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Viewing all changes in revision 13.

Committer: Package Import Robot
Author(s): Olivier Sallou
Date: 2013-06-02 11:05:35 UTC
mfrom: (6.1.3 experimental)
Revision ID: package-import@ubuntu.com-20130602110535-2moz7t9q73lnk1kb

Tags: 2.3.2+dfsg-2

Move to unstable.

files added:
.pc/.quilt_patches

.pc/.quilt_series

build_macros.xml

debian/igv.jlibs

debian/upstream

docs

docs/igvtools_readme.txt

docs/lib

docs/publishedApiDoclet

docs/readme.txt

docs/readme_src.txt

lib/StingUtils.jar

lib/apache_license.txt

lib/gson-2.2.2.jar

lib/mongo-java-driver-2.7.3.jar

lib/na12878kb.jar

lib/picard-1.89.jar

lib/sqlitejdbc-v056.jar

lib/tribble-r1414.jar

lib/variant-1.89.jar

src/apple

src/apple/dts

src/apple/dts/samplecode

src/apple/dts/samplecode/osxadapter

src/apple/dts/samplecode/osxadapter/OSXAdapter.java

src/biz

src/biz/source_code

src/biz/source_code/base64Coder

src/biz/source_code/base64Coder/Base64Coder.java

src/com

src/com/iontorrent

src/com/iontorrent/data

src/com/iontorrent/data/FlowDistribution.java

src/com/iontorrent/data/ReadInfo.java

src/com/iontorrent/utils

src/com/iontorrent/utils/ExtensionFileFilter.java

src/com/iontorrent/utils/FileTools.java

src/com/iontorrent/utils/LocationListener.java

src/com/iontorrent/utils/SimpleDialog.java

src/com/iontorrent/utils/StringTools.java

src/com/iontorrent/views

src/com/iontorrent/views/FlowSignalDistributionPanel.form

src/com/iontorrent/views/FlowSignalDistributionPanel.java

src/com/iontorrent/views/arrow-left.png

src/com/iontorrent/views/arrow-right.png

src/com/iontorrent/views/chip_16.png

src/com/iontorrent/views/configure.png

src/com/iontorrent/views/copy.png

src/com/iontorrent/views/copyj.png

src/com/iontorrent/views/copyr.png

src/com/iontorrent/views/save.png

src/log4j_all.properties

src/log4j_debug.properties

src/org/apache

src/org/apache/tomcat

src/org/apache/tomcat/util

src/org/apache/tomcat/util/Ascii.java

src/org/apache/tomcat/util/HttpDate.java

src/org/broad/igv/DirectoryManager.java

src/org/broad/igv/annotations

src/org/broad/igv/annotations/ForTesting.java

src/org/broad/igv/blat

src/org/broad/igv/blat/BlatClient.java

src/org/broad/igv/blat/BlatQueryWindow.java

src/org/broad/igv/blat/BlatQueryWindow.jfd

src/org/broad/igv/blat/BlatTableModel.java

src/org/broad/igv/cbio

src/org/broad/igv/cbio/AttributeFilter.java

src/org/broad/igv/cbio/AttributeFilter.jfd

src/org/broad/igv/cbio/FilterGeneNetworkUI.java

src/org/broad/igv/cbio/FilterGeneNetworkUI.jfd

src/org/broad/igv/cbio/GeneNetwork.java

src/org/broad/igv/cbio/resources

src/org/broad/igv/cbio/resources/post_stub.html

src/org/broad/igv/charts

src/org/broad/igv/charts/Axis.java

src/org/broad/igv/charts/AxisPanel.java

src/org/broad/igv/charts/ChartLayout.java

src/org/broad/igv/charts/ChartPanel.java

src/org/broad/igv/charts/ScatterPlot.java

src/org/broad/igv/charts/ScatterPlotData.java

src/org/broad/igv/charts/ScatterPlotDemo.java

src/org/broad/igv/charts/ScatterPlotFrame.java

src/org/broad/igv/charts/ScatterPlotFrame.jfd

src/org/broad/igv/charts/ScatterPlotUtils.java

src/org/broad/igv/charts/SelectionPath.java

src/org/broad/igv/charts/XYDataModel.java

src/org/broad/igv/charts/XYDataPoint.java

src/org/broad/igv/charts/XYSeries.java

src/org/broad/igv/cli_plugin

src/org/broad/igv/cli_plugin/AlignmentDecoder.java

src/org/broad/igv/cli_plugin/Argument.java

src/org/broad/igv/cli_plugin/AsciiDecoder.java

src/org/broad/igv/cli_plugin/AsciiEncoder.java

src/org/broad/igv/cli_plugin/BEDGraphEncoder.java

src/org/broad/igv/cli_plugin/BEDToolsDecoder.java

src/org/broad/igv/cli_plugin/FeatureDecoder.java

src/org/broad/igv/cli_plugin/FeatureEncoder.java

src/org/broad/igv/cli_plugin/FeatureIO.java

src/org/broad/igv/cli_plugin/LineFeatureDecoder.java

src/org/broad/igv/cli_plugin/LineFeatureEncoder.java

src/org/broad/igv/cli_plugin/PluginCodec.java

src/org/broad/igv/cli_plugin/PluginDataSource.java

src/org/broad/igv/cli_plugin/PluginFeatureSource.java

src/org/broad/igv/cli_plugin/PluginSource.java

src/org/broad/igv/cli_plugin/PluginSpecReader.java

src/org/broad/igv/cli_plugin/SamAlignmentEncoder.java

src/org/broad/igv/cli_plugin/resources

