From 22f8947294fbdf35f1ad01524387bdbda55807b6 Mon Sep 17 00:00:00 2001 From: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Sun, 4 Jan 2026 20:17:01 -0800 Subject: [PATCH 1/2] remove template comments --- .../java/org/igv/batch/CommandExecutor.java | 4 -- src/main/java/org/igv/blast/BlastMapping.java | 1 - .../java/org/igv/data/AbstractDataSource.java | 1 - src/main/java/org/igv/data/BasicScore.java | 4 -- src/main/java/org/igv/data/Bin.java | 4 -- src/main/java/org/igv/data/CharArrayList.java | 4 -- .../java/org/igv/data/ChromosomeSummary.java | 4 -- .../java/org/igv/data/CompositeScore.java | 1 - src/main/java/org/igv/data/DataSource.java | 4 -- .../java/org/igv/data/DataStatistics.java | 4 -- src/main/java/org/igv/data/DataTile.java | 4 -- src/main/java/org/igv/data/Dataset.java | 4 -- .../java/org/igv/data/DatasetDataSource.java | 5 --- .../java/org/igv/data/GenomeSummaryData.java | 4 -- src/main/java/org/igv/data/IGVDataset.java | 4 -- .../java/org/igv/data/IGVDatasetParser.java | 1 - src/main/java/org/igv/data/SummaryTile.java | 1 - src/main/java/org/igv/data/WiggleDataset.java | 5 --- src/main/java/org/igv/data/ZipUtils.java | 4 -- .../data/expression/ExpressionFileParser.java | 1 - .../java/org/igv/feature/AbstractFeature.java | 1 - .../igv/feature/AbstractFeatureParser.java | 4 -- .../org/igv/feature/CytoBandFileParser.java | 1 - .../igv/feature/EmblFeatureTableParser.java | 1 - src/main/java/org/igv/feature/FeatureDB.java | 1 - .../java/org/igv/feature/FeatureParser.java | 4 -- .../org/igv/feature/GisticFileParser.java | 1 - .../java/org/igv/feature/GisticScore.java | 1 - src/main/java/org/igv/feature/Locus.java | 4 -- src/main/java/org/igv/feature/LocusScore.java | 4 -- src/main/java/org/igv/feature/Mutation.java | 1 - src/main/java/org/igv/feature/Strand.java | 4 -- .../java/org/igv/feature/aa/AminoAcid.java | 4 -- .../org/igv/feature/aa/AminoAcidManager.java | 4 -- .../org/igv/feature/aa/AminoAcidSequence.java | 4 -- .../org/igv/feature/aa/CodonTableManager.java | 4 -- .../feature/basepair/BasePairRenderer.java | 1 - .../igv/feature/dranger/DRangerFeature.java | 4 -- .../igv/feature/dranger/DRangerParser.java | 4 -- .../igv/feature/dranger/DRangerRenderer.java | 4 -- .../igv/feature/genome/GenomeImporter.java | 4 -- .../igv/feature/genome/SequenceWrapper.java | 4 -- src/main/java/org/igv/maf/MAFReader.java | 4 -- src/main/java/org/igv/maf/MAFTile.java | 1 - src/main/java/org/igv/maf/MAFTileCodec.java | 4 -- src/main/java/org/igv/maf/MAFUtils.java | 4 -- .../igv/maf/Multiz44ConfigurationDialog.java | 4 -- .../java/org/igv/prefs/IGVPreferences.java | 4 -- .../org/igv/renderer/AbstractColorScale.java | 4 -- .../java/org/igv/renderer/ColorScale.java | 4 -- .../org/igv/renderer/ColorScaleFactory.java | 4 -- .../igv/renderer/ContinuousColorScale.java | 5 --- src/main/java/org/igv/renderer/DataRange.java | 4 -- .../java/org/igv/renderer/DataRenderer.java | 1 - .../org/igv/renderer/FeatureRenderer.java | 4 -- .../org/igv/renderer/GeneTrackRenderer.java | 5 --- .../org/igv/renderer/GisticTrackRenderer.java | 4 -- .../java/org/igv/renderer/GraphicUtils.java | 4 -- .../org/igv/renderer/MappedColorScale.java | 4 -- src/main/java/org/igv/renderer/Renderer.java | 4 -- .../org/igv/renderer/SequenceRenderer.java | 4 -- .../igv/renderer/SpliceJunctionRenderer.java | 1 - .../java/org/igv/renderer/XYPlotRenderer.java | 5 --- src/main/java/org/igv/sam/Alignment.java | 4 -- .../java/org/igv/sam/AlignmentBlockImpl.java | 4 -- .../java/org/igv/sam/AlignmentPacker.java | 4 -- src/main/java/org/igv/sam/CoverageTrack.java | 4 -- .../java/org/igv/sam/DotAlignedAlignment.java | 4 -- src/main/java/org/igv/sam/EWigTrack.java | 4 -- .../org/igv/sam/EmptyAlignmentIterator.java | 4 -- src/main/java/org/igv/sam/ReadMate.java | 4 -- .../org/igv/sam/ReducedMemoryAlignment.java | 4 -- src/main/java/org/igv/sam/SAMAlignment.java | 4 -- .../org/igv/sam/reader/AlignmentParser.java | 4 -- .../org/igv/sam/reader/AlignmentReader.java | 4 -- .../org/igv/sam/reader/DotAlignedCodec.java | 4 -- .../org/igv/sam/reader/DotAlignedParser.java | 4 -- .../java/org/igv/sam/reader/SAMReader.java | 4 -- .../java/org/igv/sam/reader/SamUtils.java | 1 - .../igv/sashimi/SashimiJunctionRenderer.java | 1 - .../java/org/igv/seg/SegmentFileParser.java | 1 - .../java/org/igv/seg/SegmentedDataSet.java | 1 - .../java/org/igv/session/RendererFactory.java | 4 -- src/main/java/org/igv/tdf/Accumulator.java | 4 -- .../java/org/igv/tdf/BufferedByteWriter.java | 4 -- src/main/java/org/igv/tdf/IBFAttributes.java | 4 -- src/main/java/org/igv/tdf/IBFBin.java | 4 -- src/main/java/org/igv/tdf/IBFIndex.java | 4 -- src/main/java/org/igv/tdf/LinearIndex.java | 4 -- src/main/java/org/igv/tdf/TDFBedTile.java | 4 -- src/main/java/org/igv/tdf/TDFDataSource.java | 4 -- src/main/java/org/igv/tdf/TDFDataset.java | 4 -- src/main/java/org/igv/tdf/TDFEntity.java | 4 -- src/main/java/org/igv/tdf/TDFFixedTile.java | 4 -- src/main/java/org/igv/tdf/TDFGroup.java | 4 -- src/main/java/org/igv/tdf/TDFReader.java | 4 -- src/main/java/org/igv/tdf/TDFTile.java | 4 -- src/main/java/org/igv/tdf/TDFUtils.java | 4 -- src/main/java/org/igv/tdf/TDFVaryTile.java | 4 -- src/main/java/org/igv/tdf/TDFWriter.java | 4 -- src/main/java/org/igv/tdf/TileFactory.java | 4 -- .../igv/tools/CommandLineStatusMonitor.java | 4 -- src/main/java/org/igv/tools/GenomeDesc.java | 4 -- src/main/java/org/igv/tools/IgvTools.java | 4 -- .../java/org/igv/tools/ListAccumulator.java | 4 -- .../org/igv/tools/PreprocessingException.java | 4 -- .../java/org/igv/tools/StatusMonitor.java | 4 -- .../java/org/igv/tools/TestFileGenerator.java | 4 -- src/main/java/org/igv/tools/UCSCUtils.java | 4 -- .../org/igv/tools/parsers/AbstractParser.java | 4 -- .../java/org/igv/tools/parsers/CNParser.java | 4 -- .../org/igv/tools/parsers/DataConsumer.java | 4 -- .../igv/tools/parsers/ToolsWiggleParser.java | 1 - .../igv/tools/parsers/UnsortedException.java | 4 -- .../java/org/igv/tools/sort/BedSorter.java | 4 -- .../java/org/igv/tools/sort/CNSorter.java | 4 -- .../org/igv/tools/sort/GenericSorter.java | 4 -- .../org/igv/tools/sort/InteractionSorter.java | 4 -- .../org/igv/tools/sort/RefgeneSorter.java | 4 -- .../java/org/igv/tools/sort/SAMSorter.java | 4 -- .../java/org/igv/track/AbstractTrack.java | 1 - src/main/java/org/igv/track/GisticTrack.java | 1 - .../java/org/igv/track/RegionScoreType.java | 4 -- .../java/org/igv/track/RenderContext.java | 4 -- .../java/org/igv/track/SequenceTrack.java | 1 - src/main/java/org/igv/track/TestUtils.java | 4 -- src/main/java/org/igv/track/Track.java | 4 -- src/main/java/org/igv/track/TrackGroup.java | 4 -- src/main/java/org/igv/track/TrackReader.java | 4 -- src/main/java/org/igv/track/TrackType.java | 4 -- .../java/org/igv/track/WindowFunction.java | 4 -- .../org/igv/ui/AbstractDataPanelTool.java | 4 -- .../java/org/igv/ui/AttributeCheckList.java | 4 -- .../org/igv/ui/DefaultExceptionHandler.java | 4 -- src/main/java/org/igv/ui/FontManager.java | 4 -- .../java/org/igv/ui/GlobalKeyDispatcher.java | 4 -- .../java/org/igv/ui/HeatmapScaleDialog.java | 4 -- .../java/org/igv/ui/ResourceFileBuilder.java | 1 - .../org/igv/ui/ResourceFileBuilderDialog.java | 4 -- .../igv/ui/UserDefinedGenomeCheckList.java | 4 -- .../igv/ui/action/ClearRegionsMenuAction.java | 4 -- .../ui/action/ExportRegionsMenuAction.java | 4 -- .../igv/ui/action/FilterTracksMenuAction.java | 4 -- .../ui/action/FitDataToWindowMenuAction.java | 4 -- .../igv/ui/action/GroupTracksMenuAction.java | 4 -- .../ui/action/ImportRegionsMenuAction.java | 4 -- .../igv/ui/action/LoadFilesMenuAction.java | 4 -- .../igv/ui/action/LoadFromDatabaseAction.java | 5 --- .../igv/ui/action/LoadFromServerAction.java | 5 --- .../igv/ui/action/LoadFromURLMenuAction.java | 4 -- .../ui/action/NavigateRegionsMenuAction.java | 4 -- .../igv/ui/action/NewSessionMenuAction.java | 4 -- .../igv/ui/action/OpenSessionMenuAction.java | 4 -- .../ui/action/OverlayTracksMenuAction.java | 4 -- .../ui/action/ReloadSessionMenuAction.java | 5 --- .../igv/ui/action/ReloadTracksMenuAction.java | 5 --- .../igv/ui/action/RenameTracksMenuAction.java | 4 -- .../igv/ui/action/ResetPreferencesAction.java | 4 -- .../igv/ui/action/SaveSessionMenuAction.java | 5 --- .../java/org/igv/ui/action/SearchCommand.java | 1 - .../igv/ui/action/SelectHubTracksAction.java | 4 -- .../ui/action/SetTrackHeightMenuAction.java | 5 --- .../igv/ui/action/SortTracksMenuAction.java | 4 -- .../igv/ui/panel/AttributeHeaderPanel.java | 1 - .../java/org/igv/ui/panel/AttributePanel.java | 1 - .../java/org/igv/ui/panel/CytobandPanel.java | 1 - .../org/igv/ui/panel/DataPanelPainter.java | 5 --- src/main/java/org/igv/ui/panel/IGVPanel.java | 4 -- .../org/igv/ui/panel/MouseableRegion.java | 4 -- .../org/igv/ui/panel/NameHeaderPanel.java | 4 -- src/main/java/org/igv/ui/panel/PanTool.java | 40 ------------------- .../java/org/igv/ui/panel/ReferenceFrame.java | 4 -- .../igv/ui/panel/RegionOfInterestPanel.java | 4 -- .../igv/ui/panel/RegionOfInterestTool.java | 4 -- .../org/igv/ui/panel/TrackPanelComponent.java | 5 --- .../igv/ui/panel/TrackPanelScrollPane.java | 4 -- src/main/java/org/igv/ui/util/CheckList.java | 4 -- .../java/org/igv/ui/util/DataPanelTool.java | 4 -- .../java/org/igv/ui/util/MessageUtils.java | 4 -- src/main/java/org/igv/ui/util/Packable.java | 4 -- .../igv/ui/util/TracingRepaintManager.java | 4 -- .../java/org/igv/ui/util/UIUtilities.java | 5 --- .../java/org/igv/util/ArrayHeapIntSorter.java | 4 -- .../org/igv/util/ArrayHeapObjectSorter.java | 4 -- src/main/java/org/igv/util/AsciiEcho.java | 4 -- src/main/java/org/igv/util/FilterElement.java | 4 -- src/main/java/org/igv/util/IlluminaUtils.java | 4 -- src/main/java/org/igv/util/IntComparator.java | 4 -- src/main/java/org/igv/util/RuntimeUtils.java | 4 -- src/main/java/org/igv/util/SequenceGC.java | 4 -- src/main/java/org/igv/util/TrackFilter.java | 4 -- src/main/java/org/igv/util/Utilities.java | 1 - .../igv/util/collections/StringArrayList.java | 4 -- .../java/org/igv/data/IGVDatasetTest.java | 4 -- .../org/igv/feature/FeatureUtilsTest.java | 4 -- src/test/java/org/igv/feature/GeneTest.java | 4 -- src/test/java/org/igv/feature/LocusTest.java | 4 -- .../org/igv/feature/ProbeToGeneMapTest.java | 4 -- .../org/igv/feature/TestLoadGeneManager.java | 4 -- .../igv/feature/aa/AminoAcidManagerTest.java | 4 -- .../igv/feature/genome/GenomeManagerTest.java | 4 -- .../igv/preprocess/FeatureDatasetTest.java | 4 -- .../igv/renderer/MappedColorScaleTest.java | 4 -- .../java/org/igv/sam/AlignmentPackerTest.java | 4 -- .../org/igv/sam/AlignmentTileLoaderTest.java | 4 -- .../java/org/igv/sam/AsciiLineReaderTest.java | 4 -- .../java/org/igv/sam/BAMFileReaderTest.java | 4 -- src/test/java/org/igv/sam/SamIndexTest.java | 4 -- src/test/java/org/igv/sam/SamIndexerTest.java | 4 -- .../org/igv/sam/SamQueryTextReaderTest.java | 4 -- .../java/org/igv/sam/cram/CRAMReaderTest.java | 4 -- .../org/igv/sam/reader/BAMHttpReaderTest.java | 4 -- .../java/org/igv/tdf/TDFReadWriteTest.java | 4 -- .../java/org/igv/tools/AccumulatorTest.java | 4 -- src/test/java/org/igv/util/HeapSortTest.java | 4 -- .../java/org/igv/util/SequenceGCTest.java | 4 -- .../util/collections/DoubleArrayListTest.java | 4 -- .../util/collections/IntArrayListTest.java | 4 -- 218 files changed, 829 deletions(-) mode change 100755 => 100644 src/main/java/org/igv/batch/CommandExecutor.java mode change 100755 => 100644 src/main/java/org/igv/sam/reader/AlignmentReader.java mode change 100755 => 100644 src/main/java/org/igv/tdf/TDFReader.java mode change 100755 => 100644 src/main/java/org/igv/util/ArrayHeapIntSorter.java diff --git a/src/main/java/org/igv/batch/CommandExecutor.java b/src/main/java/org/igv/batch/CommandExecutor.java old mode 100755 new mode 100644 index 631509e046..b368e633df --- a/src/main/java/org/igv/batch/CommandExecutor.java +++ b/src/main/java/org/igv/batch/CommandExecutor.