[med-svn] [mauve] 02/04: Merge tag 'upstream/2.4.0+4734'
Andreas Tille
tille at debian.org
Wed Apr 22 12:13:05 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository mauve.
commit 6503dcd83331895a06a1a2f18987e3407fc4ea6e
Merge: 0b86d17 5e3ea89
Author: Andreas Tille <tille at debian.org>
Date: Wed Apr 22 14:09:30 2015 +0200
Merge tag 'upstream/2.4.0+4734'
Upstream version 2.4.0+4734
.classpath | 20 +
.project | 17 +
.settings/org.eclipse.jdt.core.prefs | 12 +
.umlproject | 9 +
COPYING | 340 ++++++
README | 63 ++
TODO | 68 ++
build.xml | 516 +++++++++
build_support/appbundler-1.0.jar | Bin 0 -> 133599 bytes
debian/README.Debian | 7 -
debian/bin/mauve | 9 -
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 46 -
debian/copyright | 21 -
debian/get-orig-source | 39 -
debian/install | 2 -
debian/patches/build_xml.patch | 279 -----
debian/patches/debian_classes.patch | 34 -
debian/patches/series | 2 -
debian/rules | 38 -
debian/source/format | 1 -
debian/upstream/metadata | 12 -
debian/watch | 1 -
doc/overview.txt | 64 ++
ext/core-1.9.2-SNAPSHOT.jar | Bin 0 -> 2471408 bytes
ext/goose.jar | Bin 0 -> 89124 bytes
ext/gui-1.9.2-SNAPSHOT.jar | Bin 0 -> 228711 bytes
ext/jnlp.jar | Bin 0 -> 7042 bytes
ext/jsc.jar | Bin 0 -> 1075447 bytes
ext/unix-0.5.jar | Bin 0 -> 8482 bytes
ext/zeus-jscl.jar | Bin 0 -> 128804 bytes
jarAlignments.xml | 161 +++
jws/deployment.txt | 48 +
jws/index.html | 18 +
jws/mauve.jnlp.template | 29 +
linux-x64/Mauve | 34 +
mauve.dox | 1153 ++++++++++++++++++++
notes/Biojava Renderer Notes.txt | 14 +
notes/Mauve Notes.txt | 95 ++
notes/icon_with_rollover_template.psd | Bin 0 -> 149398 bytes
publish.xml | 77 ++
src/images/Back16.gif | Bin 0 -> 183 bytes
src/images/DarkHand16.gif | Bin 0 -> 636 bytes
src/images/Dcj16.gif | Bin 0 -> 355 bytes
src/images/Down16.gif | Bin 0 -> 185 bytes
src/images/DownRollover16.png | Bin 0 -> 351 bytes
src/images/Forward16.gif | Bin 0 -> 183 bytes
src/images/Grimm16.gif | Bin 0 -> 345 bytes
src/images/Hand16.gif | Bin 0 -> 1072 bytes
src/images/Home16.gif | Bin 0 -> 420 bytes
src/images/ScoreAssembly.png | Bin 0 -> 284 bytes
src/images/Up16.gif | Bin 0 -> 184 bytes
src/images/UpRollover16.png | Bin 0 -> 358 bytes
src/images/Zoom16.gif | Bin 0 -> 303 bytes
src/images/ZoomIn16.gif | Bin 0 -> 304 bytes
src/images/ZoomIn24.gif | Bin 0 -> 484 bytes
src/images/ZoomOut16.gif | Bin 0 -> 304 bytes
src/images/ZoomOut24.gif | Bin 0 -> 477 bytes
src/images/aPlus16.png | Bin 0 -> 357 bytes
src/images/fist_icon.gif | Bin 0 -> 112 bytes
src/images/hand_icon.gif | Bin 0 -> 130 bytes
src/images/mauve_icon.gif | Bin 0 -> 555 bytes
src/images/mauve_logo.png | Bin 0 -> 18351 bytes
src/images/minus16.png | Bin 0 -> 181 bytes
src/images/minusRollover16.png | Bin 0 -> 304 bytes
src/images/plus16.png | Bin 0 -> 202 bytes
src/images/plusRollover16.png | Bin 0 -> 323 bytes
src/images/r16.png | Bin 0 -> 292 bytes