src/org/broad/igv/cli_plugin/resources/awk_plugin.xml

src/org/broad/igv/cli_plugin/resources/bedtools_plugin.xml

src/org/broad/igv/cli_plugin/resources/builtin_plugins.txt

src/org/broad/igv/cli_plugin/resources/cli_plugin.dtd

src/org/broad/igv/cli_plugin/resources/cufflinks_plugin.xml

src/org/broad/igv/cli_plugin/resources/gen_plugin.xml

src/org/broad/igv/cli_plugin/ui

src/org/broad/igv/cli_plugin/ui/ArgumentPanel.java

src/org/broad/igv/cli_plugin/ui/ArgumentPanel.jfd

src/org/broad/igv/cli_plugin/ui/BoolArgument.java

src/org/broad/igv/cli_plugin/ui/BoolArgument.jfd

src/org/broad/igv/cli_plugin/ui/EnumArgument.java

src/org/broad/igv/cli_plugin/ui/EnumArgument.jfd

src/org/broad/igv/cli_plugin/ui/MultiTrackArgument.java

src/org/broad/igv/cli_plugin/ui/MultiTrackArgument.jfd

src/org/broad/igv/cli_plugin/ui/RunPlugin.java

src/org/broad/igv/cli_plugin/ui/RunPlugin.jfd

src/org/broad/igv/cli_plugin/ui/SetPluginPathDialog.java

src/org/broad/igv/cli_plugin/ui/SetPluginPathDialog.jfd

src/org/broad/igv/cli_plugin/ui/TextArgument.java

src/org/broad/igv/cli_plugin/ui/TextArgument.jfd

src/org/broad/igv/cli_plugin/ui/TrackArgument.java

src/org/broad/igv/cli_plugin/ui/TrackArgument.jfd

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

src/org/broad/igv/data/cufflinks/CufflinksCodec.java

src/org/broad/igv/data/cufflinks/CufflinksDataSource.java

src/org/broad/igv/data/cufflinks/CufflinksParser.java

src/org/broad/igv/data/cufflinks/CufflinksTrack.java

src/org/broad/igv/data/cufflinks/CufflinksValue.java

src/org/broad/igv/data/cufflinks/ExpDiffCodec.java

src/org/broad/igv/data/cufflinks/ExpDiffValue.java

src/org/broad/igv/data/cufflinks/FPKMValue.java

src/org/broad/igv/data/cufflinks/FpkmTrackingCodec.java

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

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

src/org/broad/igv/dev

src/org/broad/igv/dev/GenDataParser.java

src/org/broad/igv/dev/IParser.java

src/org/broad/igv/dev/IParserFactory.java

src/org/broad/igv/dev/README

src/org/broad/igv/dev/SegmentedReader.java

src/org/broad/igv/dev/StringArrayParser.java

src/org/broad/igv/dev/api

src/org/broad/igv/dev/api/IGVPlugin.java

src/org/broad/igv/dev/api/api.java

src/org/broad/igv/dev/api/batch

src/org/broad/igv/dev/api/batch/Command.java

src/org/broad/igv/dev/db

src/org/broad/igv/dev/db/DBManager.java

src/org/broad/igv/dev/db/DBProfile.java

src/org/broad/igv/dev/db/DBProfileEditor.java

src/org/broad/igv/dev/db/DBProfileEditor.jfd

src/org/broad/igv/dev/db/DBQueryReader.java

src/org/broad/igv/dev/db/DBReader.java

src/org/broad/igv/dev/db/SQLCodecSource.java

src/org/broad/igv/dev/db/SQLInputStream.java

src/org/broad/igv/dev/db/SQLLineParserByIndex.java

src/org/broad/igv/dev/db/SQLLineParserByLabel.java

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

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

src/org/broad/igv/dev/db/WholeTableDBReader.java

src/org/broad/igv/dev/db/database.dtd

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/exome

src/org/broad/igv/feature/exome/ExomeBlock.java

src/org/broad/igv/feature/exome/ExomeReferenceFrame.java

src/org/broad/igv/feature/exome/ExomeUtils.java

src/org/broad/igv/feature/exome/readme

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/genome/speciesMapping.txt

src/org/broad/igv/feature/resources

src/org/broad/igv/feature/resources/AANamesTable.txt

src/org/broad/igv/feature/resources/defaultTranslationTables.json

src/org/broad/igv/feature/resources/geneticCode.json

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

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

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

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

src/org/broad/igv/gitools

src/org/broad/igv/gitools/Gitools.java

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

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

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

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

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

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

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

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

