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Viewing all changes in revision 11.

Committer: Bazaar Package Importer
Author(s): Shaun Jackman
Date: 2011-07-25 11:41:18 UTC
mfrom: (1.2.5 upstream)
Revision ID: james.westby@ubuntu.com-20110725114118-irb14ppw3mru1yd5

Tags: 2.0.6-1

* New upstream release.
* debian/control: Depend and Build-Depend on libcommons-logging-java,
libhttpclient-java, libhttpcore-java, libjcommon-java and
libjfreechart-java.
* debian/igv.1: Update.
* debian/watch: Update.

files added:
igv.bat

igv.command

igv.sh

lib/goby-io-igv.jar

lib/vcf.jar

src/images/Folder-icon.png

src/images/close.png

src/images/crystal

src/images/crystal/fileclose.png

src/images/file-document.png

src/images/genomespacelogo.png

src/images/left-arrow.gif

src/images/no-tooltip.png

src/images/right-arrow.gif

src/images/tooltip.png

src/org/broad/igv/batch

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/Exec.java

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

src/org/broad/igv/bbfile

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/bigwig

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

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

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

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

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

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

src/org/broad/igv/data/cufflinks

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/genome

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

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

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

src/org/broad/igv/feature/genome/GenomeBuilderPane.jfd

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

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

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

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

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

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

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

src/org/broad/igv/feature/tribble

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

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

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

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

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

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

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

src/org/broad/igv/goby

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

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

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

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

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

src/org/broad/igv/goby/package.html

src/org/broad/igv/graph

src/org/broad/igv/graph/Edge.java

src/org/broad/igv/graph/GeneUtils.java

src/org/broad/igv/graph/Graph.java

src/org/broad/igv/graph/GraphPanel2.java

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

src/org/broad/igv/graph/Node.java

src/org/broad/igv/graph/SubGraph.java

src/org/broad/igv/gs

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/gwas

src/org/broad/igv/gwas/DescriptionCache.java

src/org/broad/igv/gwas/GWASData.java

src/org/broad/igv/gwas/GWASParser.java

src/org/broad/igv/gwas/GWASTrack.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

src/org/broad/igv/lists

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

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

src/org/broad/igv/lists/GeneListEditDialog.jfd

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

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

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

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

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

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

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

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

src/org/broad/igv/lists/VariantListNavigator.jfd

src/org/broad/igv/lists/biocarta_cancer_cp.gmt

src/org/broad/igv/lists/examples.gmt

src/org/broad/igv/lists/kegg_cancer_cp.gmt

src/org/broad/igv/lists/mckd1.gmt

src/org/broad/igv/lists/reactome_cp.gmt

src/org/broad/igv/peaks

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

src/org/broad/igv/peaks/Peak.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/PeakControlDialog.java

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

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

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

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

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

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

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

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

src/org/broad/igv/peaks/descriptor.txt

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/sam/reader/MergedAlignmentReader2.java

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/tools/converters/ExpressionFormatter.java

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

src/org/broad/igv/tools/ui/CoverageGui.java

src/org/broad/igv/tools/ui/CoverageGui.jfd

src/org/broad/igv/tools/ui/IndexGui.java

src/org/broad/igv/tools/ui/IndexGui.jfd

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/filefilters

src/org/broad/igv/ui/filefilters/AlignmentFileFilter.java

src/org/broad/igv/ui/filefilters/CoverageFileFilter.java

src/org/broad/igv/ui/legend/HeatmapLegendEditor.jfd

src/org/broad/igv/ui/legend/LegendDialog.jfd

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/panel/ReorderPanelsDialog.jfd