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.batch; diff --git a/src/main/java/org/igv/blast/BlastMapping.java b/src/main/java/org/igv/blast/BlastMapping.java index e96859fe01..e9d8852c45 100644 --- a/src/main/java/org/igv/blast/BlastMapping.java +++ b/src/main/java/org/igv/blast/BlastMapping.java @@ -1,6 +1,5 @@ package org.igv.blast; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.feature.BasicFeature; import org.igv.feature.Strand; diff --git a/src/main/java/org/igv/data/AbstractDataSource.java b/src/main/java/org/igv/data/AbstractDataSource.java index 1edf9c06f3..4dd9498dde 100644 --- a/src/main/java/org/igv/data/AbstractDataSource.java +++ b/src/main/java/org/igv/data/AbstractDataSource.java @@ -1,6 +1,5 @@ package org.igv.data; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.Globals; diff --git a/src/main/java/org/igv/data/BasicScore.java b/src/main/java/org/igv/data/BasicScore.java index dc4c21a1b3..c3e22c735a 100644 --- a/src/main/java/org/igv/data/BasicScore.java +++ b/src/main/java/org/igv/data/BasicScore.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.feature.LocusScore; diff --git a/src/main/java/org/igv/data/Bin.java b/src/main/java/org/igv/data/Bin.java index ad6af39391..c0eaa659eb 100644 --- a/src/main/java/org/igv/data/Bin.java +++ b/src/main/java/org/igv/data/Bin.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; diff --git a/src/main/java/org/igv/data/CharArrayList.java b/src/main/java/org/igv/data/CharArrayList.java index 37b7813103..72bd968de0 100644 --- a/src/main/java/org/igv/data/CharArrayList.java +++ b/src/main/java/org/igv/data/CharArrayList.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; diff --git a/src/main/java/org/igv/data/ChromosomeSummary.java b/src/main/java/org/igv/data/ChromosomeSummary.java index 7c3ddf12aa..5961f1ef5b 100644 --- a/src/main/java/org/igv/data/ChromosomeSummary.java +++ b/src/main/java/org/igv/data/ChromosomeSummary.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; /** diff --git a/src/main/java/org/igv/data/CompositeScore.java b/src/main/java/org/igv/data/CompositeScore.java index ce4585370d..f294e2d065 100644 --- a/src/main/java/org/igv/data/CompositeScore.java +++ b/src/main/java/org/igv/data/CompositeScore.java @@ -1,6 +1,5 @@ package org.igv.data; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.feature.LocusScore; import org.igv.track.WindowFunction; diff --git a/src/main/java/org/igv/data/DataSource.java b/src/main/java/org/igv/data/DataSource.java index 78713b9679..0964f6b8a6 100644 --- a/src/main/java/org/igv/data/DataSource.java +++ b/src/main/java/org/igv/data/DataSource.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; diff --git a/src/main/java/org/igv/data/DataStatistics.java b/src/main/java/org/igv/data/DataStatistics.java index 606464ca29..76cd79f90b 100644 --- a/src/main/java/org/igv/data/DataStatistics.java +++ b/src/main/java/org/igv/data/DataStatistics.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.track.WindowFunction; diff --git a/src/main/java/org/igv/data/DataTile.java b/src/main/java/org/igv/data/DataTile.java index c17199fd39..fe35a300a9 100644 --- a/src/main/java/org/igv/data/DataTile.java +++ b/src/main/java/org/igv/data/DataTile.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; /** diff --git a/src/main/java/org/igv/data/Dataset.java b/src/main/java/org/igv/data/Dataset.java index e1ebc7788d..aec2902782 100644 --- a/src/main/java/org/igv/data/Dataset.java +++ b/src/main/java/org/igv/data/Dataset.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.track.TrackProperties; diff --git a/src/main/java/org/igv/data/DatasetDataSource.java b/src/main/java/org/igv/data/DatasetDataSource.java index ee00d83993..f9713fc025 100644 --- a/src/main/java/org/igv/data/DatasetDataSource.java +++ b/src/main/java/org/igv/data/DatasetDataSource.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.Globals; diff --git a/src/main/java/org/igv/data/GenomeSummaryData.java b/src/main/java/org/igv/data/GenomeSummaryData.java index ecfc8c006d..a07377a842 100644 --- a/src/main/java/org/igv/data/GenomeSummaryData.java +++ b/src/main/java/org/igv/data/GenomeSummaryData.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.logging.*; diff --git a/src/main/java/org/igv/data/IGVDataset.java b/src/main/java/org/igv/data/IGVDataset.java index 8ce00813e3..cb6a50d4bf 100644 --- a/src/main/java/org/igv/data/IGVDataset.java +++ b/src/main/java/org/igv/data/IGVDataset.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.feature.genome.Genome; diff --git a/src/main/java/org/igv/data/IGVDatasetParser.java b/src/main/java/org/igv/data/IGVDatasetParser.java index 093d0699c6..2c86dee264 100644 --- a/src/main/java/org/igv/data/IGVDatasetParser.java +++ b/src/main/java/org/igv/data/IGVDatasetParser.java @@ -1,6 +1,5 @@ package org.igv.data; -//~--- non-JDK imports -------------------------------------------------------- import htsjdk.samtools.seekablestream.SeekableStream; import org.igv.logging.*; diff --git a/src/main/java/org/igv/data/SummaryTile.java b/src/main/java/org/igv/data/SummaryTile.java index 618c62cbf5..96c2b775ba 100644 --- a/src/main/java/org/igv/data/SummaryTile.java +++ b/src/main/java/org/igv/data/SummaryTile.java @@ -1,6 +1,5 @@ package org.igv.data; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.feature.LocusScore; diff --git a/src/main/java/org/igv/data/WiggleDataset.java b/src/main/java/org/igv/data/WiggleDataset.java index dab40d67e0..3be4c086f5 100644 --- a/src/main/java/org/igv/data/WiggleDataset.java +++ b/src/main/java/org/igv/data/WiggleDataset.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.feature.genome.Genome; import org.igv.track.TrackProperties; diff --git a/src/main/java/org/igv/data/ZipUtils.java b/src/main/java/org/igv/data/ZipUtils.java index 6b488e1ff2..3cd4ac5d77 100644 --- a/src/main/java/org/igv/data/ZipUtils.java +++ b/src/main/java/org/igv/data/ZipUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.util.FileUtils; diff --git a/src/main/java/org/igv/data/expression/ExpressionFileParser.java b/src/main/java/org/igv/data/expression/ExpressionFileParser.java index e861e3feb6..87af3ba08d 100644 --- a/src/main/java/org/igv/data/expression/ExpressionFileParser.java +++ b/src/main/java/org/igv/data/expression/ExpressionFileParser.java @@ -10,7 +10,6 @@ */ package org.igv.data.expression; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.Globals; diff --git a/src/main/java/org/igv/feature/AbstractFeature.java b/src/main/java/org/igv/feature/AbstractFeature.java index b5388a5ff0..22f650bd67 100644 --- a/src/main/java/org/igv/feature/AbstractFeature.java +++ b/src/main/java/org/igv/feature/AbstractFeature.java @@ -1,6 +1,5 @@ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.ui.IGV; diff --git a/src/main/java/org/igv/feature/AbstractFeatureParser.java b/src/main/java/org/igv/feature/AbstractFeatureParser.java index b1d6d4e91b..39ea54e1f4 100644 --- a/src/main/java/org/igv/feature/AbstractFeatureParser.java +++ b/src/main/java/org/igv/feature/AbstractFeatureParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; import org.igv.logging.*; diff --git a/src/main/java/org/igv/feature/CytoBandFileParser.java b/src/main/java/org/igv/feature/CytoBandFileParser.java index 935c53a079..84898fa4ac 100644 --- a/src/main/java/org/igv/feature/CytoBandFileParser.java +++ b/src/main/java/org/igv/feature/CytoBandFileParser.java @@ -1,6 +1,5 @@ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import htsjdk.tribble.readers.AsciiLineReader; diff --git a/src/main/java/org/igv/feature/EmblFeatureTableParser.java b/src/main/java/org/igv/feature/EmblFeatureTableParser.java index 4d424b3a69..35a867a114 100644 --- a/src/main/java/org/igv/feature/EmblFeatureTableParser.java +++ b/src/main/java/org/igv/feature/EmblFeatureTableParser.java @@ -1,6 +1,5 @@ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.feature.genome.Genome; diff --git a/src/main/java/org/igv/feature/FeatureDB.java b/src/main/java/org/igv/feature/FeatureDB.java index 08d45fe514..363c7e685c 100644 --- a/src/main/java/org/igv/feature/FeatureDB.java +++ b/src/main/java/org/igv/feature/FeatureDB.java @@ -1,6 +1,5 @@ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import com.jidesoft.utils.SortedList; import htsjdk.tribble.Feature; diff --git a/src/main/java/org/igv/feature/FeatureParser.java b/src/main/java/org/igv/feature/FeatureParser.java index 16069593c8..1e47aac147 100644 --- a/src/main/java/org/igv/feature/FeatureParser.java +++ b/src/main/java/org/igv/feature/FeatureParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; diff --git a/src/main/java/org/igv/feature/GisticFileParser.java b/src/main/java/org/igv/feature/GisticFileParser.java index e0c80fc122..4a6ecb06b5 100644 --- a/src/main/java/org/igv/feature/GisticFileParser.java +++ b/src/main/java/org/igv/feature/GisticFileParser.java @@ -8,7 +8,6 @@ */ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.exceptions.ParserException; diff --git a/src/main/java/org/igv/feature/GisticScore.java b/src/main/java/org/igv/feature/GisticScore.java index 23d91d7da4..c245915f34 100644 --- a/src/main/java/org/igv/feature/GisticScore.java +++ b/src/main/java/org/igv/feature/GisticScore.java @@ -9,7 +9,6 @@ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.track.WindowFunction; diff --git a/src/main/java/org/igv/feature/Locus.java b/src/main/java/org/igv/feature/Locus.java index b4af0ea8a7..db660e1d46 100644 --- a/src/main/java/org/igv/feature/Locus.java +++ b/src/main/java/org/igv/feature/Locus.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; import java.text.NumberFormat; diff --git a/src/main/java/org/igv/feature/LocusScore.java b/src/main/java/org/igv/feature/LocusScore.java index 46b53e46c0..5a29483685 100644 --- a/src/main/java/org/igv/feature/LocusScore.java +++ b/src/main/java/org/igv/feature/LocusScore.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; import org.igv.track.WindowFunction; diff --git a/src/main/java/org/igv/feature/Mutation.java b/src/main/java/org/igv/feature/Mutation.java index 93f77d913b..8e49fd5d9e 100644 --- a/src/main/java/org/igv/feature/Mutation.java +++ b/src/main/java/org/igv/feature/Mutation.java @@ -1,6 +1,5 @@ package org.igv.feature; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.feature.genome.GenomeManager; import org.igv.logging.*; diff --git a/src/main/java/org/igv/feature/Strand.java b/src/main/java/org/igv/feature/Strand.java index 41b559fe02..4f2b16e028 100644 --- a/src/main/java/org/igv/feature/Strand.java +++ b/src/main/java/org/igv/feature/Strand.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; diff --git a/src/main/java/org/igv/feature/aa/AminoAcid.java b/src/main/java/org/igv/feature/aa/AminoAcid.java index 6d7e246a7f..5e6517ec74 100644 --- a/src/main/java/org/igv/feature/aa/AminoAcid.java +++ b/src/main/java/org/igv/feature/aa/AminoAcid.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.aa; /** diff --git a/src/main/java/org/igv/feature/aa/AminoAcidManager.java b/src/main/java/org/igv/feature/aa/AminoAcidManager.java index 0af284b86c..fd8175ad62 100644 --- a/src/main/java/org/igv/feature/aa/AminoAcidManager.java +++ b/src/main/java/org/igv/feature/aa/AminoAcidManager.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.aa; import org.igv.logging.*; diff --git a/src/main/java/org/igv/feature/aa/AminoAcidSequence.java b/src/main/java/org/igv/feature/aa/AminoAcidSequence.java index d481828fd9..51dfac7d6a 100644 --- a/src/main/java/org/igv/feature/aa/AminoAcidSequence.java +++ b/src/main/java/org/igv/feature/aa/AminoAcidSequence.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.aa; import org.igv.feature.Strand; diff --git a/src/main/java/org/igv/feature/aa/CodonTableManager.java b/src/main/java/org/igv/feature/aa/CodonTableManager.java index b4ed808a02..26eab38708 100644 --- a/src/main/java/org/igv/feature/aa/CodonTableManager.java +++ b/src/main/java/org/igv/feature/aa/CodonTableManager.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.aa; import org.igv.logging.*; diff --git a/src/main/java/org/igv/feature/basepair/BasePairRenderer.java b/src/main/java/org/igv/feature/basepair/BasePairRenderer.java index d1084825de..a30555a105 100644 --- a/src/main/java/org/igv/feature/basepair/BasePairRenderer.java +++ b/src/main/java/org/igv/feature/basepair/BasePairRenderer.java @@ -1,6 +1,5 @@ package org.igv.feature.basepair; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.feature.basepair.BasePairTrack.