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JAL-2050 make SequenceFeature.score final, adjust constructor calls
[jalview.git] / src / jalview / io /
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const... tree | commitdiff
2017-05-25 gmungocJAL-2490 test coverage of empty and null feature group... tree | commitdiff
2017-05-23 gmungocJAL-2490 find features for export as GFF, JAL-2548... tree | commitdiff
2017-05-23 gmungocJAL-2490 tidy code and tests for feature export in... tree | commitdiff
2017-05-23 gmungocJAL-2490 improved lookup of features for Export Feature... tree | commitdiff
2017-05-22 gmungocJAL-2505 use setter not direct access to sf.description tree | commitdiff
2017-05-22 gmungocJAL-2543 identify as JSON before HTML tree | commitdiff
2017-05-22 gmungocJAL-2546 JAL-2490 efficient lookup of features, correct... tree | commitdiff
2017-05-19 gmungocJAL-2490 refactored test for 'hasFeatures' tree | commitdiff
2017-05-16 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-16 gmungocJAL-2505 refactor to set type and group in SequenceFeat... tree | commitdiff
2017-05-15 Jim ProcterMerge branch 'bug/JAL-2507_rnasecstrstockholm' into... tree | commitdiff
2017-05-15 Jim ProcterJAL-2507 capitalisation for annotation lines generated... tree | commitdiff
2017-05-15 Jim ProcterJAL-2507 case insensitive recognition of annotation... tree | commitdiff
2017-05-15 Jim ProcterJAL-2535 quick hack to implement posterior probabilitie... tree | commitdiff
2017-05-15 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-12 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... tree | commitdiff
2017-05-11 Jim ProcterJAL-2509 JAL-2507 allow whitespace in GS annotation... tree | commitdiff
2017-05-09 Jim ProcterJAL-2509 extend set of brackets recognised by stockholm... tree | commitdiff
2017-05-09 Jim ProcterJAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS... tree | commitdiff
2017-05-09 Jim ProcterJAL-2507 output secondary structure regardless of prese... tree | commitdiff
2017-05-09 gmungocJAL-2505 use constructors to set (what will be) final... tree | commitdiff
2017-05-08 gmungocJAL-2505 set type,desc,begin,end,group,score in Sequenc... tree | commitdiff
2017-05-08 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into tree | commitdiff
2017-05-04 Jim Procterfix for JAL-2509 - don’t replace all bracket types... tree | commitdiff
2017-05-04 Jim Procterfix for JAL-2507 - resolve stockholm per residue annota... tree | commitdiff
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside... tree | commitdiff
2017-05-02 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-05-01 gmungocMerge branch 'develop' into features/JAL-2446NCList tree | commitdiff
2017-05-01 gmungocJAL-2489 JAL-2371 reinstate calls to tree | commitdiff
2017-04-28 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-04-27 gmungocJAL-2492 use SequenceFeatures.getNonPositionalFeatures() tree | commitdiff
2017-04-26 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-04-26 kiramtMerge remote-tracking branch 'origin/develop' into... tree | commitdiff
2017-04-26 gmungocJAL-2490 findFeaturesAtRes with performant feature... tree | commitdiff
2017-04-25 tcofoegbuJAL-2489 bug fix tree | commitdiff
2017-04-25 kiramtJAL-2388 Working hidden regions hide/show in desktop tree | commitdiff
2017-04-24 kiramtJAL-2388 Finished split of hidden columns and selected... tree | commitdiff
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... tree | commitdiff
2017-03-28 gmungocJAL-2416 more test coverage of matrix parser tree | commitdiff
2017-03-27 gmungocJAL-2416 parse score matrices in either NCBI or AAindex... tree | commitdiff
2017-03-27 gmungocJAL-2416 class Javadoc updates prior to parsing changes tree | commitdiff
2017-03-24 gmungocJAL-2428 simplify TreeModel constructors, add getOrigin... tree | commitdiff
2017-03-24 gmungocJAL-1632 TreeChooser renamed CalculationChooser, text... tree | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-13 gmungocJAL-2438 FeatureColourFinder refactored from FeatureRen... tree | commitdiff