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

src/org/broad/igv/ui/panel/flowlayout.txt

src/org/broad/igv/ui/svg

src/org/broad/igv/ui/svg/SVGGraphics.java

src/org/broad/igv/ui/svg/SVGTest.java

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

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

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

src/org/broad/igv/ui/util/FontChooser.jfd

src/org/broad/igv/ui/util/FontChooser2.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/util/collections/StringArrayList.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/sigma

src/org/broad/igv/util/sigma.zip

src/org/broad/igv/util/stats

src/org/broad/igv/util/stats/Distribution.java

src/org/broad/igv/util/stats/KMPlotFrame.java

src/org/broad/igv/util/stats/KMPlotFrame.jfd

src/org/broad/igv/util/stats/KaplanMeierEstimator.java

src/org/broad/igv/util/stream

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

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

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

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

src/org/broad/igv/util/stream/SeekablePicardFtpStream.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/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/FeatureSource.java

src/org/broad/tribble/NameAwareCodec.java

src/org/broad/tribble/Tribble.java

src/org/broad/tribble/TribbleException.java

src/org/broad/tribble/annotation

src/org/broad/tribble/annotation/DiploidGenotype.java

src/org/broad/tribble/annotation/Strand.java

src/org/broad/tribble/annotation/VariantType.java

src/org/broad/tribble/bed

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

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

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

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

src/org/broad/tribble/dbsnp

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

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

src/org/broad/tribble/example

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

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

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

src/org/broad/tribble/gelitext

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

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

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

src/org/broad/tribble/iterators

src/org/broad/tribble/iterators/CloseableTribbleIterator.java

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

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

src/org/broad/tribble/readme.txt

src/org/broad/tribble/source

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

src/org/broad/tribble/source/query

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

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

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

src/org/broad/tribble/source/tabix

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/tribble/util/ftp

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

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

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

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

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

src/org/broad/tribble/util/popgen

src/org/broad/tribble/util/popgen/HardyWeinbergCalculation.java

src/org/json

src/org/json/CDL.java

src/org/json/Cookie.java

src/org/json/CookieList.java

src/org/json/HTTP.java

src/org/json/HTTPTokener.java

src/org/json/JSONArray.java

src/org/json/JSONException.java

src/org/json/JSONML.java

src/org/json/JSONObject.java

src/org/json/JSONString.java

src/org/json/JSONStringer.java

src/org/json/JSONTokener.java

src/org/json/JSONWriter.java

src/org/json/README

src/org/json/Test.java

src/org/json/XML.java

src/org/json/XMLTokener.java

files removed:
igv_linux-64.sh

igv_linux.sh

igv_mac-intel.command

igv_mac-powerpc.sh

igv_win.bat

src/demos

src/demos/ColorBlocks.java

src/demos/ColorComposite.java

src/demos/GradientPaintDemo.java

src/demos/GradientPaintDemo2.java

src/demos/JArgsTest.java

src/demos/Paints.java

src/demos/RubberBand.java

src/demos/ScreenCapture.java

src/edu/mit/broad/picard

src/edu/mit/broad/picard/PicardException.java

src/edu/mit/broad/picard/cmdline

src/edu/mit/broad/picard/illumina

src/edu/mit/broad/picard/illumina/SolexaQualityConverter.java

src/edu/mit/broad/picard/util

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

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

src/edu/mit/broad/sam

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

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

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

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

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

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

src/org/broad/igv/feature/Bed4Feature.java

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/main

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/track/tribble

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

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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/ApplicationStatusBar.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/util/MD5Checksum.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/util/collections/DoubleArrayList.java

src/org/broad/igv/util/collections/FloatArrayList.java

src/org/broad/igv/util/collections/IntArrayList.java

src/org/broad/igv/util/index/Interval.java

src/org/broad/igv/util/index/IntervalTree.java

src/org/broad/tribble/AbstractFeatureCodec.java

src/org/broad/tribble/FeatureCodec.java

src/org/broad/tribble/FeatureIterator.java

src/org/broad/tribble/exception/CodecLineParsingException.java

src/org/broad/tribble/exception/UnsortedFileException.java

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

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

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

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

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

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

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

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

src/org/broad/tribble/index/interval/IntervalTree.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/util/LittleEndianInputStream.java