src/org/broad/igv/maf/Multiz44ConfigurationDialog.java

src/org/broad/igv/methyl

src/org/broad/igv/methyl/BBMethylDataSource.java

src/org/broad/igv/methyl/CachingMethylSource.java

src/org/broad/igv/methyl/MethylDataSource.java

src/org/broad/igv/methyl/MethylScore.java

src/org/broad/igv/methyl/MethylTrack.java

src/org/broad/igv/methyl/ZillerDataSource2.java

src/org/broad/igv/methyl/readme

src/org/broad/igv/plugin

src/org/broad/igv/plugin/AddMenuSeparator.java

src/org/broad/igv/plugin/mongovariant

src/org/broad/igv/plugin/mongovariant/MongoVCFVariant.java

src/org/broad/igv/plugin/mongovariant/VariantReviewDialog.java

src/org/broad/igv/plugin/mongovariant/VariantReviewDialog.jfd

src/org/broad/igv/plugin/mongovariant/VariantReviewPlugin.java

src/org/broad/igv/plugin/mongovariant/VariantReviewRenderer.java

src/org/broad/igv/plugin/mongovariant/VariantReviewSource.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/tools/motiffinder

src/org/broad/igv/tools/motiffinder/MotifFinderDialog.java

src/org/broad/igv/tools/motiffinder/MotifFinderDialog.jfd

src/org/broad/igv/tools/motiffinder/MotifFinderSource.java

src/org/broad/igv/tools/motiffinder/resources

src/org/broad/igv/tools/motiffinder/resources/iupac_regex_table.txt

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

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

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

src/org/broad/igv/track/AnalysisDialog.jfd

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/JList7.java

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

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

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

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

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

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

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

src/org/broad/igv/ui/color

src/org/broad/igv/ui/color/ColorChooserPanel.java

src/org/broad/igv/ui/color/ColorPalette.java

src/org/broad/igv/ui/color/ColorPanel.java

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

src/org/broad/igv/ui/color/ColorUtilities.java

src/org/broad/igv/ui/color/PaletteColorTable.java

src/org/broad/igv/ui/color/PaletteToolFrame.java

src/org/broad/igv/ui/color/PaletteToolFrame.jfd

src/org/broad/igv/ui/color/resources

src/org/broad/igv/ui/color/resources/colorPalettes.txt

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/legend/ColorMapEditor.java

src/org/broad/igv/ui/mainframeicon.png

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

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

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

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

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

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

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

src/org/broad/igv/ui/panel/resources

src/org/broad/igv/ui/panel/resources/IGV_64.png

src/org/broad/igv/ui/resources

src/org/broad/igv/ui/resources/IGV_64.png

src/org/broad/igv/ui/resources/builtin_plugin_list.txt

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/resources/bedtools_help.txt

src/slider

src/slider/LICENSE.txt

src/slider/RangeSlider.java

src/slider/RangeSliderDemo.java

src/slider/RangeSliderUI.java

files removed:
igv.bat

igv.command

lib/AbsoluteLayout.jar

lib/jide-action.jar

lib/jide-common.jar

lib/jide-components.jar

lib/jide-dialogs.jar

lib/jide-dock.jar

lib/jide-grids.jar

lib/vcf.jar

readme_src.txt

src/edu

src/edu/mit

src/edu/mit/broad

src/edu/mit/broad/prodinfo

src/edu/mit/broad/prodinfo/chromosome

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

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

src/edu/mit/broad/prodinfo/datastrutures

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

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

src/edu/mit/broad/prodinfo/genomicplot

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/GenomeSelectionDialog.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/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/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/TrackConfigurationDialog.java