*; diff --git a/src/main/java/org/igv/feature/dranger/DRangerFeature.java b/src/main/java/org/igv/feature/dranger/DRangerFeature.java index e3d3768734..efe808086b 100644 --- a/src/main/java/org/igv/feature/dranger/DRangerFeature.java +++ b/src/main/java/org/igv/feature/dranger/DRangerFeature.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.dranger; import org.igv.feature.AbstractFeature; diff --git a/src/main/java/org/igv/feature/dranger/DRangerParser.java b/src/main/java/org/igv/feature/dranger/DRangerParser.java index 228f8a7001..d9aa765800 100644 --- a/src/main/java/org/igv/feature/dranger/DRangerParser.java +++ b/src/main/java/org/igv/feature/dranger/DRangerParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.dranger; import org.igv.logging.*; diff --git a/src/main/java/org/igv/feature/dranger/DRangerRenderer.java b/src/main/java/org/igv/feature/dranger/DRangerRenderer.java index 387a322a2c..cbe2d2dff0 100644 --- a/src/main/java/org/igv/feature/dranger/DRangerRenderer.java +++ b/src/main/java/org/igv/feature/dranger/DRangerRenderer.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.dranger; import org.igv.feature.IGVFeature; diff --git a/src/main/java/org/igv/feature/genome/GenomeImporter.java b/src/main/java/org/igv/feature/genome/GenomeImporter.java index 46e7e29ec6..1d9e01a200 100644 --- a/src/main/java/org/igv/feature/genome/GenomeImporter.java +++ b/src/main/java/org/igv/feature/genome/GenomeImporter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.genome; import org.igv.logging.*; diff --git a/src/main/java/org/igv/feature/genome/SequenceWrapper.java b/src/main/java/org/igv/feature/genome/SequenceWrapper.java index a59bb22345..2853458f6d 100644 --- a/src/main/java/org/igv/feature/genome/SequenceWrapper.java +++ b/src/main/java/org/igv/feature/genome/SequenceWrapper.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.genome; import org.igv.feature.Chromosome; diff --git a/src/main/java/org/igv/maf/MAFReader.java b/src/main/java/org/igv/maf/MAFReader.java index 8d45b6f675..4d33f9fac1 100644 --- a/src/main/java/org/igv/maf/MAFReader.java +++ b/src/main/java/org/igv/maf/MAFReader.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.maf; diff --git a/src/main/java/org/igv/maf/MAFTile.java b/src/main/java/org/igv/maf/MAFTile.java index dd00312f2d..6cfb57629a 100644 --- a/src/main/java/org/igv/maf/MAFTile.java +++ b/src/main/java/org/igv/maf/MAFTile.java @@ -1,6 +1,5 @@ package org.igv.maf; -//~--- non-JDK imports -------------------------------------------------------- import java.util.ArrayList; import java.util.LinkedHashMap; diff --git a/src/main/java/org/igv/maf/MAFTileCodec.java b/src/main/java/org/igv/maf/MAFTileCodec.java index e89d467286..a211d4c989 100644 --- a/src/main/java/org/igv/maf/MAFTileCodec.java +++ b/src/main/java/org/igv/maf/MAFTileCodec.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.maf; import org.igv.maf.MAFTile.MASequence; diff --git a/src/main/java/org/igv/maf/MAFUtils.java b/src/main/java/org/igv/maf/MAFUtils.java index 2767f08406..a1d7c74c1b 100644 --- a/src/main/java/org/igv/maf/MAFUtils.java +++ b/src/main/java/org/igv/maf/MAFUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.maf; diff --git a/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java b/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java index ceefe1c810..73046eadf6 100644 --- a/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java +++ b/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ /* * MAFConfigurationDialog.java diff --git a/src/main/java/org/igv/prefs/IGVPreferences.java b/src/main/java/org/igv/prefs/IGVPreferences.java index babc6d93e8..583b5d6a6d 100644 --- a/src/main/java/org/igv/prefs/IGVPreferences.java +++ b/src/main/java/org/igv/prefs/IGVPreferences.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.prefs; diff --git a/src/main/java/org/igv/renderer/AbstractColorScale.java b/src/main/java/org/igv/renderer/AbstractColorScale.java index 2ccaab25f8..eb5d98ae4a 100644 --- a/src/main/java/org/igv/renderer/AbstractColorScale.java +++ b/src/main/java/org/igv/renderer/AbstractColorScale.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; diff --git a/src/main/java/org/igv/renderer/ColorScale.java b/src/main/java/org/igv/renderer/ColorScale.java index 0c970be6eb..0a3909635a 100644 --- a/src/main/java/org/igv/renderer/ColorScale.java +++ b/src/main/java/org/igv/renderer/ColorScale.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import java.awt.*; diff --git a/src/main/java/org/igv/renderer/ColorScaleFactory.java b/src/main/java/org/igv/renderer/ColorScaleFactory.java index a1eac78fb4..48eb389b9d 100644 --- a/src/main/java/org/igv/renderer/ColorScaleFactory.java +++ b/src/main/java/org/igv/renderer/ColorScaleFactory.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import java.util.HashMap; diff --git a/src/main/java/org/igv/renderer/ContinuousColorScale.java b/src/main/java/org/igv/renderer/ContinuousColorScale.java index 015452bf5d..170b2369f6 100644 --- a/src/main/java/org/igv/renderer/ContinuousColorScale.java +++ b/src/main/java/org/igv/renderer/ContinuousColorScale.java @@ -1,10 +1,5 @@ -/* -* To change this template, choose Tools | Templates -* and open the template in the editor. -*/ package org.igv.renderer; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.prefs.Constants; import org.igv.prefs.PreferencesManager; diff --git a/src/main/java/org/igv/renderer/DataRange.java b/src/main/java/org/igv/renderer/DataRange.java index 55601bde94..7ae5c6361f 100644 --- a/src/main/java/org/igv/renderer/DataRange.java +++ b/src/main/java/org/igv/renderer/DataRange.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import org.igv.session.Persistable; diff --git a/src/main/java/org/igv/renderer/DataRenderer.java b/src/main/java/org/igv/renderer/DataRenderer.java index e9d8bf7e2f..8f239e3f8e 100644 --- a/src/main/java/org/igv/renderer/DataRenderer.java +++ b/src/main/java/org/igv/renderer/DataRenderer.java @@ -10,7 +10,6 @@ package org.igv.renderer; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.Globals; diff --git a/src/main/java/org/igv/renderer/FeatureRenderer.java b/src/main/java/org/igv/renderer/FeatureRenderer.java index 163d4c887f..04da18904b 100644 --- a/src/main/java/org/igv/renderer/FeatureRenderer.java +++ b/src/main/java/org/igv/renderer/FeatureRenderer.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import org.igv.Globals; diff --git a/src/main/java/org/igv/renderer/GeneTrackRenderer.java b/src/main/java/org/igv/renderer/GeneTrackRenderer.java index 7c6ef41c11..b6a9d44051 100644 --- a/src/main/java/org/igv/renderer/GeneTrackRenderer.java +++ b/src/main/java/org/igv/renderer/GeneTrackRenderer.java @@ -1,10 +1,5 @@ -/* -* To change this template, choose Tools | Templates -* and open the template in the editor. -*/ package org.igv.renderer; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; diff --git a/src/main/java/org/igv/renderer/GisticTrackRenderer.java b/src/main/java/org/igv/renderer/GisticTrackRenderer.java index 8584dc7bbc..7f7c2e5221 100644 --- a/src/main/java/org/igv/renderer/GisticTrackRenderer.java +++ b/src/main/java/org/igv/renderer/GisticTrackRenderer.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import org.igv.feature.GisticScore; diff --git a/src/main/java/org/igv/renderer/GraphicUtils.java b/src/main/java/org/igv/renderer/GraphicUtils.java index c953f4a3be..778c4b25b9 100644 --- a/src/main/java/org/igv/renderer/GraphicUtils.java +++ b/src/main/java/org/igv/renderer/GraphicUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import org.igv.Globals; diff --git a/src/main/java/org/igv/renderer/MappedColorScale.java b/src/main/java/org/igv/renderer/MappedColorScale.java index 6ec6626957..9d6fc0bf42 100644 --- a/src/main/java/org/igv/renderer/MappedColorScale.java +++ b/src/main/java/org/igv/renderer/MappedColorScale.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; diff --git a/src/main/java/org/igv/renderer/Renderer.java b/src/main/java/org/igv/renderer/Renderer.java index d702567bee..3161c9a900 100644 --- a/src/main/java/org/igv/renderer/Renderer.java +++ b/src/main/java/org/igv/renderer/Renderer.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; diff --git a/src/main/java/org/igv/renderer/SequenceRenderer.java b/src/main/java/org/igv/renderer/SequenceRenderer.java index 9ac39e556e..9fbb37e4b5 100644 --- a/src/main/java/org/igv/renderer/SequenceRenderer.java +++ b/src/main/java/org/igv/renderer/SequenceRenderer.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; import org.igv.Globals; diff --git a/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java b/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java index 5a89603df4..b01843fd2a 100644 --- a/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java +++ b/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java @@ -1,6 +1,5 @@ package org.igv.renderer; -//~--- non-JDK imports -------------------------------------------------------- import htsjdk.tribble.Feature; import org.igv.Globals; diff --git a/src/main/java/org/igv/renderer/XYPlotRenderer.java b/src/main/java/org/igv/renderer/XYPlotRenderer.java index 166ecd518d..45f30b6264 100644 --- a/src/main/java/org/igv/renderer/XYPlotRenderer.java +++ b/src/main/java/org/igv/renderer/XYPlotRenderer.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.feature.LocusScore; import org.igv.prefs.IGVPreferences; diff --git a/src/main/java/org/igv/sam/Alignment.java b/src/main/java/org/igv/sam/Alignment.java index c1559a55b0..c89b8d27b9 100644 --- a/src/main/java/org/igv/sam/Alignment.java +++ b/src/main/java/org/igv/sam/Alignment.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import htsjdk.samtools.Cigar; diff --git a/src/main/java/org/igv/sam/AlignmentBlockImpl.java b/src/main/java/org/igv/sam/AlignmentBlockImpl.java index 8345a56721..ee08041ef8 100644 --- a/src/main/java/org/igv/sam/AlignmentBlockImpl.java +++ b/src/main/java/org/igv/sam/AlignmentBlockImpl.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; public class AlignmentBlockImpl implements AlignmentBlock { diff --git a/src/main/java/org/igv/sam/AlignmentPacker.java b/src/main/java/org/igv/sam/AlignmentPacker.java index 50c81afd20..ec02ced9d6 100644 --- a/src/main/java/org/igv/sam/AlignmentPacker.java +++ b/src/main/java/org/igv/sam/AlignmentPacker.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import htsjdk.samtools.SAMTag; diff --git a/src/main/java/org/igv/sam/CoverageTrack.java b/src/main/java/org/igv/sam/CoverageTrack.java index 3a8a5a559d..6c0448e1c6 100644 --- a/src/main/java/org/igv/sam/CoverageTrack.java +++ b/src/main/java/org/igv/sam/CoverageTrack.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import org.igv.Globals; diff --git a/src/main/java/org/igv/sam/DotAlignedAlignment.java b/src/main/java/org/igv/sam/DotAlignedAlignment.java index e1ff0029bf..6136f9ff3e 100644 --- a/src/main/java/org/igv/sam/DotAlignedAlignment.java +++ b/src/main/java/org/igv/sam/DotAlignedAlignment.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import org.igv.feature.LocusScore; diff --git a/src/main/java/org/igv/sam/EWigTrack.java b/src/main/java/org/igv/sam/EWigTrack.java index c51ea81f57..a8715fbdeb 100644 --- a/src/main/java/org/igv/sam/EWigTrack.java +++ b/src/main/java/org/igv/sam/EWigTrack.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import org.igv.feature.Locus; diff --git a/src/main/java/org/igv/sam/EmptyAlignmentIterator.java b/src/main/java/org/igv/sam/EmptyAlignmentIterator.java index abffe64428..45e1aa2496 100644 --- a/src/main/java/org/igv/sam/EmptyAlignmentIterator.java +++ b/src/main/java/org/igv/sam/EmptyAlignmentIterator.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import htsjdk.samtools.util.CloseableIterator; diff --git a/src/main/java/org/igv/sam/ReadMate.java b/src/main/java/org/igv/sam/ReadMate.java index 5629d0b2d5..293ceb6c8d 100644 --- a/src/main/java/org/igv/sam/ReadMate.java +++ b/src/main/java/org/igv/sam/ReadMate.