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

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

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

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

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

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

src/resources/about.properties

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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

lib/goby-io-igv.jar

src/copyright.txt

src/demos/ColorBlocks.java

src/demos/ColorComposite.java

src/demos/GradientPaintDemo.java

src/demos/GradientPaintDemo2.java

src/demos/JArgsTest.java

src/demos/Paints.java

src/demos/RubberBand.java

src/demos/ScreenCapture.java

src/edu/mit/broad/picard/

src/edu/mit/broad/picard/PicardException.java

src/edu/mit/broad/picard/cmdline/

src/edu/mit/broad/picard/illumina/

src/edu/mit/broad/picard/illumina/SolexaQualityConverter.java

src/edu/mit/broad/picard/util/

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

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

src/edu/mit/broad/prodinfo/chromosome/BasicGenomicAnnotation.java

src/edu/mit/broad/prodinfo/chromosome/BasicTwoSubjectAnnotation.java

src/edu/mit/broad/prodinfo/datastrutures/Interval.java

src/edu/mit/broad/prodinfo/datastrutures/IntervalTree.java

src/edu/mit/broad/prodinfo/genomicplot/Feature.java

src/edu/mit/broad/prodinfo/genomicplot/GenomicAnnotation.java

src/edu/mit/broad/prodinfo/genomicplot/ParseException.java

src/edu/mit/broad/prodinfo/genomicplot/TwoSubjectAnnotation.java

src/edu/mit/broad/prodinfo/multiplealignment/MAFAlignment.java

src/edu/mit/broad/prodinfo/multiplealignment/MAFIO.java

src/edu/mit/broad/prodinfo/multiplealignment/MultipleAlignment.java

src/edu/mit/broad/prodinfo/multiplealignment/MultipleAlignmentIO.java

src/edu/mit/broad/prodinfo/multiplealignment/ReadTest.java

src/edu/mit/broad/prodinfo/sequence/Sequence.java

src/edu/mit/broad/prodinfo/sequence/SequenceRegion.java

src/edu/mit/broad/prodinfo/sequence/WindowSlider.java

src/edu/mit/broad/sam/

src/images/Folder-icon.png

src/images/close.png

src/images/crystal/

src/images/crystal/fileclose.png

src/images/file-document.png

src/images/genomespacelogo.png

src/images/left-arrow.gif

src/images/no-tooltip.png

src/images/right-arrow.gif

src/images/tooltip.png

src/log4j.properties

src/org/broad/igv/Globals.java

src/org/broad/igv/IGVPreferences.java

src/org/broad/igv/PreferenceManager.java

src/org/broad/igv/batch/

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/Exec.java

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

src/org/broad/igv/bbfile/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/bigwig/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/data/DataTile2D.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/data/SummaryTile2D.java

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

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

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

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

src/org/broad/igv/data/cufflinks/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/data/seg/Segment.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/SegmentedBinaryLocalReader.java

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

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

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

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

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

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

src/org/broad/igv/event/StatusChangeEvent.java

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/Bed4Feature.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/genome/

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

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

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

src/org/broad/igv/feature/genome/GenomeBuilderPane.jfd

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

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

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

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

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

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

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

src/org/broad/igv/feature/tribble/

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

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

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

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

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

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

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

src/org/broad/igv/goby/

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

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

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

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

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

src/org/broad/igv/goby/package.html

src/org/broad/igv/graph/

src/org/broad/igv/graph/Edge.java

src/org/broad/igv/graph/GeneUtils.java

src/org/broad/igv/graph/Graph.java

src/org/broad/igv/graph/GraphPanel2.java

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

src/org/broad/igv/graph/Node.java

src/org/broad/igv/graph/SubGraph.java

src/org/broad/igv/gs/

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/gwas/

src/org/broad/igv/gwas/DescriptionCache.java

src/org/broad/igv/gwas/GWASData.java

src/org/broad/igv/gwas/GWASParser.java

src/org/broad/igv/gwas/GWASTrack.java

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/listener/StatusListener.java

