribble/AbstractFeatureCodec.java

src/org/broad/tribble/Feature.java

src/org/broad/tribble/FeatureCodec.java

src/org/broad/tribble/bed/BEDCodec.java

src/org/broad/tribble/dbsnp/DbSNPCodec.java

src/org/broad/tribble/dbsnp/DbSNPFeature.java

src/org/broad/tribble/dbsnp/OldDbSNPCodec.java

src/org/broad/tribble/dbsnp/OldDbSNPFeature.java

src/org/broad/tribble/example/CountRecords.java

src/org/broad/tribble/example/IndexToTable.java

src/org/broad/tribble/example/ProfileIndexReading.java

src/org/broad/tribble/gelitext/GeliTextCodec.java

src/org/broad/tribble/index/AbstractIndex.java

src/org/broad/tribble/index/Index.java

src/org/broad/tribble/index/IndexFactory.java

src/org/broad/tribble/index/interval/IntervalTreeIndex.java

src/org/broad/tribble/index/linear/LinearIndex.java

src/org/broad/tribble/index/linear/LinearIndexCreator.java

src/org/broad/tribble/source/BasicFeatureSource.java

src/org/broad/tribble/source/PerformanceLoggingFeatureSource.java

src/org/broad/tribble/source/query/AsciiQuerySource.java

src/org/broad/tribble/source/query/IndexFreeAsciiQuerySource.java

src/org/broad/tribble/source/tabix/TabixReader.java

src/org/broad/tribble/util/LittleEndianInputStream.java

src/org/broad/tribble/util/LittleEndianOutputStream.java

src/org/broad/tribble/util/SeekableBufferedStream.java

src/org/broad/tribble/util/SeekableFTPStreamHelper.java

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

src/org/broad/tribble/util/SeekableHTTPStream.java

src/org/broad/tribble/util/ftp/FTPClient.java

src/org/broad/tribble/util/ftp/FTPReply.java

src/org/broad/tribble/util/ftp/FTPUtils.java

src/resources/about.properties

src/resources/codonTable.txt

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