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; diff --git a/src/main/java/org/igv/sam/ReducedMemoryAlignment.java b/src/main/java/org/igv/sam/ReducedMemoryAlignment.java index fa1291d07b..e672b8284e 100644 --- a/src/main/java/org/igv/sam/ReducedMemoryAlignment.java +++ b/src/main/java/org/igv/sam/ReducedMemoryAlignment.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import org.igv.logging.*; diff --git a/src/main/java/org/igv/sam/SAMAlignment.java b/src/main/java/org/igv/sam/SAMAlignment.java index d422d6cd94..a849ba3755 100644 --- a/src/main/java/org/igv/sam/SAMAlignment.java +++ b/src/main/java/org/igv/sam/SAMAlignment.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import htsjdk.samtools.*; diff --git a/src/main/java/org/igv/sam/reader/AlignmentParser.java b/src/main/java/org/igv/sam/reader/AlignmentParser.java index fc4efde09d..a77f3d8c97 100644 --- a/src/main/java/org/igv/sam/reader/AlignmentParser.java +++ b/src/main/java/org/igv/sam/reader/AlignmentParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.reader; diff --git a/src/main/java/org/igv/sam/reader/AlignmentReader.java b/src/main/java/org/igv/sam/reader/AlignmentReader.java old mode 100755 new mode 100644 index 891a2e480a..9629912825 --- a/src/main/java/org/igv/sam/reader/AlignmentReader.java +++ b/src/main/java/org/igv/sam/reader/AlignmentReader.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.reader; diff --git a/src/main/java/org/igv/sam/reader/DotAlignedCodec.java b/src/main/java/org/igv/sam/reader/DotAlignedCodec.java index b2f80bd9ad..892a2077aa 100644 --- a/src/main/java/org/igv/sam/reader/DotAlignedCodec.java +++ b/src/main/java/org/igv/sam/reader/DotAlignedCodec.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.reader; import org.igv.util.collections.SortingCollection; diff --git a/src/main/java/org/igv/sam/reader/DotAlignedParser.java b/src/main/java/org/igv/sam/reader/DotAlignedParser.java index 343760f8f9..7da86b4aa7 100644 --- a/src/main/java/org/igv/sam/reader/DotAlignedParser.java +++ b/src/main/java/org/igv/sam/reader/DotAlignedParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.reader; import org.igv.logging.*; diff --git a/src/main/java/org/igv/sam/reader/SAMReader.java b/src/main/java/org/igv/sam/reader/SAMReader.java index 6352a70420..786a9da099 100644 --- a/src/main/java/org/igv/sam/reader/SAMReader.java +++ b/src/main/java/org/igv/sam/reader/SAMReader.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.reader; import htsjdk.samtools.*; diff --git a/src/main/java/org/igv/sam/reader/SamUtils.java b/src/main/java/org/igv/sam/reader/SamUtils.java index 30a1357307..c360fa3126 100644 --- a/src/main/java/org/igv/sam/reader/SamUtils.java +++ b/src/main/java/org/igv/sam/reader/SamUtils.java @@ -1,6 +1,5 @@ package org.igv.sam.reader; -//~--- non-JDK imports -------------------------------------------------------- //~--- JDK imports ------------------------------------------------------------ diff --git a/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java b/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java index 541369dec8..0ea75cd2a7 100644 --- a/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java +++ b/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java @@ -1,6 +1,5 @@ package org.igv.sashimi; -//~--- non-JDK imports -------------------------------------------------------- import htsjdk.tribble.Feature; import org.igv.Globals; diff --git a/src/main/java/org/igv/seg/SegmentFileParser.java b/src/main/java/org/igv/seg/SegmentFileParser.java index fd783db79d..487545b575 100644 --- a/src/main/java/org/igv/seg/SegmentFileParser.java +++ b/src/main/java/org/igv/seg/SegmentFileParser.java @@ -1,6 +1,5 @@ package org.igv.seg; -//~--- non-JDK imports -------------------------------------------------------- import htsjdk.tribble.readers.AsciiLineReader; import org.igv.Globals; diff --git a/src/main/java/org/igv/seg/SegmentedDataSet.java b/src/main/java/org/igv/seg/SegmentedDataSet.java index 4c8158f30c..0ce8c6aadc 100644 --- a/src/main/java/org/igv/seg/SegmentedDataSet.java +++ b/src/main/java/org/igv/seg/SegmentedDataSet.java @@ -5,7 +5,6 @@ */ package org.igv.seg; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.Globals; import org.igv.feature.FeatureUtils; diff --git a/src/main/java/org/igv/session/RendererFactory.java b/src/main/java/org/igv/session/RendererFactory.java index a778acc2fc..f46bef265e 100644 --- a/src/main/java/org/igv/session/RendererFactory.java +++ b/src/main/java/org/igv/session/RendererFactory.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.session; import org.igv.renderer.*; diff --git a/src/main/java/org/igv/tdf/Accumulator.java b/src/main/java/org/igv/tdf/Accumulator.java index 8b7898e8ec..03a71bc7de 100644 --- a/src/main/java/org/igv/tdf/Accumulator.java +++ b/src/main/java/org/igv/tdf/Accumulator.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.apache.commons.math3.stat.StatUtils; diff --git a/src/main/java/org/igv/tdf/BufferedByteWriter.java b/src/main/java/org/igv/tdf/BufferedByteWriter.java index 0ec7a5c589..07f9e92aed 100644 --- a/src/main/java/org/igv/tdf/BufferedByteWriter.java +++ b/src/main/java/org/igv/tdf/BufferedByteWriter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import java.io.ByteArrayOutputStream; diff --git a/src/main/java/org/igv/tdf/IBFAttributes.java b/src/main/java/org/igv/tdf/IBFAttributes.java index cebd376dec..376661da4a 100644 --- a/src/main/java/org/igv/tdf/IBFAttributes.java +++ b/src/main/java/org/igv/tdf/IBFAttributes.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; diff --git a/src/main/java/org/igv/tdf/IBFBin.java b/src/main/java/org/igv/tdf/IBFBin.java index c8bd8bb716..b529110c0a 100644 --- a/src/main/java/org/igv/tdf/IBFBin.java +++ b/src/main/java/org/igv/tdf/IBFBin.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; diff --git a/src/main/java/org/igv/tdf/IBFIndex.java b/src/main/java/org/igv/tdf/IBFIndex.java index c88beb92ba..cd29bf5cca 100644 --- a/src/main/java/org/igv/tdf/IBFIndex.java +++ b/src/main/java/org/igv/tdf/IBFIndex.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; diff --git a/src/main/java/org/igv/tdf/LinearIndex.java b/src/main/java/org/igv/tdf/LinearIndex.java index 7cb21bdb55..8fc709e323 100644 --- a/src/main/java/org/igv/tdf/LinearIndex.java +++ b/src/main/java/org/igv/tdf/LinearIndex.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; diff --git a/src/main/java/org/igv/tdf/TDFBedTile.java b/src/main/java/org/igv/tdf/TDFBedTile.java index 0042e87a90..6932fbee84 100644 --- a/src/main/java/org/igv/tdf/TDFBedTile.java +++ b/src/main/java/org/igv/tdf/TDFBedTile.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.util.StringUtils; diff --git a/src/main/java/org/igv/tdf/TDFDataSource.java b/src/main/java/org/igv/tdf/TDFDataSource.java index 57ee55502b..c90a20f2c0 100644 --- a/src/main/java/org/igv/tdf/TDFDataSource.java +++ b/src/main/java/org/igv/tdf/TDFDataSource.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.feature.genome.ChromAliasManager; diff --git a/src/main/java/org/igv/tdf/TDFDataset.java b/src/main/java/org/igv/tdf/TDFDataset.java index 5674f39910..581cee07c2 100644 --- a/src/main/java/org/igv/tdf/TDFDataset.java +++ b/src/main/java/org/igv/tdf/TDFDataset.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.util.StringUtils; diff --git a/src/main/java/org/igv/tdf/TDFEntity.java b/src/main/java/org/igv/tdf/TDFEntity.java index d9187689a0..22ce657e8d 100644 --- a/src/main/java/org/igv/tdf/TDFEntity.java +++ b/src/main/java/org/igv/tdf/TDFEntity.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.util.StringUtils; diff --git a/src/main/java/org/igv/tdf/TDFFixedTile.java b/src/main/java/org/igv/tdf/TDFFixedTile.java index aa90f32fc7..fef34b3cef 100644 --- a/src/main/java/org/igv/tdf/TDFFixedTile.java +++ b/src/main/java/org/igv/tdf/TDFFixedTile.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import java.io.IOException; diff --git a/src/main/java/org/igv/tdf/TDFGroup.java b/src/main/java/org/igv/tdf/TDFGroup.java index 12ad6f7941..a476583db6 100644 --- a/src/main/java/org/igv/tdf/TDFGroup.java +++ b/src/main/java/org/igv/tdf/TDFGroup.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import java.io.IOException; diff --git a/src/main/java/org/igv/tdf/TDFReader.java b/src/main/java/org/igv/tdf/TDFReader.java old mode 100755 new mode 100644 index 0e4979ef12..2d18a697aa --- a/src/main/java/org/igv/tdf/TDFReader.java +++ b/src/main/java/org/igv/tdf/TDFReader.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import htsjdk.samtools.seekablestream.SeekableStream; diff --git a/src/main/java/org/igv/tdf/TDFTile.java b/src/main/java/org/igv/tdf/TDFTile.java index fd03569224..f12e68f696 100644 --- a/src/main/java/org/igv/tdf/TDFTile.java +++ b/src/main/java/org/igv/tdf/TDFTile.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; diff --git a/src/main/java/org/igv/tdf/TDFUtils.java b/src/main/java/org/igv/tdf/TDFUtils.java index 46ab308381..22a2588627 100644 --- a/src/main/java/org/igv/tdf/TDFUtils.java +++ b/src/main/java/org/igv/tdf/TDFUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.Globals; diff --git a/src/main/java/org/igv/tdf/TDFVaryTile.java b/src/main/java/org/igv/tdf/TDFVaryTile.java index 45ebc0dcbb..6fb5ecffb5 100644 --- a/src/main/java/org/igv/tdf/TDFVaryTile.java +++ b/src/main/java/org/igv/tdf/TDFVaryTile.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import java.io.IOException; diff --git a/src/main/java/org/igv/tdf/TDFWriter.java b/src/main/java/org/igv/tdf/TDFWriter.java index 6d56d76f03..6bb7e99477 100644 --- a/src/main/java/org/igv/tdf/TDFWriter.java +++ b/src/main/java/org/igv/tdf/TDFWriter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.logging.*; diff --git a/src/main/java/org/igv/tdf/TileFactory.java b/src/main/java/org/igv/tdf/TileFactory.java index 29ed8e72d1..702af96c91 100644 --- a/src/main/java/org/igv/tdf/TileFactory.java +++ b/src/main/java/org/igv/tdf/TileFactory.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; diff --git a/src/main/java/org/igv/tools/CommandLineStatusMonitor.java b/src/main/java/org/igv/tools/CommandLineStatusMonitor.java index adb4527ae8..632e3ca246 100644 --- a/src/main/java/org/igv/tools/CommandLineStatusMonitor.java +++ b/src/main/java/org/igv/tools/CommandLineStatusMonitor.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; import java.io.PrintStream; diff --git a/src/main/java/org/igv/tools/GenomeDesc.java b/src/main/java/org/igv/tools/GenomeDesc.java index 20c613c54d..3add40ce1e 100644 --- a/src/main/java/org/igv/tools/GenomeDesc.java +++ b/src/main/java/org/igv/tools/GenomeDesc.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; import java.util.List; diff --git a/src/main/java/org/igv/tools/IgvTools.java b/src/main/java/org/igv/tools/IgvTools.java index d956b7158f..425595b90e 100644 --- a/src/main/java/org/igv/tools/IgvTools.java +++ b/src/main/java/org/igv/tools/IgvTools.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; diff --git a/src/main/java/org/igv/tools/ListAccumulator.java b/src/main/java/org/igv/tools/ListAccumulator.java index b4f7c915c1..6ab703643d 100644 --- a/src/main/java/org/igv/tools/ListAccumulator.java +++ b/src/main/java/org/igv/tools/ListAccumulator.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; import org.igv.util.collections.DoubleArrayList; diff --git a/src/main/java/org/igv/tools/PreprocessingException.java b/src/main/java/org/igv/tools/PreprocessingException.java index 3db05eb215..93ec315645 100644 --- a/src/main/java/org/igv/tools/PreprocessingException.java +++ b/src/main/java/org/igv/tools/PreprocessingException.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; diff --git a/src/main/java/org/igv/tools/StatusMonitor.java b/src/main/java/org/igv/tools/StatusMonitor.java index d62de67e3a..81fb9665e9 100644 --- a/src/main/java/org/igv/tools/StatusMonitor.java +++ b/src/main/java/org/igv/tools/StatusMonitor.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; diff --git a/src/main/java/org/igv/tools/TestFileGenerator.java b/src/main/java/org/igv/tools/TestFileGenerator.java index cafe3f8560..66f7fac796 100644 --- a/src/main/java/org/igv/tools/TestFileGenerator.java +++ b/src/main/java/org/igv/tools/TestFileGenerator.