src/org/broad/igv/lists/

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

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

src/org/broad/igv/lists/GeneListEditDialog.jfd

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

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

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

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

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

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

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

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

src/org/broad/igv/lists/VariantListNavigator.jfd

src/org/broad/igv/lists/biocarta_cancer_cp.gmt

src/org/broad/igv/lists/examples.gmt

src/org/broad/igv/lists/kegg_cancer_cp.gmt

src/org/broad/igv/lists/mckd1.gmt

src/org/broad/igv/lists/reactome_cp.gmt

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/maf/species.properties

src/org/broad/igv/main/

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

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

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

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

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

src/org/broad/igv/peaks/

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

src/org/broad/igv/peaks/Peak.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/PeakControlDialog.java

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

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

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

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

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

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

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

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

src/org/broad/igv/peaks/descriptor.txt

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/repeats/RepeatMaskSplitter.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/sam/reader/MergedAlignmentReader2.java

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

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

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

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

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

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

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

src/org/broad/igv/sam/reader/SamQueryReader.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/sam/reader/SolexaQualityConverter.java

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

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

src/org/broad/igv/scatterplot/ScatterData.java

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

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

src/org/broad/igv/session/RendererFactory.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/svg/TestSVGGen.java

src/org/broad/igv/synteny/BlastMapping.java

src/org/broad/igv/synteny/BlastMappingUtils.java

src/org/broad/igv/synteny/BlastParser.java

src/org/broad/igv/synteny/SyntenyMapping.java

src/org/broad/igv/synteny/SyntenyUtils.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/tools/converters/ExpressionFormatter.java

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

src/org/broad/igv/tools/converters/IlluminaToCN.java

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

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

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

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

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

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

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

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

src/org/broad/igv/tools/sort/BedSorter.java

src/org/broad/igv/tools/sort/CNSorter.java

src/org/broad/igv/tools/sort/GFFSorter.java

src/org/broad/igv/tools/sort/Parser.java

src/org/broad/igv/tools/sort/SAMSorter.java

src/org/broad/igv/tools/sort/SortableRecord.java

src/org/broad/igv/tools/sort/SortableRecordCodec.java

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src/org/broad/igv/tools/ui/CoverageGui.java

src/org/broad/igv/tools/ui/CoverageGui.jfd

src/org/broad/igv/tools/ui/IndexGui.java

src/org/broad/igv/tools/ui/IndexGui.jfd

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

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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/FeatureTrackUtils.java

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/track/TrackClickEvent.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/TrackReader.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/GenomeBuilderPane.form

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/action/NewSessionMenuAction.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/ResetPreferencesAction.java

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

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

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

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

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

src/org/broad/igv/ui/dnd/AbstractGhostDropManager.java

src/org/broad/igv/ui/dnd/GhostDropAdapter.java

src/org/broad/igv/ui/dnd/GhostDropEvent.java

src/org/broad/igv/ui/dnd/GhostDropListener.java

src/org/broad/igv/ui/dnd/GhostGlassPane.java

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

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src/org/broad/igv/ui/filefilters/AlignmentFileFilter.java

src/org/broad/igv/ui/filefilters/CoverageFileFilter.java

src/org/broad/igv/ui/legend/ChrColorDialog.java

src/org/broad/igv/ui/legend/ChromosomeColorLegend.java

src/org/broad/igv/ui/legend/HeatmapLegendEditor.form

src/org/broad/igv/ui/legend/HeatmapLegendEditor.java

src/org/broad/igv/ui/legend/HeatmapLegendEditor.jfd

src/org/broad/igv/ui/legend/HeatmapLegendPanel.java

src/org/broad/igv/ui/legend/LegendDialog.form

src/org/broad/igv/ui/legend/LegendDialog.java

src/org/broad/igv/ui/legend/LegendDialog.jfd

src/org/broad/igv/ui/legend/LegendPanel.java

src/org/broad/igv/ui/legend/LohLegendPanel.java

src/org/broad/igv/ui/legend/MutationLegendPanel.java

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

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

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

src/org/broad/igv/ui/panel/CytobandPanel.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/DragAndDropTransferHandler.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/panel/ReorderPanelsDialog.jfd