src/images/searchBinoculars16.png | Bin 0 -> 992 bytes
src/images/searchBinoculars24.png | Bin 0 -> 1766 bytes
src/images/searchBinoculars32.png | Bin 0 -> 1735 bytes
src/org/gel/air/util/GroupHelpers.java | 29 +
src/org/gel/air/util/IOUtils.java | 129 +++
src/org/gel/air/util/MathUtils.java | 34 +
src/org/gel/air/util/StatusBox.java | 40 +
src/org/gel/mauve/BaseViewerModel.java | 971 +++++++++++++++++
src/org/gel/mauve/BrowserLauncher.java | 824 ++++++++++++++
src/org/gel/mauve/Chromosome.java | 56 +
src/org/gel/mauve/ColorScheme.java | 25 +
src/org/gel/mauve/DbXrefFactory.java | 155 +++
src/org/gel/mauve/DbXrefHandler.java | 23 +
src/org/gel/mauve/FilterCacheSpec.java | 48 +
src/org/gel/mauve/Genome.java | 204 ++++
src/org/gel/mauve/GenomeBuilder.java | 213 ++++
src/org/gel/mauve/HighlightListener.java | 7 +
src/org/gel/mauve/LCB.java | 172 +++
src/org/gel/mauve/LCBLeftComparator.java | 32 +
src/org/gel/mauve/LCBlist.java | 409 +++++++
src/org/gel/mauve/LcbIdComparator.java | 15 +
src/org/gel/mauve/LcbViewerModel.java | 759 +++++++++++++
src/org/gel/mauve/Match.java | 170 +++
src/org/gel/mauve/MatchStartComparator.java | 41 +
src/org/gel/mauve/MauveConstants.java | 182 +++
src/org/gel/mauve/MauveFormatException.java | 11 +
src/org/gel/mauve/MauveHelperFunctions.java | 303 +++++
src/org/gel/mauve/ModelBuilder.java | 566 ++++++++++
src/org/gel/mauve/ModelEvent.java | 13 +
src/org/gel/mauve/ModelListener.java | 22 +
src/org/gel/mauve/ModelProgressListener.java | 15 +
src/org/gel/mauve/MyConsole.java | 47 +
src/org/gel/mauve/OptionsBuilder.java | 84 ++
src/org/gel/mauve/PreferencesDump.java | 23 +
src/org/gel/mauve/SeqFeatureData.java | 315 ++++++
src/org/gel/mauve/SimilarityIndex.java | 380 +++++++
src/org/gel/mauve/SupportedFormat.java | 90 ++
src/org/gel/mauve/ViewerMode.java | 10 +
src/org/gel/mauve/XMFAAlignment.java | 885 +++++++++++++++
src/org/gel/mauve/XmfaViewerModel.java | 561 ++++++++++
src/org/gel/mauve/analysis/BrokenCDS.java | 208 ++++
src/org/gel/mauve/analysis/CDSErrorExporter.java | 640 +++++++++++
src/org/gel/mauve/analysis/Gap.java | 240 ++++
src/org/gel/mauve/analysis/IdentityMatrix.java | 104 ++
src/org/gel/mauve/analysis/LiteWeightFeature.java | 130 +++
.../mauve/analysis/OneToOneOrthologExporter.java | 1122 +++++++++++++++++++
.../gel/mauve/analysis/PermutationExporter.java | 696 ++++++++++++
src/org/gel/mauve/analysis/SNP.java | 331 ++++++
src/org/gel/mauve/analysis/Segment.java | 169 +++
src/org/gel/mauve/analysis/SegmentComparator.java | 65 ++
src/org/gel/mauve/analysis/SnpExporter.java | 502 +++++++++
src/org/gel/mauve/analysis/TreeAnalysis.java | 58 +
src/org/gel/mauve/assembly/AssemblyScorer.java | 810 ++++++++++++++
src/org/gel/mauve/assembly/ScoreAssembly.java | 427 ++++++++
src/org/gel/mauve/backbone/Backbone.java | 82 ++
src/org/gel/mauve/backbone/BackboneList.java | 150 +++
.../gel/mauve/backbone/BackboneListBuilder.java | 121 ++