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

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

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

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

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

src/org/broad/igv/ui/action/LoadFromURLMenuAction.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/RemoveUserDefinedGenomeMenuAction.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/event/GlobalKeyDispatcher.java

src/org/broad/igv/ui/legend/ChromosomeColorLegend.java

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

src/org/broad/igv/ui/legend/HeatmapLegendPanel.java

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/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/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/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/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/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/ConfirmDialog.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/FontChooser2.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/resources/about.properties

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removed removed

.pc/.quilt_patches

.pc/.quilt_series

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

build_macros.xml

debian/changelog

debian/copyright

debian/igv.jlibs

debian/patches/01-build.xml

debian/upstream

docs/igvtools_readme.txt

docs/publishedApiDoclet/

docs/readme.txt

docs/readme_src.txt

lib/AbsoluteLayout.jar

lib/StingUtils.jar

lib/apache_license.txt

lib/goby-io-igv.jar

lib/gson-2.2.2.jar

lib/jide-action.jar

lib/jide-common.jar

lib/jide-components.jar

lib/jide-dialogs.jar

lib/jide-dock.jar

lib/jide-grids.jar

lib/mongo-java-driver-2.7.3.jar

lib/na12878kb.jar

lib/picard-1.89.jar

lib/sqlitejdbc-v056.jar

lib/tribble-r1414.jar

lib/variant-1.89.jar

src/apple/dts/samplecode/

src/apple/dts/samplecode/osxadapter/

src/apple/dts/samplecode/osxadapter/OSXAdapter.java

src/biz/source_code/

src/biz/source_code/base64Coder/

src/biz/source_code/base64Coder/Base64Coder.java

src/com/iontorrent/

src/com/iontorrent/data/

src/com/iontorrent/data/FlowDistribution.java

src/com/iontorrent/data/ReadInfo.java

src/com/iontorrent/utils/

src/com/iontorrent/utils/ExtensionFileFilter.java

src/com/iontorrent/utils/FileTools.java

src/com/iontorrent/utils/LocationListener.java

src/com/iontorrent/utils/SimpleDialog.java

src/com/iontorrent/utils/StringTools.java

src/com/iontorrent/views/

src/com/iontorrent/views/FlowSignalDistributionPanel.form

src/com/iontorrent/views/FlowSignalDistributionPanel.java

src/com/iontorrent/views/arrow-left.png

src/com/iontorrent/views/arrow-right.png

src/com/iontorrent/views/chip_16.png

src/com/iontorrent/views/configure.png

src/com/iontorrent/views/copy.png

src/com/iontorrent/views/copyj.png

src/com/iontorrent/views/copyr.png

src/com/iontorrent/views/save.png

src/edu/mit/broad/

src/edu/mit/broad/prodinfo/

src/edu/mit/broad/prodinfo/chromosome/

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

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

src/edu/mit/broad/prodinfo/datastrutures/

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

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

src/edu/mit/broad/prodinfo/genomicplot/

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/

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/

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/log4j.properties

src/log4j_all.properties

src/log4j_debug.properties

src/org/apache/

src/org/apache/tomcat/

src/org/apache/tomcat/util/

src/org/apache/tomcat/util/Ascii.java

src/org/apache/tomcat/util/HttpDate.java

src/org/broad/igv/DirectoryManager.java

src/org/broad/igv/Globals.java

src/org/broad/igv/IGVPreferences.java

src/org/broad/igv/PreferenceManager.java

src/org/broad/igv/annotations/

src/org/broad/igv/annotations/ForTesting.java

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

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

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/BPTreeHeader.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/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/ZoomDataBlock.java