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/panel/ZoomSliderPanel.java

src/org/broad/igv/ui/panel/flowlayout.txt

src/org/broad/igv/ui/svg/

src/org/broad/igv/ui/svg/SVGGraphics.java

src/org/broad/igv/ui/svg/SVGTest.java

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/util/FontChooser.jfd

src/org/broad/igv/ui/util/FontChooser2.java

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

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

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

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

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

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

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

src/org/broad/igv/ui/util/MessageUtils.java

src/org/broad/igv/ui/util/OkCancelDialog.java

src/org/broad/igv/ui/util/Packable.java

src/org/broad/igv/ui/util/ProgressBar.java

src/org/broad/igv/ui/util/ProgressMonitor.java

src/org/broad/igv/ui/util/PropertyDialog.java

src/org/broad/igv/ui/util/PropertyManager.java

src/org/broad/igv/ui/util/ReorderableJList.java

src/org/broad/igv/ui/util/SnapshotUtilities.java

src/org/broad/igv/ui/util/SortDialog.java

src/org/broad/igv/ui/util/SwitchingLabelUI.java

src/org/broad/igv/ui/util/Tool.java

src/org/broad/igv/ui/util/TracingRepaintManager.java

src/org/broad/igv/ui/util/UIUtilities.java

src/org/broad/igv/ui/util/VerticalLabelUI.java

src/org/broad/igv/util/AlphaColorGradient.java

src/org/broad/igv/util/AltSequenceGenerator.java

src/org/broad/igv/util/ArrayHeapIntSorter.java

src/org/broad/igv/util/ArrayHeapObjectSorter.java

src/org/broad/igv/util/AsciiEcho.java

src/org/broad/igv/util/AsciiLineReader.java

src/org/broad/igv/util/BrowserLauncher.java

src/org/broad/igv/util/ByteConverter.java

src/org/broad/igv/util/ChromosomeColors.java

src/org/broad/igv/util/ColorUtilities.java

src/org/broad/igv/util/CompressionUtils.java

src/org/broad/igv/util/CompressionUtilsTest.java

src/org/broad/igv/util/ConnectionTimerTask.java

src/org/broad/igv/util/ConvertPlasmodium.java

src/org/broad/igv/util/DumpHttpHeaders.java

src/org/broad/igv/util/EpigeneticsUtils.java

src/org/broad/igv/util/FileUtils.java

src/org/broad/igv/util/Filter.java

src/org/broad/igv/util/GapToWigConverter.java

src/org/broad/igv/util/GenomeUtils.java

src/org/broad/igv/util/IGVHttpClientUtils.java

src/org/broad/igv/util/IGVHttpUtils.java

src/org/broad/igv/util/IlluminaUtils.java

src/org/broad/igv/util/IntComparator.java

src/org/broad/igv/util/IntHashMap.java

src/org/broad/igv/util/JavaLibTests.java

src/org/broad/igv/util/LRUCache.java

src/org/broad/igv/util/LoggingUtils.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/MD5Checksum.java