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; import org.igv.logging.*; diff --git a/src/main/java/org/igv/tools/UCSCUtils.java b/src/main/java/org/igv/tools/UCSCUtils.java index 78476bdc99..af3f41389f 100644 --- a/src/main/java/org/igv/tools/UCSCUtils.java +++ b/src/main/java/org/igv/tools/UCSCUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; import org.igv.logging.*; diff --git a/src/main/java/org/igv/tools/parsers/AbstractParser.java b/src/main/java/org/igv/tools/parsers/AbstractParser.java index c35a9824e3..970cc23fee 100644 --- a/src/main/java/org/igv/tools/parsers/AbstractParser.java +++ b/src/main/java/org/igv/tools/parsers/AbstractParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.parsers; diff --git a/src/main/java/org/igv/tools/parsers/CNParser.java b/src/main/java/org/igv/tools/parsers/CNParser.java index c2fe52137b..6a607b4a91 100644 --- a/src/main/java/org/igv/tools/parsers/CNParser.java +++ b/src/main/java/org/igv/tools/parsers/CNParser.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.parsers; import org.igv.logging.*; diff --git a/src/main/java/org/igv/tools/parsers/DataConsumer.java b/src/main/java/org/igv/tools/parsers/DataConsumer.java index 23add440bf..b1fac6be9b 100644 --- a/src/main/java/org/igv/tools/parsers/DataConsumer.java +++ b/src/main/java/org/igv/tools/parsers/DataConsumer.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.parsers; import org.igv.track.TrackType; diff --git a/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java b/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java index fa27268ead..a9a5af4a06 100644 --- a/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java +++ b/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java @@ -1,6 +1,5 @@ package org.igv.tools.parsers; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.Globals; diff --git a/src/main/java/org/igv/tools/parsers/UnsortedException.java b/src/main/java/org/igv/tools/parsers/UnsortedException.java index 9d7250689b..d463eca598 100644 --- a/src/main/java/org/igv/tools/parsers/UnsortedException.java +++ b/src/main/java/org/igv/tools/parsers/UnsortedException.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.parsers; diff --git a/src/main/java/org/igv/tools/sort/BedSorter.java b/src/main/java/org/igv/tools/sort/BedSorter.java index f685a0dcf6..98633a98a5 100644 --- a/src/main/java/org/igv/tools/sort/BedSorter.java +++ b/src/main/java/org/igv/tools/sort/BedSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.sort; import htsjdk.tribble.readers.AsciiLineReader; diff --git a/src/main/java/org/igv/tools/sort/CNSorter.java b/src/main/java/org/igv/tools/sort/CNSorter.java index 0d6828656d..05459bc8e7 100644 --- a/src/main/java/org/igv/tools/sort/CNSorter.java +++ b/src/main/java/org/igv/tools/sort/CNSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.sort; import org.igv.logging.*; diff --git a/src/main/java/org/igv/tools/sort/GenericSorter.java b/src/main/java/org/igv/tools/sort/GenericSorter.java index a839a58748..24bd931873 100644 --- a/src/main/java/org/igv/tools/sort/GenericSorter.java +++ b/src/main/java/org/igv/tools/sort/GenericSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.sort; import htsjdk.tribble.readers.AsciiLineReader; diff --git a/src/main/java/org/igv/tools/sort/InteractionSorter.java b/src/main/java/org/igv/tools/sort/InteractionSorter.java index 514dbe1f9b..85bb87c4ae 100644 --- a/src/main/java/org/igv/tools/sort/InteractionSorter.java +++ b/src/main/java/org/igv/tools/sort/InteractionSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.sort; import htsjdk.tribble.readers.AsciiLineReader; diff --git a/src/main/java/org/igv/tools/sort/RefgeneSorter.java b/src/main/java/org/igv/tools/sort/RefgeneSorter.java index f9257c9523..252c953853 100644 --- a/src/main/java/org/igv/tools/sort/RefgeneSorter.java +++ b/src/main/java/org/igv/tools/sort/RefgeneSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.sort; import htsjdk.tribble.readers.AsciiLineReader; diff --git a/src/main/java/org/igv/tools/sort/SAMSorter.java b/src/main/java/org/igv/tools/sort/SAMSorter.java index d72966266f..be066c25b0 100644 --- a/src/main/java/org/igv/tools/sort/SAMSorter.java +++ b/src/main/java/org/igv/tools/sort/SAMSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools.sort; import htsjdk.tribble.readers.AsciiLineReader; diff --git a/src/main/java/org/igv/track/AbstractTrack.java b/src/main/java/org/igv/track/AbstractTrack.java index da7b8b77a1..6b69a8f5de 100644 --- a/src/main/java/org/igv/track/AbstractTrack.java +++ b/src/main/java/org/igv/track/AbstractTrack.java @@ -1,6 +1,5 @@ package org.igv.track; -//~--- non-JDK imports -------------------------------------------------------- import htsjdk.tribble.Feature; import org.igv.Globals; diff --git a/src/main/java/org/igv/track/GisticTrack.java b/src/main/java/org/igv/track/GisticTrack.java index 51330f74f8..06c92d3b84 100644 --- a/src/main/java/org/igv/track/GisticTrack.java +++ b/src/main/java/org/igv/track/GisticTrack.java @@ -8,7 +8,6 @@ */ package org.igv.track; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.feature.IGVFeature; diff --git a/src/main/java/org/igv/track/RegionScoreType.java b/src/main/java/org/igv/track/RegionScoreType.java index 02974352be..b3fddb932f 100644 --- a/src/main/java/org/igv/track/RegionScoreType.java +++ b/src/main/java/org/igv/track/RegionScoreType.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; diff --git a/src/main/java/org/igv/track/RenderContext.java b/src/main/java/org/igv/track/RenderContext.java index b4d7c5048e..bbc7d8d7e6 100644 --- a/src/main/java/org/igv/track/RenderContext.java +++ b/src/main/java/org/igv/track/RenderContext.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; import org.igv.prefs.PreferencesManager; diff --git a/src/main/java/org/igv/track/SequenceTrack.java b/src/main/java/org/igv/track/SequenceTrack.java index cd2891b372..1a6ad0ac95 100644 --- a/src/main/java/org/igv/track/SequenceTrack.java +++ b/src/main/java/org/igv/track/SequenceTrack.java @@ -1,6 +1,5 @@ package org.igv.track; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.event.IGVEvent; import org.igv.logging.*; diff --git a/src/main/java/org/igv/track/TestUtils.java b/src/main/java/org/igv/track/TestUtils.java index 1f34d92fca..807c4599af 100644 --- a/src/main/java/org/igv/track/TestUtils.java +++ b/src/main/java/org/igv/track/TestUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; diff --git a/src/main/java/org/igv/track/Track.java b/src/main/java/org/igv/track/Track.java index f8c39b84fb..d2490a85ba 100644 --- a/src/main/java/org/igv/track/Track.java +++ b/src/main/java/org/igv/track/Track.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; diff --git a/src/main/java/org/igv/track/TrackGroup.java b/src/main/java/org/igv/track/TrackGroup.java index 565fdf3159..9d70ceca86 100644 --- a/src/main/java/org/igv/track/TrackGroup.java +++ b/src/main/java/org/igv/track/TrackGroup.java @@ -1,7 +1,3 @@ -/* -* To change this template, choose Tools | Templates -* and open the template in the editor. - */ package org.igv.track; //~--- JDK imports ------------------------------------------------------------ diff --git a/src/main/java/org/igv/track/TrackReader.java b/src/main/java/org/igv/track/TrackReader.java index 9eca9bb4c2..26a655f4de 100644 --- a/src/main/java/org/igv/track/TrackReader.java +++ b/src/main/java/org/igv/track/TrackReader.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; diff --git a/src/main/java/org/igv/track/TrackType.java b/src/main/java/org/igv/track/TrackType.java index 809195cdca..be21c180d5 100644 --- a/src/main/java/org/igv/track/TrackType.java +++ b/src/main/java/org/igv/track/TrackType.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; diff --git a/src/main/java/org/igv/track/WindowFunction.java b/src/main/java/org/igv/track/WindowFunction.java index 6be7f66ddf..47508b1cbf 100644 --- a/src/main/java/org/igv/track/WindowFunction.java +++ b/src/main/java/org/igv/track/WindowFunction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.track; diff --git a/src/main/java/org/igv/ui/AbstractDataPanelTool.java b/src/main/java/org/igv/ui/AbstractDataPanelTool.java index 0b8accad5f..a28f9fd083 100644 --- a/src/main/java/org/igv/ui/AbstractDataPanelTool.java +++ b/src/main/java/org/igv/ui/AbstractDataPanelTool.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; diff --git a/src/main/java/org/igv/ui/AttributeCheckList.java b/src/main/java/org/igv/ui/AttributeCheckList.java index 21f6abfd8d..c3ed6de28c 100644 --- a/src/main/java/org/igv/ui/AttributeCheckList.java +++ b/src/main/java/org/igv/ui/AttributeCheckList.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; diff --git a/src/main/java/org/igv/ui/DefaultExceptionHandler.java b/src/main/java/org/igv/ui/DefaultExceptionHandler.java index cdd540e7fa..9e5b43636d 100644 --- a/src/main/java/org/igv/ui/DefaultExceptionHandler.java +++ b/src/main/java/org/igv/ui/DefaultExceptionHandler.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/FontManager.java b/src/main/java/org/igv/ui/FontManager.java index 64dc496176..df90ae4b14 100644 --- a/src/main/java/org/igv/ui/FontManager.java +++ b/src/main/java/org/igv/ui/FontManager.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; diff --git a/src/main/java/org/igv/ui/GlobalKeyDispatcher.java b/src/main/java/org/igv/ui/GlobalKeyDispatcher.java index 443c93ce21..0624ea31cc 100644 --- a/src/main/java/org/igv/ui/GlobalKeyDispatcher.java +++ b/src/main/java/org/igv/ui/GlobalKeyDispatcher.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; import htsjdk.tribble.Feature; diff --git a/src/main/java/org/igv/ui/HeatmapScaleDialog.java b/src/main/java/org/igv/ui/HeatmapScaleDialog.java index 5e5356e77d..dcfd59322f 100644 --- a/src/main/java/org/igv/ui/HeatmapScaleDialog.java +++ b/src/main/java/org/igv/ui/HeatmapScaleDialog.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ /* * HeatmapScaleDialog.java diff --git a/src/main/java/org/igv/ui/ResourceFileBuilder.java b/src/main/java/org/igv/ui/ResourceFileBuilder.java index ba278bc029..93bb9ab857 100644 --- a/src/main/java/org/igv/ui/ResourceFileBuilder.java +++ b/src/main/java/org/igv/ui/ResourceFileBuilder.java @@ -1,6 +1,5 @@ package org.igv.ui; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.ui.color.ColorUtilities; diff --git a/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java b/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java index 928130ea51..8168d49391 100644 --- a/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java +++ b/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; import com.jidesoft.plaf.LookAndFeelFactory; diff --git a/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java b/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java index 19b0f13ddc..008419ee83 100644 --- a/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java +++ b/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui; diff --git a/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java b/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java index 66dca678e1..7b0990ebc6 100644 --- a/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java +++ b/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java b/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java index 8439838c56..08dc272540 100644 --- a/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java +++ b/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java b/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java index bfcdacca07..4514e57e9f 100644 --- a/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java +++ b/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.event.IGVEventBus; diff --git a/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java b/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java index 73c9357362..cb540479c9 100644 --- a/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java +++ b/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java b/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java index 2e5fb33b9d..66fcca0aa4 100644 --- a/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java +++ b/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.ui.AttributeSelectionDialog; diff --git a/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java b/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java index 3d08722ad9..2c5b2c07bc 100644 --- a/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java +++ b/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java b/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java index 7715c6ed1d..28322cd2d4 100644 --- a/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java +++ b/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.LogManager; diff --git a/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java b/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java index 218025816c..7e296d64d2 100644 --- a/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java +++ b/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.prefs.IGVPreferences; diff --git a/src/main/java/org/igv/ui/action/LoadFromServerAction.java b/src/main/java/org/igv/ui/action/LoadFromServerAction.java index 3db2aed463..f85d05c9ba 100644 --- a/src/main/java/org/igv/ui/action/LoadFromServerAction.java +++ b/src/main/java/org/igv/ui/action/LoadFromServerAction.