src/org/gel/mauve/chado/ChadoDB.java | 79 ++
src/org/gel/mauve/chado/ChadoFeatureLoader.java | 52 +
src/org/gel/mauve/chado/ChadoReader.java | 41 +
src/org/gel/mauve/chado/ChadoWriter.java | 41 +
src/org/gel/mauve/chado/DBUtils.java | 18 +
src/org/gel/mauve/color/BackboneLcbColor.java | 34 +
.../gel/mauve/color/BackboneMultiplicityColor.java | 209 ++++
src/org/gel/mauve/color/ColorMenu.java | 126 +++
src/org/gel/mauve/color/LCBColorScheme.java | 57 +
.../gel/mauve/color/MultiplicityColorScheme.java | 78 ++
.../mauve/color/MultiplicityTypeColorScheme.java | 46 +
.../NormalizedMultiplicityTypeColorScheme.java | 73 ++
.../mauve/color/NormalizedOffsetColorScheme.java | 82 ++
src/org/gel/mauve/color/OffsetColorScheme.java | 57 +
src/org/gel/mauve/contigs/ChangedFastaFormat.java | 25 +
.../gel/mauve/contigs/ChangedFeatureWriter.java | 110 ++
src/org/gel/mauve/contigs/ContigFeatureWriter.java | 129 +++
src/org/gel/mauve/contigs/ContigGrouper.java | 349 ++++++
src/org/gel/mauve/contigs/ContigHandler.java | 37 +
src/org/gel/mauve/contigs/ContigInverter.java | 496 +++++++++
.../gel/mauve/contigs/ContigMauveAlignFrame.java | 168 +++
src/org/gel/mauve/contigs/ContigOrderer.java | 345 ++++++
src/org/gel/mauve/contigs/ContigRenamer.java | 67 ++
src/org/gel/mauve/contigs/ContigReorderer.java | 574 ++++++++++
.../gel/mauve/contigs/DefaultContigHandler.java | 60 +
.../gel/mauve/contigs/FastAContigChangeWriter.java | 175 +++
src/org/gel/mauve/contigs/FeatureFixer.java | 84 ++
.../gel/mauve/contigs/ListSequenceIterator.java | 31 +
src/org/gel/mauve/dcj/DCJ.java | 758 +++++++++++++
src/org/gel/mauve/dcj/DCJWindow.java | 261 +++++
src/org/gel/mauve/dcjx/Adjacency.java | 102 ++
src/org/gel/mauve/dcjx/AdjacencyGraph.java | 255 +++++
src/org/gel/mauve/dcjx/Block.java | 61 ++
src/org/gel/mauve/dcjx/BlockEnd.java | 12 +
src/org/gel/mauve/dcjx/Constants.java | 12 +
src/org/gel/mauve/dcjx/Contig.java | 109 ++
src/org/gel/mauve/dcjx/DCJ.java | 116 ++
src/org/gel/mauve/dcjx/DCJDistance.java | 231 ++++
src/org/gel/mauve/dcjx/FastAccessTable.java | 38 +
src/org/gel/mauve/dcjx/Head.java | 18 +
src/org/gel/mauve/dcjx/Permutation.java | 196 ++++
src/org/gel/mauve/dcjx/Tail.java | 18 +
src/org/gel/mauve/dcjx/VestigialDCJ.java | 96 ++
src/org/gel/mauve/format/BaseFormat.java | 129 +++
src/org/gel/mauve/format/DelegatingSequence.java | 429 ++++++++
src/org/gel/mauve/format/EmblFormat.java | 26 +
src/org/gel/mauve/format/FastaFormat.java | 43 +
src/org/gel/mauve/format/FileFinder.java | 73 ++
src/org/gel/mauve/format/GenbankEmblFormat.java | 248 +++++
src/org/gel/mauve/format/GenbankFileFormat.java | 28 +
src/org/gel/mauve/format/INSDseqFormat.java | 33 +
.../mauve/format/RawFastaBridgeFilterReader.java | 100 ++
src/org/gel/mauve/format/RawFormat.java | 26 +
.../gel/mauve/format/RichDelegatingSequence.java | 171 +++
.../mauve/format/RichStrandedFeatureTemplate.java | 28 +
.../gel/mauve/format/SequenceIteratorCache.java | 116 ++