src/org/broad/igv/util/MacroSnapshotAction.java

src/org/broad/igv/util/MiscTests.java

src/org/broad/igv/util/NamedRunnable.java

src/org/broad/igv/util/ObjectCache.java

src/org/broad/igv/util/ObserverForObject.java

src/org/broad/igv/util/ParsingUtils.java

src/org/broad/igv/util/ResourceLocator.java

src/org/broad/igv/util/RuntimeUtils.java

src/org/broad/igv/util/SOLIDUtils.java

src/org/broad/igv/util/SeekableFTPStream.java

src/org/broad/igv/util/SeekableFileStream.java

src/org/broad/igv/util/SeekableHTTPStream.java

src/org/broad/igv/util/SeekableServiceStream.java

src/org/broad/igv/util/SeekableSplitStream.java

src/org/broad/igv/util/SeekableStream.java

src/org/broad/igv/util/SeekableStreamFactory.java

src/org/broad/igv/util/SequenceGC.java

src/org/broad/igv/util/StreamUtils.java

src/org/broad/igv/util/StringUtils.java

src/org/broad/igv/util/Temp.java

src/org/broad/igv/util/TestS3Access.java

src/org/broad/igv/util/TestThreadTiming.java

src/org/broad/igv/util/UCSCUtils.java

src/org/broad/igv/util/UnzipGenomes.java

src/org/broad/igv/util/UserPasswordDialog.java

src/org/broad/igv/util/UserPasswordDialog.jfd

src/org/broad/igv/util/Utilities.java

src/org/broad/igv/util/ZipArchiveWrapper.java

src/org/broad/igv/util/collections/DoubleArrayList.java

src/org/broad/igv/util/collections/FloatArrayList.java

src/org/broad/igv/util/collections/IntArrayList.java

src/org/broad/igv/util/collections/StringArrayList.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/index/Interval.java

src/org/broad/igv/util/index/IntervalTree.java

src/org/broad/igv/util/sigma.zip

src/org/broad/igv/util/sigma/

src/org/broad/igv/util/stats/

src/org/broad/igv/util/stats/Distribution.java

src/org/broad/igv/util/stats/KMPlotFrame.java

src/org/broad/igv/util/stats/KMPlotFrame.jfd

src/org/broad/igv/util/stats/KaplanMeierEstimator.java

src/org/broad/igv/util/stream/

src/org/broad/igv/util/stream/ApacheURLHelper.java

src/org/broad/igv/util/stream/IGVSeekableStreamFactory.java

src/org/broad/igv/util/stream/SeekableFTPStream.java

src/org/broad/igv/util/stream/SeekableFTPStreamHelper.java

src/org/broad/igv/util/stream/SeekablePicardFtpStream.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/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/FeatureCodec.java

src/org/broad/tribble/FeatureIterator.java

src/org/broad/tribble/FeatureReader.java

src/org/broad/tribble/FeatureSource.java

src/org/broad/tribble/NameAwareCodec.java

src/org/broad/tribble/Tribble.java

src/org/broad/tribble/TribbleException.java

src/org/broad/tribble/annotation/

src/org/broad/tribble/annotation/DiploidGenotype.java

src/org/broad/tribble/annotation/Strand.java

src/org/broad/tribble/annotation/VariantType.java

src/org/broad/tribble/bed/

src/org/broad/tribble/bed/BEDCodec.java

src/org/broad/tribble/bed/BEDFeature.java

src/org/broad/tribble/bed/FullBEDFeature.java

src/org/broad/tribble/bed/SimpleBEDFeature.java

src/org/broad/tribble/dbsnp/

src/org/broad/tribble/dbsnp/DbSNPCodec.java

src/org/broad/tribble/dbsnp/DbSNPFeature.java

src/org/broad/tribble/example/

src/org/broad/tribble/example/CountRecords.java

src/org/broad/tribble/example/IndexToTable.java

src/org/broad/tribble/example/IndicesAreEqual.java

src/org/broad/tribble/exception/CodecLineParsingException.java

src/org/broad/tribble/exception/UnsortedFileException.java

src/org/broad/tribble/gelitext/

src/org/broad/tribble/gelitext/GeliTextCodec.java

src/org/broad/tribble/gelitext/GeliTextFeature.java

src/org/broad/tribble/index/AbstractIndex.java

src/org/broad/tribble/index/Block.java

src/org/broad/tribble/index/ChrIndex.java

src/org/broad/tribble/index/DynamicIndexCreator.java

src/org/broad/tribble/index/Index.java

src/org/broad/tribble/index/IndexCreator.java

src/org/broad/tribble/index/IndexFactory.java

src/org/broad/tribble/index/interval/Interval.java

src/org/broad/tribble/index/interval/IntervalIndexCreator.java

src/org/broad/tribble/index/interval/IntervalTree.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/index/linear/LinearIndexerTest.java