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.feature.genome.GenomeManager; diff --git a/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java b/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java index 219173df7e..06876da92d 100644 --- a/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java +++ b/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.feature.genome.Genome; diff --git a/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java b/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java index 27d359cc82..2d564435b4 100644 --- a/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java +++ b/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/NewSessionMenuAction.java b/src/main/java/org/igv/ui/action/NewSessionMenuAction.java index 90b3cd39a3..a7aa6172e7 100644 --- a/src/main/java/org/igv/ui/action/NewSessionMenuAction.java +++ b/src/main/java/org/igv/ui/action/NewSessionMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.ui.IGV; diff --git a/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java b/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java index d09e796719..4a0b5f6fa7 100644 --- a/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java +++ b/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.logging.LogManager; diff --git a/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java b/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java index 1803992d83..c317eefd91 100644 --- a/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java +++ b/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.track.DataTrack; diff --git a/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java b/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java index 17d9469e71..e475a8f562 100644 --- a/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java +++ b/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.ui.IGV; diff --git a/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java b/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java index f45db1980b..6ef9381684 100644 --- a/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java +++ b/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.session.Session; diff --git a/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java b/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java index a030f55ef4..973f1c35ba 100644 --- a/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java +++ b/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.prefs.Constants; diff --git a/src/main/java/org/igv/ui/action/ResetPreferencesAction.java b/src/main/java/org/igv/ui/action/ResetPreferencesAction.java index 7e859599f8..ea8009d3dd 100644 --- a/src/main/java/org/igv/ui/action/ResetPreferencesAction.java +++ b/src/main/java/org/igv/ui/action/ResetPreferencesAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.ui.IGV; diff --git a/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java b/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java index 8267e73d0b..9c139b193b 100644 --- a/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java +++ b/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.DirectoryManager; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/SearchCommand.java b/src/main/java/org/igv/ui/action/SearchCommand.java index 7f565c8c6a..27e844485a 100644 --- a/src/main/java/org/igv/ui/action/SearchCommand.java +++ b/src/main/java/org/igv/ui/action/SearchCommand.java @@ -1,6 +1,5 @@ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import htsjdk.tribble.Feature; import htsjdk.tribble.NamedFeature; diff --git a/src/main/java/org/igv/ui/action/SelectHubTracksAction.java b/src/main/java/org/igv/ui/action/SelectHubTracksAction.java index 512af33d7f..91b33efe0b 100644 --- a/src/main/java/org/igv/ui/action/SelectHubTracksAction.java +++ b/src/main/java/org/igv/ui/action/SelectHubTracksAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.feature.genome.load.TrackConfig; diff --git a/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java b/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java index 030fa07b39..98b84e6869 100644 --- a/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java +++ b/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java @@ -1,10 +1,5 @@ -/* -* To change this template, choose Tools | Templates -* and open the template in the editor. -*/ package org.igv.ui.action; -//~--- non-JDK imports -------------------------------------------------------- import org.apache.commons.math3.stat.StatUtils; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/action/SortTracksMenuAction.java b/src/main/java/org/igv/ui/action/SortTracksMenuAction.java index c4b5f6f96a..ff6d3dd644 100644 --- a/src/main/java/org/igv/ui/action/SortTracksMenuAction.java +++ b/src/main/java/org/igv/ui/action/SortTracksMenuAction.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.action; import org.igv.track.AttributeManager; diff --git a/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java b/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java index 3ea297364a..5b217d7f8f 100644 --- a/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java +++ b/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java @@ -9,7 +9,6 @@ package org.igv.ui.panel; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.Globals; import org.igv.prefs.Constants; diff --git a/src/main/java/org/igv/ui/panel/AttributePanel.java b/src/main/java/org/igv/ui/panel/AttributePanel.java index 3ed04ffe7f..4bdf2b867b 100644 --- a/src/main/java/org/igv/ui/panel/AttributePanel.java +++ b/src/main/java/org/igv/ui/panel/AttributePanel.java @@ -8,7 +8,6 @@ */ package org.igv.ui.panel; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.LogManager; import org.igv.logging.Logger; diff --git a/src/main/java/org/igv/ui/panel/CytobandPanel.java b/src/main/java/org/igv/ui/panel/CytobandPanel.java index 5a96653d49..23d251f440 100644 --- a/src/main/java/org/igv/ui/panel/CytobandPanel.java +++ b/src/main/java/org/igv/ui/panel/CytobandPanel.java @@ -8,7 +8,6 @@ */ package org.igv.ui.panel; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.Globals; import org.igv.event.IGVEventBus; diff --git a/src/main/java/org/igv/ui/panel/DataPanelPainter.java b/src/main/java/org/igv/ui/panel/DataPanelPainter.java index 1928fe3e89..1cb118c652 100644 --- a/src/main/java/org/igv/ui/panel/DataPanelPainter.java +++ b/src/main/java/org/igv/ui/panel/DataPanelPainter.java @@ -1,12 +1,7 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.sam.AlignmentTrack; diff --git a/src/main/java/org/igv/ui/panel/IGVPanel.java b/src/main/java/org/igv/ui/panel/IGVPanel.java index b687d348ae..9c65b3b7b2 100644 --- a/src/main/java/org/igv/ui/panel/IGVPanel.java +++ b/src/main/java/org/igv/ui/panel/IGVPanel.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import org.igv.logging.*; diff --git a/src/main/java/org/igv/ui/panel/MouseableRegion.java b/src/main/java/org/igv/ui/panel/MouseableRegion.java index 9400250159..a70fee064d 100644 --- a/src/main/java/org/igv/ui/panel/MouseableRegion.java +++ b/src/main/java/org/igv/ui/panel/MouseableRegion.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import org.igv.track.Track; diff --git a/src/main/java/org/igv/ui/panel/NameHeaderPanel.java b/src/main/java/org/igv/ui/panel/NameHeaderPanel.java index be2288bc91..760161a468 100644 --- a/src/main/java/org/igv/ui/panel/NameHeaderPanel.java +++ b/src/main/java/org/igv/ui/panel/NameHeaderPanel.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import org.igv.Globals; diff --git a/src/main/java/org/igv/ui/panel/PanTool.java b/src/main/java/org/igv/ui/panel/PanTool.java index e00433b842..c0302d7177 100644 --- a/src/main/java/org/igv/ui/panel/PanTool.java +++ b/src/main/java/org/igv/ui/panel/PanTool.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; -//~--- non-JDK imports -------------------------------------------------------- import org.apache.commons.math3.stat.StatUtils; import org.igv.ui.AbstractDataPanelTool; @@ -24,15 +19,10 @@ public class PanTool extends AbstractDataPanelTool { private static int throttleTimeMS = 50; - private static double [] repaintTimes = new double[100]; - private static int repaintTimeCount = 0; - private int previousYDirection = 0; // Drag Directions: 1=up, 0=none 0r -1=down - //private int lastMousePressedY; private int cumulativeDeltaX; private int cumulativeDeltaY; private Point lastMousePoint; - //private JViewport viewport; private JScrollBar verticalScrollBar; private boolean isDragging = false; private long lastDragEventTime = 0; @@ -44,25 +34,14 @@ public PanTool(DataPanel owner) { setName("Pan"); if (owner != null) { verticalScrollBar = owner.getVerticalScrollbar(); - Container parentContainer = owner.getParent(); - if (parentContainer != null) { - Container parentOfParent = parentContainer.getParent(); - if ((parentOfParent != null) && (parentOfParent instanceof JViewport)) { - //viewport = (JViewport) parentOfParent; - } - } } } - @Override public Cursor getCursor() { return Cursor.getDefaultCursor(); } - public Point getLastMousePoint() { - return lastMousePoint; - } @Override public void mousePressed(final MouseEvent e) { @@ -74,7 +53,6 @@ public void mousePressed(final MouseEvent e) { lastMousePoint = e.getPoint(); cumulativeDeltaX = 0; cumulativeDeltaY = 0; - } public void setReferenceFrame(ReferenceFrame frame) { @@ -111,11 +89,9 @@ final public void mouseDragged(final MouseEvent e) { return; } - //System.out.println("T=" + ctr); lastDragEventTime = currentTime; try { - Component panel = (Component) e.getSource(); if (lastMousePoint == null) { lastMousePoint = e.getPoint(); return; @@ -180,20 +156,4 @@ final public void mouseDragged(final MouseEvent e) { lastMousePoint = e.getPoint(); // Always save the last Point } } - - /** - * Adaptively throttle the drag time based on repaint times. Its pointless to drag faster than we can repaint. - * - * @param t - */ - public static void repaintTime(double t) { - repaintTimes[repaintTimeCount++] = t; - if (repaintTimeCount == repaintTimes.length) { - double p = StatUtils.percentile(repaintTimes, 95); - throttleTimeMS = Math.max(5, Math.min(200, (int) p)); - repaintTimeCount = 0; - } - - } - } diff --git a/src/main/java/org/igv/ui/panel/ReferenceFrame.java b/src/main/java/org/igv/ui/panel/ReferenceFrame.java index 2111d57a0c..1a67376a1f 100644 --- a/src/main/java/org/igv/ui/panel/ReferenceFrame.java +++ b/src/main/java/org/igv/ui/panel/ReferenceFrame.