.../gel/mauve/format/SupportedFormatFactory.java | 83 ++
src/org/gel/mauve/format/TestMain.java | 12 +
src/org/gel/mauve/gaggle/SampleGoose.java | 696 ++++++++++++
src/org/gel/mauve/gui/AlignFrame.java | 717 ++++++++++++
src/org/gel/mauve/gui/AlignWorker.java | 139 +++
.../gel/mauve/gui/AlignmentProcessListener.java | 7 +
src/org/gel/mauve/gui/AnalysisDisplayWindow.java | 278 +++++
src/org/gel/mauve/gui/ConsoleDialog.java | 35 +
src/org/gel/mauve/gui/ExportFrame.java | 464 ++++++++
src/org/gel/mauve/gui/ExportMenu.java | 166 +++
src/org/gel/mauve/gui/FillLayout.java | 85 ++
src/org/gel/mauve/gui/FrameLoader.java | 102 ++
src/org/gel/mauve/gui/GenomeCellRenderer.java | 26 +
src/org/gel/mauve/gui/HintMessageEvent.java | 17 +
src/org/gel/mauve/gui/HintMessageListener.java | 7 +
src/org/gel/mauve/gui/LCBStatusBar.java | 195 ++++
src/org/gel/mauve/gui/LcbLinePanel.java | 283 +++++
src/org/gel/mauve/gui/Mauve.java | 379 +++++++
src/org/gel/mauve/gui/MauveAlignFrame.java | 320 ++++++
src/org/gel/mauve/gui/MauveFrame.java | 766 +++++++++++++
src/org/gel/mauve/gui/MauveRenderingHints.java | 19 +
.../gel/mauve/gui/MySymbolSequenceRenderer.java | 116 ++
src/org/gel/mauve/gui/PrintPreviewCanvas.java | 77 ++
src/org/gel/mauve/gui/PrintPreviewDialog.java | 51 +
src/org/gel/mauve/gui/PrintUtilities.java | 34 +
.../gel/mauve/gui/ProgressiveMauveAlignFrame.java | 602 ++++++++++
src/org/gel/mauve/gui/QualifierPanel.java | 68 ++
src/org/gel/mauve/gui/RearrangementPanel.java | 976 +++++++++++++++++
src/org/gel/mauve/gui/SequenceNavigator.java | 745 +++++++++++++
src/org/gel/mauve/gui/SplashScreen.java | 91 ++
src/org/gel/mauve/gui/StyleMenu.java | 285 +++++
src/org/gel/mauve/gui/SwingWorker.java | 137 +++
src/org/gel/mauve/gui/dnd/DnDList.java | 264 +++++
src/org/gel/mauve/gui/dnd/FileDrop.java | 572 ++++++++++
src/org/gel/mauve/gui/dnd/TransferableObject.java | 262 +++++
.../gui/navigation/AnnotationContainsFilter.java | 120 ++
.../gel/mauve/gui/navigation/NavigationPanel.java | 203 ++++
.../mauve/gui/navigation/SearchResultPanel.java | 524 +++++++++
.../mauve/gui/sequence/AbstractSequencePanel.java | 151 +++
src/org/gel/mauve/gui/sequence/ControlPanel.java | 263 +++++
.../gel/mauve/gui/sequence/FeatureFilterer.java | 329 ++++++
src/org/gel/mauve/gui/sequence/FeaturePanel.java | 505 +++++++++
.../gui/sequence/FlatFileFeatureConstants.java | 68 ++
.../gui/sequence/FlatFileFeatureImporter.java | 318 ++++++
src/org/gel/mauve/gui/sequence/HighlightPanel.java | 99 ++
src/org/gel/mauve/gui/sequence/HistogramPanel.java | 68 ++
src/org/gel/mauve/gui/sequence/MatchPanel.java | 1031 +++++++++++++++++
src/org/gel/mauve/gui/sequence/MatchPopupMenu.java | 94 ++
.../MultiGenomeRectangularBeadRenderer.java | 86 ++
.../gel/mauve/gui/sequence/RRSequencePanel.java | 193 ++++
.../mauve/gui/sequence/RangeHighlightPanel.java | 92 ++
src/org/gel/mauve/gui/sequence/RulerPanel.java | 90 ++