src/org/broad/tribble/iterators/

src/org/broad/tribble/iterators/CloseableTribbleIterator.java

src/org/broad/tribble/readers/AsciiLineReader.java

src/org/broad/tribble/readers/AsciiQueryReader.java

src/org/broad/tribble/readers/BasicFeatureReader.java

src/org/broad/tribble/readers/LineReader.java

src/org/broad/tribble/readers/QueryReader.java

src/org/broad/tribble/readers/TabixReader.java

src/org/broad/tribble/readme.txt

src/org/broad/tribble/source/

src/org/broad/tribble/source/BasicFeatureSource.java

src/org/broad/tribble/source/query/

src/org/broad/tribble/source/query/AsciiQuerySource.java

src/org/broad/tribble/source/query/IndexFreeAsciiQuerySource.java

src/org/broad/tribble/source/query/QuerySource.java

src/org/broad/tribble/source/tabix/

src/org/broad/tribble/source/tabix/TabixLineReader.java

src/org/broad/tribble/source/tabix/TabixReader.java

src/org/broad/tribble/util/AsciiLineReader.java

src/org/broad/tribble/util/BlockCompressedInputStream.java

src/org/broad/tribble/util/BlockCompressedStreamConstants.java

src/org/broad/tribble/util/BlockGunzipper.java

src/org/broad/tribble/util/CloseableTribbleIterator.java

src/org/broad/tribble/util/HTTPHelper.java

src/org/broad/tribble/util/HttpUtils.java

src/org/broad/tribble/util/IOUtil.java

src/org/broad/tribble/util/LineReader.java

src/org/broad/tribble/util/LittleEndianInputStream.java

src/org/broad/tribble/util/LittleEndianOutputStream.java

src/org/broad/tribble/util/MathUtils.java

src/org/broad/tribble/util/ParsingUtils.java

src/org/broad/tribble/util/Positional.java

src/org/broad/tribble/util/PositionalStream.java

src/org/broad/tribble/util/SeekableBufferedStream.java

src/org/broad/tribble/util/SeekableFTPStream.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/SeekableSplitStream.java

src/org/broad/tribble/util/SeekableStream.java

src/org/broad/tribble/util/SeekableStreamFactory.java

src/org/broad/tribble/util/TabixUtils.java

src/org/broad/tribble/util/URLHelper.java

src/org/broad/tribble/util/ftp/

src/org/broad/tribble/util/ftp/FTPClient.java

src/org/broad/tribble/util/ftp/FTPReply.java

src/org/broad/tribble/util/ftp/FTPStream.java

src/org/broad/tribble/util/ftp/FTPUtils.java

src/org/broad/tribble/util/ftp/UserPasswordInput.java

src/org/broad/tribble/util/popgen/

src/org/broad/tribble/util/popgen/HardyWeinbergCalculation.java

src/org/json/CDL.java

src/org/json/CookieList.java

src/org/json/HTTP.java

src/org/json/HTTPTokener.java

src/org/json/JSONArray.java

src/org/json/JSONException.java

src/org/json/JSONML.java

src/org/json/JSONObject.java

src/org/json/JSONString.java

src/org/json/JSONStringer.java

src/org/json/JSONTokener.java

src/org/json/JSONWriter.java

src/org/json/README

src/org/json/Test.java

src/org/json/XML.java

src/org/json/XMLTokener.java

src/resources/about.properties

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