2017-03-06 gmungocJAL-2428 separate TreeModel from TreeBuilder/NJTree... tree | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... tree | commitdiff
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... tree | commitdiff
2017-02-21 gmungocJAL-2416 support roundtrip print/parse of ScoreMatrix tree | commitdiff
2017-02-17 gmungocJAL-2416 allow space in score matrix name tree | commitdiff
2017-02-17 gmungocJAL-2403 constants for "NJ", "AV" tree | commitdiff
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop... tree | commitdiff
2017-01-26 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-26 gmungocJAL-2344 test fix and code tidy for review comments tree | commitdiff
2017-01-25 gmungocJAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid... tree | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2017-01-17 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-12 gmungocJAL-2344 now flagging formats as 'identifiable' instead... tree | commitdiff
2017-01-11 gmungocJAL-2344 separated AlignmentFileI into AlignmentFileRea... tree | commitdiff
2017-01-11 gmungocJAL-2344 FileFormats singleton for formats, FileFormatI... tree | commitdiff
2017-01-11 gmungocJAL-2344 addSequence() method added to support Groovy... tree | commitdiff
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-06 gmungocJAL-2360 findColour() with no args removed from ColourS... tree | commitdiff
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI tree | commitdiff
2016-12-21 gmungocJAL-2360 tidy spelling and file contents order only tree | commitdiff
2016-12-16 Jim ProcterJAL-2360 report line number when threshold cannot be... tree | commitdiff
2016-12-16 gmungocJAL-2360 getColour() renamed to getColourScheme(),... tree | commitdiff
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum, tree | commitdiff
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-12-07 gmungocJAL-2344 handle null format, simplify JalviewFileChoose... tree | commitdiff
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-29 gmungocJAL-2344 FileFormat.isStructureFile replaces tree | commitdiff
2016-11-28 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-28 tcofoegbuMerge branch 'features/JAL-2326_JOptionPane-refactoring... tree | commitdiff
2016-11-28 gmungocJAL-2344 added FileFormatI.isStructureFile() tree | commitdiff
2016-11-28 gmungocJAL-2345 cache generated ImageIcon per file path tree | commitdiff
2016-11-25 gmungocJAL-2344 dynamically determine recognised extensions... tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-25 gmungocJAL-2344 override to ignore (obsolete?) JalviewFileView tree | commitdiff
2016-11-25 gmungocJAL-2344 use .equals() to compare FileFormatI objects tree | commitdiff
2016-11-24 gmungocDistinguish text-only output formats and others (.jar... tree | commitdiff
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane tree | commitdiff
2016-11-24 gmungocFurther tweaks to get tests passing tree | commitdiff
2016-11-24 gmungocFileFormatI further tweaks, clean compile tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'documentation/JAL-2325_release2101' into... tree | commitdiff
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-22 Jim ProcterJAL-2197 changed tooltip for Jnet annotation rows to... tree | commitdiff
2016-11-22 tcofoegbuMerge branch 'bug/JAL-2277_refactorPrintUnwrapped'... tree | commitdiff
2016-11-22 tcofoegbuJAL-2322 added runnable interface to HTMLOutput class... tree | commitdiff
2016-11-22 gmungocJAL-2277 refactored AlignmentPanel.printUnwrapped to... tree | commitdiff
2016-11-21 gmungocMerge branch 'develop' into bug/JAL-2323disulfideOverview tree | commitdiff
2016-11-17 gmungocJAL-2327 disulfide bond abstracted to SequenceFeature... tree | commitdiff
2016-11-16 Jim ProcterMerge branch 'features/JAL-1723_sequenceReport' into... tree | commitdiff
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