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import org.igv.Globals; diff --git a/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java b/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java index 7c336b3bca..23cc7aa956 100644 --- a/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java +++ b/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import org.igv.Globals; diff --git a/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java b/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java index a84020efb8..740f421760 100644 --- a/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java +++ b/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import org.igv.feature.RegionOfInterest; diff --git a/src/main/java/org/igv/ui/panel/TrackPanelComponent.java b/src/main/java/org/igv/ui/panel/TrackPanelComponent.java index 9c916b7769..88162cdcec 100644 --- a/src/main/java/org/igv/ui/panel/TrackPanelComponent.java +++ b/src/main/java/org/igv/ui/panel/TrackPanelComponent.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.logging.*; import org.igv.Globals; diff --git a/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java b/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java index d9ebe59e52..b2e27a23a6 100644 --- a/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java +++ b/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.panel; import com.jidesoft.swing.JideScrollPane; diff --git a/src/main/java/org/igv/ui/util/CheckList.java b/src/main/java/org/igv/ui/util/CheckList.java index 6db58bea10..4908b0f2ce 100644 --- a/src/main/java/org/igv/ui/util/CheckList.java +++ b/src/main/java/org/igv/ui/util/CheckList.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.util; diff --git a/src/main/java/org/igv/ui/util/DataPanelTool.java b/src/main/java/org/igv/ui/util/DataPanelTool.java index ea9cc3f6ad..b1e505277d 100644 --- a/src/main/java/org/igv/ui/util/DataPanelTool.java +++ b/src/main/java/org/igv/ui/util/DataPanelTool.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.util; diff --git a/src/main/java/org/igv/ui/util/MessageUtils.java b/src/main/java/org/igv/ui/util/MessageUtils.java index 9cee1c717b..30075d2b8d 100644 --- a/src/main/java/org/igv/ui/util/MessageUtils.java +++ b/src/main/java/org/igv/ui/util/MessageUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.util; import org.igv.Globals; diff --git a/src/main/java/org/igv/ui/util/Packable.java b/src/main/java/org/igv/ui/util/Packable.java index 1169805659..ce146c3772 100644 --- a/src/main/java/org/igv/ui/util/Packable.java +++ b/src/main/java/org/igv/ui/util/Packable.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.util; diff --git a/src/main/java/org/igv/ui/util/TracingRepaintManager.java b/src/main/java/org/igv/ui/util/TracingRepaintManager.java index d29909ac66..352fae166c 100644 --- a/src/main/java/org/igv/ui/util/TracingRepaintManager.java +++ b/src/main/java/org/igv/ui/util/TracingRepaintManager.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.util; diff --git a/src/main/java/org/igv/ui/util/UIUtilities.java b/src/main/java/org/igv/ui/util/UIUtilities.java index 83e3f39b81..818d6d5138 100644 --- a/src/main/java/org/igv/ui/util/UIUtilities.java +++ b/src/main/java/org/igv/ui/util/UIUtilities.java @@ -1,10 +1,5 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.ui.util; -//~--- non-JDK imports -------------------------------------------------------- import org.igv.Globals; import org.igv.logging.*; diff --git a/src/main/java/org/igv/util/ArrayHeapIntSorter.java b/src/main/java/org/igv/util/ArrayHeapIntSorter.java old mode 100755 new mode 100644 index 155eb67cff..030fc517c9 --- a/src/main/java/org/igv/util/ArrayHeapIntSorter.java +++ b/src/main/java/org/igv/util/ArrayHeapIntSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; public class ArrayHeapIntSorter { diff --git a/src/main/java/org/igv/util/ArrayHeapObjectSorter.java b/src/main/java/org/igv/util/ArrayHeapObjectSorter.java index 9d03b15cf0..c49be5ab75 100644 --- a/src/main/java/org/igv/util/ArrayHeapObjectSorter.java +++ b/src/main/java/org/igv/util/ArrayHeapObjectSorter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; import java.util.Comparator; diff --git a/src/main/java/org/igv/util/AsciiEcho.java b/src/main/java/org/igv/util/AsciiEcho.java index 6a355fe08b..0f7b64c66f 100644 --- a/src/main/java/org/igv/util/AsciiEcho.java +++ b/src/main/java/org/igv/util/AsciiEcho.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; diff --git a/src/main/java/org/igv/util/FilterElement.java b/src/main/java/org/igv/util/FilterElement.java index 31f8dbbf9c..c6c725c2f5 100644 --- a/src/main/java/org/igv/util/FilterElement.java +++ b/src/main/java/org/igv/util/FilterElement.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; import org.igv.track.AttributeManager; diff --git a/src/main/java/org/igv/util/IlluminaUtils.java b/src/main/java/org/igv/util/IlluminaUtils.java index 6725d346fc..013e90696f 100644 --- a/src/main/java/org/igv/util/IlluminaUtils.java +++ b/src/main/java/org/igv/util/IlluminaUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; import java.io.*; diff --git a/src/main/java/org/igv/util/IntComparator.java b/src/main/java/org/igv/util/IntComparator.java index d734c3537d..7d0c06b677 100644 --- a/src/main/java/org/igv/util/IntComparator.java +++ b/src/main/java/org/igv/util/IntComparator.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; diff --git a/src/main/java/org/igv/util/RuntimeUtils.java b/src/main/java/org/igv/util/RuntimeUtils.java index 02bd545eb3..4f64938657 100644 --- a/src/main/java/org/igv/util/RuntimeUtils.java +++ b/src/main/java/org/igv/util/RuntimeUtils.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; import org.igv.logging.*; diff --git a/src/main/java/org/igv/util/SequenceGC.java b/src/main/java/org/igv/util/SequenceGC.java index 9c80c51a4f..0b31023a0e 100644 --- a/src/main/java/org/igv/util/SequenceGC.java +++ b/src/main/java/org/igv/util/SequenceGC.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; diff --git a/src/main/java/org/igv/util/TrackFilter.java b/src/main/java/org/igv/util/TrackFilter.java index 9c1c9af10e..1dc3559387 100644 --- a/src/main/java/org/igv/util/TrackFilter.java +++ b/src/main/java/org/igv/util/TrackFilter.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; diff --git a/src/main/java/org/igv/util/Utilities.java b/src/main/java/org/igv/util/Utilities.java index 302e0090b6..e39d14063e 100644 --- a/src/main/java/org/igv/util/Utilities.java +++ b/src/main/java/org/igv/util/Utilities.java @@ -1,6 +1,5 @@ package org.igv.util; -//~--- non-JDK imports -------------------------------------------------------- import biz.source_code.base64Coder.Base64Coder; import org.igv.logging.*; diff --git a/src/main/java/org/igv/util/collections/StringArrayList.java b/src/main/java/org/igv/util/collections/StringArrayList.java index 8010d0d61c..23a93896df 100644 --- a/src/main/java/org/igv/util/collections/StringArrayList.java +++ b/src/main/java/org/igv/util/collections/StringArrayList.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util.collections; diff --git a/src/test/java/org/igv/data/IGVDatasetTest.java b/src/test/java/org/igv/data/IGVDatasetTest.java index 5d728e5249..59b07e2388 100644 --- a/src/test/java/org/igv/data/IGVDatasetTest.java +++ b/src/test/java/org/igv/data/IGVDatasetTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.data; import org.igv.AbstractHeadlessTest; diff --git a/src/test/java/org/igv/feature/FeatureUtilsTest.java b/src/test/java/org/igv/feature/FeatureUtilsTest.java index bb8a3bc0d8..9be53022b4 100644 --- a/src/test/java/org/igv/feature/FeatureUtilsTest.java +++ b/src/test/java/org/igv/feature/FeatureUtilsTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; import org.igv.feature.genome.Genome; diff --git a/src/test/java/org/igv/feature/GeneTest.java b/src/test/java/org/igv/feature/GeneTest.java index 6ab3316334..c3a9bbb707 100644 --- a/src/test/java/org/igv/feature/GeneTest.java +++ b/src/test/java/org/igv/feature/GeneTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; import org.igv.AbstractHeadlessTest; diff --git a/src/test/java/org/igv/feature/LocusTest.java b/src/test/java/org/igv/feature/LocusTest.java index 6676a18701..e0dbd2f9d3 100644 --- a/src/test/java/org/igv/feature/LocusTest.java +++ b/src/test/java/org/igv/feature/LocusTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; diff --git a/src/test/java/org/igv/feature/ProbeToGeneMapTest.java b/src/test/java/org/igv/feature/ProbeToGeneMapTest.java index da6fb0fd6b..bc1eceebe0 100644 --- a/src/test/java/org/igv/feature/ProbeToGeneMapTest.java +++ b/src/test/java/org/igv/feature/ProbeToGeneMapTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; import org.igv.util.TestUtils; diff --git a/src/test/java/org/igv/feature/TestLoadGeneManager.java b/src/test/java/org/igv/feature/TestLoadGeneManager.java index 930c96ef79..b1f79a3980 100644 --- a/src/test/java/org/igv/feature/TestLoadGeneManager.java +++ b/src/test/java/org/igv/feature/TestLoadGeneManager.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature; diff --git a/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java b/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java index 699bf7a583..da14a2e03e 100644 --- a/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java +++ b/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.aa; import org.igv.AbstractHeadlessTest; diff --git a/src/test/java/org/igv/feature/genome/GenomeManagerTest.java b/src/test/java/org/igv/feature/genome/GenomeManagerTest.java index de6fb76e17..27d295e51d 100644 --- a/src/test/java/org/igv/feature/genome/GenomeManagerTest.java +++ b/src/test/java/org/igv/feature/genome/GenomeManagerTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.feature.genome; diff --git a/src/test/java/org/igv/preprocess/FeatureDatasetTest.java b/src/test/java/org/igv/preprocess/FeatureDatasetTest.java index 1e7761a5d2..972e6f6ec7 100644 --- a/src/test/java/org/igv/preprocess/FeatureDatasetTest.java +++ b/src/test/java/org/igv/preprocess/FeatureDatasetTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.preprocess; import org.igv.AbstractHeadlessTest; diff --git a/src/test/java/org/igv/renderer/MappedColorScaleTest.java b/src/test/java/org/igv/renderer/MappedColorScaleTest.java index ba6e6c3456..f36ab772aa 100644 --- a/src/test/java/org/igv/renderer/MappedColorScaleTest.java +++ b/src/test/java/org/igv/renderer/MappedColorScaleTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.renderer; diff --git a/src/test/java/org/igv/sam/AlignmentPackerTest.java b/src/test/java/org/igv/sam/AlignmentPackerTest.java index c0b131548d..e3fcce6abf 100644 --- a/src/test/java/org/igv/sam/AlignmentPackerTest.java +++ b/src/test/java/org/igv/sam/AlignmentPackerTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; diff --git a/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java b/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java index 5073bb17b5..0e08ca42be 100644 --- a/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java +++ b/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import org.igv.AbstractHeadlessTest; diff --git a/src/test/java/org/igv/sam/AsciiLineReaderTest.java b/src/test/java/org/igv/sam/AsciiLineReaderTest.java index 83aed69eeb..62ff5087f8 100644 --- a/src/test/java/org/igv/sam/AsciiLineReaderTest.java +++ b/src/test/java/org/igv/sam/AsciiLineReaderTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import org.igv.util.TestUtils; diff --git a/src/test/java/org/igv/sam/BAMFileReaderTest.java b/src/test/java/org/igv/sam/BAMFileReaderTest.java index 78c032ef21..ed50520351 100644 --- a/src/test/java/org/igv/sam/BAMFileReaderTest.java +++ b/src/test/java/org/igv/sam/BAMFileReaderTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; diff --git a/src/test/java/org/igv/sam/SamIndexTest.java b/src/test/java/org/igv/sam/SamIndexTest.java index a6082f243a..fc136fe844 100644 --- a/src/test/java/org/igv/sam/SamIndexTest.java +++ b/src/test/java/org/igv/sam/SamIndexTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; diff --git a/src/test/java/org/igv/sam/SamIndexerTest.java b/src/test/java/org/igv/sam/SamIndexerTest.java index 672a0d82a2..932438d2a7 100644 --- a/src/test/java/org/igv/sam/SamIndexerTest.java +++ b/src/test/java/org/igv/sam/SamIndexerTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; diff --git a/src/test/java/org/igv/sam/SamQueryTextReaderTest.java