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

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

src/org/broad/igv/blat/

src/org/broad/igv/blat/BlatClient.java

src/org/broad/igv/blat/BlatQueryWindow.java

src/org/broad/igv/blat/BlatQueryWindow.jfd

src/org/broad/igv/blat/BlatTableModel.java

src/org/broad/igv/cbio/

src/org/broad/igv/cbio/FilterGeneNetworkUI.java

src/org/broad/igv/cbio/FilterGeneNetworkUI.jfd

src/org/broad/igv/cbio/GeneNetwork.java

src/org/broad/igv/cbio/resources/

src/org/broad/igv/cbio/resources/post_stub.html

src/org/broad/igv/charts/

src/org/broad/igv/charts/Axis.java

src/org/broad/igv/charts/AxisPanel.java

src/org/broad/igv/charts/ChartLayout.java

src/org/broad/igv/charts/ChartPanel.java

src/org/broad/igv/charts/ScatterPlot.java

src/org/broad/igv/charts/ScatterPlotData.java

src/org/broad/igv/charts/ScatterPlotDemo.java

src/org/broad/igv/charts/ScatterPlotFrame.java

src/org/broad/igv/charts/ScatterPlotFrame.jfd

src/org/broad/igv/charts/ScatterPlotUtils.java

src/org/broad/igv/charts/SelectionPath.java

src/org/broad/igv/charts/XYDataModel.java

src/org/broad/igv/charts/XYDataPoint.java

src/org/broad/igv/charts/XYSeries.java

src/org/broad/igv/cli_plugin/

src/org/broad/igv/cli_plugin/AlignmentDecoder.java

src/org/broad/igv/cli_plugin/Argument.java

src/org/broad/igv/cli_plugin/AsciiDecoder.java

src/org/broad/igv/cli_plugin/AsciiEncoder.java

src/org/broad/igv/cli_plugin/BEDGraphEncoder.java

src/org/broad/igv/cli_plugin/BEDToolsDecoder.java

src/org/broad/igv/cli_plugin/FeatureDecoder.java

src/org/broad/igv/cli_plugin/FeatureEncoder.java

src/org/broad/igv/cli_plugin/FeatureIO.java

src/org/broad/igv/cli_plugin/LineFeatureDecoder.java

src/org/broad/igv/cli_plugin/LineFeatureEncoder.java

src/org/broad/igv/cli_plugin/PluginCodec.java

src/org/broad/igv/cli_plugin/PluginDataSource.java

src/org/broad/igv/cli_plugin/PluginFeatureSource.java

src/org/broad/igv/cli_plugin/PluginSource.java

src/org/broad/igv/cli_plugin/PluginSpecReader.java

src/org/broad/igv/cli_plugin/SamAlignmentEncoder.java

src/org/broad/igv/cli_plugin/resources/

src/org/broad/igv/cli_plugin/resources/awk_plugin.xml

src/org/broad/igv/cli_plugin/resources/bedtools_plugin.xml

src/org/broad/igv/cli_plugin/resources/builtin_plugins.txt

src/org/broad/igv/cli_plugin/resources/cli_plugin.dtd

src/org/broad/igv/cli_plugin/resources/cufflinks_plugin.xml

src/org/broad/igv/cli_plugin/resources/gen_plugin.xml

src/org/broad/igv/cli_plugin/ui/

src/org/broad/igv/cli_plugin/ui/ArgumentPanel.java

src/org/broad/igv/cli_plugin/ui/ArgumentPanel.jfd

src/org/broad/igv/cli_plugin/ui/BoolArgument.java

src/org/broad/igv/cli_plugin/ui/BoolArgument.jfd

src/org/broad/igv/cli_plugin/ui/EnumArgument.java

src/org/broad/igv/cli_plugin/ui/EnumArgument.jfd

src/org/broad/igv/cli_plugin/ui/MultiTrackArgument.java

src/org/broad/igv/cli_plugin/ui/MultiTrackArgument.jfd

src/org/broad/igv/cli_plugin/ui/RunPlugin.java

src/org/broad/igv/cli_plugin/ui/RunPlugin.jfd

src/org/broad/igv/cli_plugin/ui/SetPluginPathDialog.java

src/org/broad/igv/cli_plugin/ui/SetPluginPathDialog.jfd

src/org/broad/igv/cli_plugin/ui/TextArgument.java

src/org/broad/igv/cli_plugin/ui/TextArgument.jfd

src/org/broad/igv/cli_plugin/ui/TrackArgument.java

src/org/broad/igv/cli_plugin/ui/TrackArgument.jfd

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

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

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

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

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

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

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

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

src/org/broad/igv/data/Interval.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/CufflinksCodec.java

src/org/broad/igv/data/cufflinks/CufflinksDataSource.java

src/org/broad/igv/data/cufflinks/CufflinksParser.java

src/org/broad/igv/data/cufflinks/CufflinksTrack.java

src/org/broad/igv/data/cufflinks/CufflinksValue.java

src/org/broad/igv/data/cufflinks/ExpDiffCodec.java

src/org/broad/igv/data/cufflinks/ExpDiffValue.java

src/org/broad/igv/data/cufflinks/FPKMValue.java

src/org/broad/igv/data/cufflinks/FpkmTrackingCodec.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/ExpressionDataset.java