src/org/gel/mauve/gui/sequence/SeqPanel.java | 317 ++++++
.../gui/sequence/ZiggyRectangularBeadRenderer.java | 276 +++++
src/org/gel/mauve/histogram/HistogramBuilder.java | 122 +++
src/org/gel/mauve/histogram/ZoomHistogram.java | 382 +++++++
src/org/gel/mauve/module/MauveModule.java | 22 +
src/org/gel/mauve/module/MauveModuleFrame.java | 23 +
src/org/gel/mauve/module/ModuleListener.java | 9 +
.../gel/mauve/recombination/WeakArgDataModel.java | 18 +
.../mauve/recombination/WeakArgModelBuilder.java | 268 +++++
.../gel/mauve/remote/MauveDisplayCommunicator.java | 17 +
src/org/gel/mauve/remote/MauveInterface.java | 14 +
src/org/gel/mauve/remote/MauveInterfaceImpl.java | 75 ++
src/org/gel/mauve/remote/RemoteApplet.java | 182 +++
src/org/gel/mauve/remote/RemoteControl.java | 9 +
src/org/gel/mauve/remote/RemoteControlImpl.java | 38 +
.../gel/mauve/remote/WargDisplayCommunicator.java | 32 +
src/org/gel/mauve/remote/WargInterface.java | 8 +
src/org/gel/mauve/summary/AnalysisModuleFrame.java | 117 ++
src/org/gel/mauve/summary/MauveInterfacer.java | 60 +
src/org/gel/mauve/summary/ProcessBackboneFile.java | 183 ++++
.../mauve/summary/output/AbstractIslandWriter.java | 22 +
.../summary/output/AbstractMatchDataWriter.java | 185 ++++
.../summary/output/AbstractTabbedDataWriter.java | 198 ++++
.../summary/output/AlignedSequenceWriter.java | 124 +++
.../mauve/summary/output/BackboneCompareFile.java | 37 +
.../summary/output/IslandCoordinateWriter.java | 55 +
.../mauve/summary/output/IslandFeatureWriter.java | 84 ++
.../summary/output/IslandGeneFeatureWriter.java | 208 ++++
.../mauve/summary/output/OverviewFileWriter.java | 238 ++++
.../mauve/summary/output/PartialFastaWriter.java | 68 ++
.../mauve/summary/output/SegmentDataProcessor.java | 285 +++++
.../mauve/summary/output/TroubleMatchWriter.java | 98 ++
src/org/gel/mauve/tree/FileKey.java | 71 ++
src/org/gel/mauve/tree/GISTree.java | 414 +++++++
src/org/gel/mauve/tree/GapKey.java | 45 +
src/org/gel/mauve/tree/IntervalSequenceTree.java | 320 ++++++
src/org/gel/mauve/tree/IstIterator.java | 31 +
src/org/gel/mauve/tree/IstNode.java | 67 ++
src/org/gel/mauve/tree/Key.java | 17 +
src/org/gel/mauve/tree/TreeStore.java | 98 ++
test/org/gel/mauve/LcbViewerModelTest.java | 59 +
test/org/gel/mauve/ModelLoader.java | 44 +
test/org/gel/mauve/XMFAAlignmentTest.java | 95 ++
.../gel/mauve/format/DelegatingSequenceTest.java | 89 ++
test/org/gel/mauve/format/MockFormat.java | 118 ++
test/org/gel/mauve/tree/GistNode.java | 58 +
test/org/gel/mauve/tree/GistTest.java | 194 ++++
testdata/S_bayanus_small.fasta | 12 +
testdata/S_bayanus_small.raw | 9 +
testdata/S_cerevisiae_small.gbk | 207 ++++
testdata/small.alignment | 58 +
testdata/small.mauve | 28 +
testdata/small.mums | 128 +++
testdata/small_raw.alignment | 58 +
288 files changed, 43136 insertions(+), 497 deletions(-)
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