b/src/test/java/org/igv/sam/SamQueryTextReaderTest.java index 8ae7a8d568..4054a6e826 100644 --- a/src/test/java/org/igv/sam/SamQueryTextReaderTest.java +++ b/src/test/java/org/igv/sam/SamQueryTextReaderTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam; import htsjdk.samtools.util.CloseableIterator; diff --git a/src/test/java/org/igv/sam/cram/CRAMReaderTest.java b/src/test/java/org/igv/sam/cram/CRAMReaderTest.java index 7b518da0e6..d077eafd82 100644 --- a/src/test/java/org/igv/sam/cram/CRAMReaderTest.java +++ b/src/test/java/org/igv/sam/cram/CRAMReaderTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.cram; diff --git a/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java b/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java index b023b9afce..b0a8d8a547 100644 --- a/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java +++ b/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.sam.reader; diff --git a/src/test/java/org/igv/tdf/TDFReadWriteTest.java b/src/test/java/org/igv/tdf/TDFReadWriteTest.java index f5501f7489..e8f5c6727b 100644 --- a/src/test/java/org/igv/tdf/TDFReadWriteTest.java +++ b/src/test/java/org/igv/tdf/TDFReadWriteTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tdf; import org.igv.track.TrackType; diff --git a/src/test/java/org/igv/tools/AccumulatorTest.java b/src/test/java/org/igv/tools/AccumulatorTest.java index fd52ec4834..df36b27dfa 100644 --- a/src/test/java/org/igv/tools/AccumulatorTest.java +++ b/src/test/java/org/igv/tools/AccumulatorTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.tools; import org.igv.track.WindowFunction; diff --git a/src/test/java/org/igv/util/HeapSortTest.java b/src/test/java/org/igv/util/HeapSortTest.java index bc5ee83752..dd807cc92c 100644 --- a/src/test/java/org/igv/util/HeapSortTest.java +++ b/src/test/java/org/igv/util/HeapSortTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; import org.junit.AfterClass; diff --git a/src/test/java/org/igv/util/SequenceGCTest.java b/src/test/java/org/igv/util/SequenceGCTest.java index 8eaebe9211..41753938e9 100644 --- a/src/test/java/org/igv/util/SequenceGCTest.java +++ b/src/test/java/org/igv/util/SequenceGCTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util; diff --git a/src/test/java/org/igv/util/collections/DoubleArrayListTest.java b/src/test/java/org/igv/util/collections/DoubleArrayListTest.java index 411cd4ba1d..2c6e08189d 100644 --- a/src/test/java/org/igv/util/collections/DoubleArrayListTest.java +++ b/src/test/java/org/igv/util/collections/DoubleArrayListTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util.collections; diff --git a/src/test/java/org/igv/util/collections/IntArrayListTest.java b/src/test/java/org/igv/util/collections/IntArrayListTest.java index 8c40ba83c2..a270ce2105 100644 --- a/src/test/java/org/igv/util/collections/IntArrayListTest.java +++ b/src/test/java/org/igv/util/collections/IntArrayListTest.java @@ -1,7 +1,3 @@ -/* - * To change this template, choose Tools | Templates - * and open the template in the editor. - */ package org.igv.util.collections; From 590c87553dffa4c56ddad69f306a7d1087c8618e Mon Sep 17 00:00:00 2001 From: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Sun, 4 Jan 2026 22:32:39 -0800 Subject: [PATCH 2/2] Fix potential threading bugs in repaint logic --- src/main/java/org/igv/ui/IGV.java | 125 ++++++++++++------ src/main/java/org/igv/ui/panel/DataPanel.java | 21 +-- .../java/org/igv/ui/panel/TrackPanel.java | 9 ++ 3 files changed, 97 insertions(+), 58 deletions(-) diff --git a/src/main/java/org/igv/ui/IGV.java b/src/main/java/org/igv/ui/IGV.java index c97004ca62..8fbe3bdc44 100644 --- a/src/main/java/org/igv/ui/IGV.java +++ b/src/main/java/org/igv/ui/IGV.java @@ -17,7 +17,6 @@ import org.igv.batch.CommandListener; import org.igv.event.*; import org.igv.exceptions.DataLoadException; -import org.igv.feature.Range; import org.igv.feature.RegionOfInterest; import org.igv.feature.Strand; import org.igv.feature.genome.Genome; @@ -31,9 +30,7 @@ import org.igv.prefs.PreferencesEditor; import org.igv.prefs.PreferencesManager; import org.igv.sam.AlignmentTrack; -import org.igv.sam.AlignmentTrackUtils; import org.igv.sam.InsertionSelectionEvent; -import org.igv.sam.SortOption; import org.igv.session.*; import org.igv.session.autosave.AutosaveTimerTask; import org.igv.session.autosave.SessionAutosaveManager; @@ -2111,7 +2108,7 @@ public void resetFrames() { public void revalidateTrackPanels() { UIUtilities.invokeOnEventThread(() -> { getMainPanel().revalidateTrackPanels(); - repaint(rootPane); + repaint(); }); } @@ -2135,36 +2132,55 @@ public void fitTracksToPanel() { repaint(); } + /** + * Repaint all visible tracks. + */ public void repaint() { - repaint(contentPane); - } - - public void repaint(Track track) { - this.repaint(contentPane, List.of(track)); + Collection trackList = new ArrayList<>(); + for (TrackPanel tp : getTrackPanels()) { + trackList.addAll(visibleTracks(tp.getDataPanelContainer())); + } + getAllTracks(); + repaint(contentPane, trackList); } + /** + * Repaint a collection of tracks.Rather than search for panels containing the tracks we paint the entire content + * pane. In practice this is not significantly different from a full repaint(), but has the potential of + * being optimized. Also, we only need to check and potentially load the specified tracks. + * + * @param tracks + */ public void repaint(Collection tracks) { this.repaint(contentPane, tracks); } - private void repaint(final JComponent component) { - Collection trackList = new ArrayList<>(); + + /** + * Repaint a single track. In practice this repaints the entire panel containing the track + * + * @param track + */ + public void repaint(Track track) { + // Find the panel containing this track for (TrackPanel tp : getTrackPanels()) { - trackList.addAll(visibleTracks(tp.getDataPanelContainer())); + if (tp.containsTrack(track)) { + this.repaint(tp, List.of(track)); + return; + } } - repaint(component, trackList); } - private boolean isLoading = false; - private Collection pending = null; + + private volatile boolean isLoading = false; + private Set pendingTracks = null; + private final Object repaintLock = new Object(); private void repaint(final JComponent component, Collection trackList) { if (Globals.isBatch()) { // In batch mode everything is done synchronously on the event thread UIUtilities.invokeAndWaitOnEventThread(() -> { - - CursorToken token = WaitCursorManager.showWaitCursor(); try { for (ReferenceFrame frame : FrameManager.getFrames()) { for (Track track : trackList) { @@ -2177,7 +2193,6 @@ private void repaint(final JComponent component, Collection tra checkPanelLayouts(); component.paintImmediately(component.getBounds()); } finally { - WaitCursorManager.removeWaitCursor(token); synchronized (IGV.getInstance()) { IGV.getInstance().notifyAll(); } @@ -2186,13 +2201,20 @@ private void repaint(final JComponent component, Collection tra } else { - if (isLoading) { - // Track data is being loaded, do a repaint with existing data and mark this request for future execution - UIUtilities.invokeOnEventThread(contentPane::repaint); - pending = trackList; - return; + synchronized (repaintLock) { + if (isLoading) { + // Track data is being loaded. Paint the component with available data and queue these tracks for + // the next repaint cycle + UIUtilities.invokeOnEventThread(contentPane::repaint); + if (pendingTracks == null) { + pendingTracks = new HashSet<>(); + } + pendingTracks.addAll(trackList); + return; + } } + // Not currently loading // Find tracks that need loading (not ready to paint) List> futures = new ArrayList<>(); for (ReferenceFrame frame : FrameManager.getFrames()) { @@ -2205,37 +2227,52 @@ private void repaint(final JComponent component, Collection tra if (futures.isEmpty()) { // All tracks are ready to paint + Autoscaler.autoscale(getAllTracks()); UIUtilities.invokeOnEventThread(() -> { - Autoscaler.autoscale(getAllTracks()); checkPanelLayouts(); component.repaint(); + }); - } else { - // One or more tracks require loading before repaint. + return; + } + + + // One or more tracks require loading before repaint. + synchronized (repaintLock) { isLoading = true; - final WaitCursorManager.CursorToken token = WaitCursorManager.showWaitCursor(); + } + final WaitCursorManager.CursorToken token = WaitCursorManager.showWaitCursor(); - CompletableFuture.allOf(futures.toArray(new CompletableFuture[0])).whenCompleteAsync((ignored, ex) -> { - WaitCursorManager.removeWaitCursor(token); + CompletableFuture.allOf(futures.toArray(new CompletableFuture[0])).whenComplete((ignored, ex) -> { + WaitCursorManager.removeWaitCursor(token); + + if (ex != null) { + log.error("Error loading track data", ex); + } + + // Collect pending tracks and reset state under lock + Set tracksToRepaint; + synchronized (repaintLock) { isLoading = false; + tracksToRepaint = pendingTracks; + pendingTracks = null; + } - if (ex != null) { - log.error("Error loading track data", ex); - } + // Autoscale (modifies track internal state, not UI) + Autoscaler.autoscale(getAllTracks()); - // Autoscale as required, check layouts, and repaint. - Autoscaler.autoscale(getAllTracks()); - UIUtilities.invokeOnEventThread(() -> { - checkPanelLayouts(); + // Check layouts and repaint on EDT + UIUtilities.invokeOnEventThread(() -> { + checkPanelLayouts(); + if (tracksToRepaint != null && !tracksToRepaint.isEmpty()) { + // Pending tracks exist - repaint will be called by the recursive invocation + repaint(component, tracksToRepaint); + } else { component.repaint(); - if (pending != null) { - Collection tmp = pending; - pending = null; - repaint(tmp); - } - }); - }, SwingUtilities::invokeLater); - } + } + }); + }); + } } diff --git a/src/main/java/org/igv/ui/panel/DataPanel.java b/src/main/java/org/igv/ui/panel/DataPanel.java index 57ffed9c6b..8f5d3fec05 100644 --- a/src/main/java/org/igv/ui/panel/DataPanel.java +++ b/src/main/java/org/igv/ui/panel/DataPanel.java @@ -69,7 +69,12 @@ public DataPanel(ReferenceFrame frame, DataPanelContainer parent) { setAutoscrolls(true); setToolTipText(""); painter = new DataPanelPainter(); - setBackground(PreferencesManager.getPreferences().getAsColor(Constants.BACKGROUND_COLOR)); + + if(darkMode && !PreferencesManager.getPreferences().hasExplicitValue(Constants.BACKGROUND_COLOR)){ + setBackground(UIManager.getColor("Panel.background")); + } else { + setBackground(PreferencesManager.getPreferences().getAsColor(Constants.BACKGROUND_COLOR)); + } ToolTipManager.sharedInstance().registerComponent(this); } @@ -101,26 +106,18 @@ public void setCurrentTool(final AbstractDataPanelTool tool) { } } - long lastPaintTime = 0; - @Override public void paintComponent(final Graphics g) { super.paintComponent(g); - if(darkMode){ - setBackground(UIManager.getColor("Panel.background")); - } - RenderContext context = null; try { - lastPaintTime = System.currentTimeMillis(); - Rectangle clipBounds = g.getClipBounds(); final Rectangle visibleRect = getVisibleRect(); final Rectangle damageRect = clipBounds == null ? visibleRect : clipBounds.intersection(visibleRect); - Graphics2D graphics2D = (Graphics2D) g; //(Graphics2D) g.create(); + Graphics2D graphics2D = (Graphics2D) g; context = new RenderContext(this, graphics2D, frame, visibleRect); @@ -144,10 +141,6 @@ public void paintComponent(final Graphics g) { drawAllRegions(g); - - long dt = System.currentTimeMillis() - lastPaintTime; - PanTool.repaintTime(dt); - } catch (Exception e) { MessageUtils.showMessage("Unexpected error repainting view. See igv.log for details."); log.error("Error painting DataPanel", e); diff --git a/src/main/java/org/igv/ui/panel/TrackPanel.java b/src/main/java/org/igv/ui/panel/TrackPanel.java index 5b04140bb2..464f4414b9 100644 --- a/src/main/java/org/igv/ui/panel/TrackPanel.java +++ b/src/main/java/org/igv/ui/panel/TrackPanel.java @@ -148,6 +148,15 @@ public List getTracks() { return tracks; } + public boolean containsTrack(Track track) { + for (TrackGroup tg : trackGroups) { + if (tg.contains(track)) { + return true; + } + } + return false; + } + public void clearTracks() { for (Track t : getTracks()) {