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

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/expression/ProbeToLocusMap.java

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

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

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

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

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

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

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

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

src/org/broad/igv/dev/

src/org/broad/igv/dev/GenDataParser.java

src/org/broad/igv/dev/IParser.java

src/org/broad/igv/dev/IParserFactory.java

src/org/broad/igv/dev/README

src/org/broad/igv/dev/SegmentedReader.java

src/org/broad/igv/dev/StringArrayParser.java

src/org/broad/igv/dev/api/

src/org/broad/igv/dev/api/IGVPlugin.java

src/org/broad/igv/dev/api/api.java

src/org/broad/igv/dev/api/batch/

src/org/broad/igv/dev/api/batch/Command.java

src/org/broad/igv/dev/db/

src/org/broad/igv/dev/db/DBManager.java

src/org/broad/igv/dev/db/DBProfile.java

src/org/broad/igv/dev/db/DBProfileEditor.java

src/org/broad/igv/dev/db/DBProfileEditor.jfd

src/org/broad/igv/dev/db/DBQueryReader.java

src/org/broad/igv/dev/db/DBReader.java

src/org/broad/igv/dev/db/SQLCodecSource.java

src/org/broad/igv/dev/db/SQLInputStream.java

src/org/broad/igv/dev/db/SQLLineParserByIndex.java

src/org/broad/igv/dev/db/SQLLineParserByLabel.java

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

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

src/org/broad/igv/dev/db/WholeTableDBReader.java

src/org/broad/igv/dev/db/database.dtd

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

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

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

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

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

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

src/org/broad/igv/feature/AlternativeSpliceGraph.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/CachingFeatureSource.java

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

src/org/broad/igv/feature/Codon.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/FeatureCodecParser.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/FeatureUtils.java

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/WrappedIterator.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/exome/

src/org/broad/igv/feature/exome/ExomeBlock.java

src/org/broad/igv/feature/exome/ExomeReferenceFrame.java

src/org/broad/igv/feature/exome/ExomeUtils.java

src/org/broad/igv/feature/exome/readme

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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/GenomeImporter.java

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/feature/genome/speciesMapping.txt

src/org/broad/igv/feature/resources/

src/org/broad/igv/feature/resources/AANamesTable.txt

src/org/broad/igv/feature/resources/defaultTranslationTables.json

src/org/broad/igv/feature/resources/geneticCode.json

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/EncodePeakCodec.java

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

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

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

src/org/broad/igv/feature/tribble/MUTCodec.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/UCSCGeneTableCodec.java

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

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

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

src/org/broad/igv/gitools/

src/org/broad/igv/gitools/Gitools.java

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/graph/GeneUtils.java

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

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

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

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

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

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/WebToolDescriptor.java

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

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

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/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/listener/

src/org/broad/igv/listener/StatusListener.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/maf/Multiz44ConfigurationDialog.java

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

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

src/org/broad/igv/maf/conservation/

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/methyl/

src/org/broad/igv/methyl/BBMethylDataSource.java

src/org/broad/igv/methyl/CachingMethylSource.java

src/org/broad/igv/methyl/MethylDataSource.java

src/org/broad/igv/methyl/MethylScore.java

src/org/broad/igv/methyl/MethylTrack.java

src/org/broad/igv/methyl/ZillerDataSource2.java

src/org/broad/igv/methyl/readme

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/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/PeakTrack.java

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

src/org/broad/igv/plugin/

src/org/broad/igv/plugin/AddMenuSeparator.java

src/org/broad/igv/plugin/mongovariant/

src/org/broad/igv/plugin/mongovariant/MongoVCFVariant.java

src/org/broad/igv/plugin/mongovariant/VariantReviewDialog.java

src/org/broad/igv/plugin/mongovariant/VariantReviewDialog.jfd

src/org/broad/igv/plugin/mongovariant/VariantReviewPlugin.java

src/org/broad/igv/plugin/mongovariant/VariantReviewRenderer.java

src/org/broad/igv/plugin/mongovariant/VariantReviewSource.java

src/org/broad/igv/renderer/AbstractColorScale.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/FeatureRenderer.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/IGVExomeFeatureRenderer.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/MutationRenderer.java

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

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

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

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

src/org/broad/igv/renderer/SelectableFeatureRenderer.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/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/AlignmentBlockFS.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/AlignmentPacker.java

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/sam/FlowSignalSubContext.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/SAMWriter.java

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

src/org/broad/igv/sam/SparseAlignmentCounts.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/AlignmentReader.java

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/sam/reader/GeraldReader.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/SAMQueryIterator.java

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

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

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

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

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

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

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

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

src/org/broad/igv/scatterplot/

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

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

src/org/broad/igv/session/IGVSessionReader.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/SessionXmlAdapters.java

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

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

src/org/broad/igv/svg/

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/tools/motiffinder/

src/org/broad/igv/tools/motiffinder/MotifFinderDialog.java

src/org/broad/igv/tools/motiffinder/MotifFinderDialog.jfd

src/org/broad/igv/tools/motiffinder/MotifFinderSource.java

src/org/broad/igv/tools/motiffinder/resources/

src/org/broad/igv/tools/motiffinder/resources/iupac_regex_table.txt

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/WiggleParser.java

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/track/AnalysisDialog.jfd

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/track/GisticTrack.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/MutationDataManager.java

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

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

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

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

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

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

src/org/broad/igv/track/SelectableFeatureTrack.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/TrackMenuItemBuilder.java

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

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

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

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

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

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

src/org/broad/igv/ui/AboutDialog.form

src/org/broad/igv/ui/AttributeSelectionDialog.form

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

src/org/broad/igv/ui/DataRangeDialog.form

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

src/org/broad/igv/ui/GenomeSelectionDialog.form

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

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

src/org/broad/igv/ui/HeatmapDialog.form

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/IGVMenuBar.java

src/org/broad/igv/ui/JList7.java

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

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

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

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

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

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

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

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/SashimiPlot.java

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/color/ColorChooserPanel.java

src/org/broad/igv/ui/color/ColorPalette.java

src/org/broad/igv/ui/color/ColorPanel.java

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

src/org/broad/igv/ui/color/ColorUtilities.java

src/org/broad/igv/ui/color/PaletteColorTable.java

src/org/broad/igv/ui/color/PaletteToolFrame.java

src/org/broad/igv/ui/color/PaletteToolFrame.jfd

src/org/broad/igv/ui/color/resources/

src/org/broad/igv/ui/color/resources/colorPalettes.txt

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

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

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

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

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

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

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

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

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

src/org/broad/igv/ui/legend/ChrColorDialog.form

src/org/broad/igv/ui/legend/ChrColorDialog.java

src/org/broad/igv/ui/legend/ChromosomeColorLegend.java

src/org/broad/igv/ui/legend/ColorMapEditor.java

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

src/org/broad/igv/ui/legend/HeatmapLegendPanel.java

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/mainframeicon.png

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

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

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

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

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

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

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

src/org/broad/igv/ui/panel/RadioButtonSelectionList.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/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/TrackSelectionDialog.java

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

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

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

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

src/org/broad/igv/ui/panel/resources/

src/org/broad/igv/ui/panel/resources/IGV_64.png

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src/org/broad/igv/ui/resources/IGV_64.png

src/org/broad/igv/ui/resources/builtin_plugin_list.txt

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/CancellableProgressDialog.java

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

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.form

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

src/org/broad/tribble/

src/org/broad/tribble/AbstractFeatureCodec.java

src/org/broad/tribble/Feature.java

src/org/broad/tribble/FeatureCodec.java

src/org/broad/tribble/FeatureIterator.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

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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

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

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

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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/example/ProfileIndexReading.java

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

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

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

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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

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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

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

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

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

src/org/broad/tribble/readers/

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/PerformanceLoggingFeatureSource.java

src/org/broad/tribble/source/query/

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

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

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

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

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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/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/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

src/resources/bedtools_help.txt

src/resources/hg18_cytoBand.txt

src/slider/LICENSE.txt

src/slider/RangeSlider.java

src/slider/RangeSliderDemo.java

src/slider/RangeSliderUI.java

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