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JAL-3116 parse EMBL XML with JAXB (todo: update unit tests)
[jalview.git] / src / jalview / gui / AlignFrame.java
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit... blob | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch blob | commitdiff | diff to current
2018-09-07 Jim ProcterJAL-3107 update any group associated annotation rows... blob | commitdiff | diff to current
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2... blob | commitdiff | diff to current
2018-05-23 gmungocJAL-2993 AlignFrame listen for keystrokes in OverviewPanel blob | commitdiff | diff to current
2018-05-09 gmungocJAL-2984 add pdb as sequence(s) if associate structure... blob | commitdiff | diff to current
2018-03-16 gmungocMerge branch 'bug/JAL-2865removeGC' into develop blob | commitdiff | diff to current
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... blob | commitdiff | diff to current
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 blob | commitdiff | diff to current
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... blob | commitdiff | diff to current
2018-02-13 Jim ProcterJAL-2781 refactor ‘trim retrieved sequence’ preference... blob | commitdiff | diff to current
2018-01-15 kiramtJAL-2759 Refactor of hideInsertionsFor after review blob | commitdiff | diff to current
2018-01-10 gmungocJAL-2865 unhelpful System.gc() calls removed bug/JAL-2865removeGC blob | commitdiff | diff to current
2018-01-10 gmungocJAL-1793 update spike branch to latest blob | commitdiff | diff to current
2017-12-08 gmungocJAL-2843 refactor / tidy for feature filter input/output blob | commitdiff | diff to current
2017-12-04 gmungocJAL-2850 JAL-1766 option to load contig sequence refere... blob | commitdiff | diff to current
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759 blob | commitdiff | diff to current
2017-10-27 gmungocJAL-1793 spike branch updated to latest blob | commitdiff | diff to current
2017-10-27 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-10-26 Jim ProcterMerge branch 'feature/JAL-2488finalize' into develop blob | commitdiff | diff to current
2017-10-26 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2727closeAllFreeMemory' into... blob | commitdiff | diff to current
2017-10-24 gmungocJAL-2738 update spike branch with latest blob | commitdiff | diff to current
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd... blob | commitdiff | diff to current
2017-10-20 gmungocPush 1793 latest to spike branch blob | commitdiff | diff to current
2017-10-19 gmungocJAL-2755 find gene loci for fetched xrefs where possible blob | commitdiff | diff to current
2017-10-12 Jim ProcterJAL-2773 add new flag to paintAlignment(updateOverview... features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-26 kiramtJAL-2674 more List<int[]> -> HiddenColumns copy changes blob | commitdiff | diff to current
2017-09-26 kiramtJAL-2674 Changes to pasting blob | commitdiff | diff to current
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes blob | commitdiff | diff to current
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence blob | commitdiff | diff to current
2017-09-12 gmungocJAL-2727 ensure ViewportRanges (and gapcounts) are... blob | commitdiff | diff to current
2017-09-01 gmungocJAL-2488 remove finalize methods blob | commitdiff | diff to current
2017-08-29 Jim ProcterJAL-2698 spawn a thread to test for and raise auto... blob | commitdiff | diff to current
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-08-09 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-08-07 Jim ProcterMerge branch 'bug/JAL-2592userDefinedScheme' into develop blob | commitdiff | diff to current
2017-08-02 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-07-28 kiramtJAL-2632 Added paintAlignment(true) to show cols code blob | commitdiff | diff to current
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 blob | commitdiff | diff to current
2017-07-19 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-07-04 gmungocJAL-147 remove redundant calls to update overview panel blob | commitdiff | diff to current
2017-07-04 gmungocJAL-2608 tidy up OverviewPanel when closed blob | commitdiff | diff to current
2017-06-29 gmungocJAL-147 improved wrapped scrolling (including Overview... blob | commitdiff | diff to current
2017-06-27 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-06-26 gmungocJAL-1858 ensure full redraw on 'remove all selections' blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2592 distinguish "User Defined" (scheme name) from... bug/JAL-2592userDefinedScheme blob | commitdiff | diff to current
2017-06-08 kiramtJAL-2591 Refactor HiddenColumns to use ArrayList instea... blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 Further refactoring (still incomplete) blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 More refactoring (incomplete) blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 More rationalising of hiddencols blob | commitdiff | diff to current
2017-06-07 kiramtJAL-2591 simplifying hidden columns usage blob | commitdiff | diff to current
2017-05-29 Jim ProcterMerge branch 'bug/JAL-2536' into develop blob | commitdiff | diff to current
2017-05-16 kiramtJAL-2536 Overview window sizing not subject to min... bug/JAL-2536 blob | commitdiff | diff to current
2017-05-15 kiramtMerge remote-tracking branch 'origin/develop' into... blob | commitdiff | diff to current
2017-05-12 Jim ProcterMerge branch 'features/JAL-2388OverviewWindow' into... blob | commitdiff | diff to current
2017-05-11 kiramtJAL-2491 Unit tests and updates blob | commitdiff | diff to current
2017-05-08 gmungocJAL-1632 i18n for warning messages blob | commitdiff | diff to current
2017-05-08 kiramtJAL-2491 Started moving other scrolling fns into viewpo... blob | commitdiff | diff to current
2017-05-05 kiramtMerge remote-tracking branch blob | commitdiff | diff to current
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges blob | commitdiff | diff to current
2017-05-02 gmungocJAL-2499 JAL-2403 push 'configure for view' inside... blob | commitdiff | diff to current
2017-04-25 kiramtJAL-2388 Working hidden regions hide/show in desktop blob | commitdiff | diff to current
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... blob | commitdiff | diff to current
2017-04-12 gmungocJAL-1632 removed check for aligned sequences for Tree... blob | commitdiff | diff to current
2017-04-12 gmungocJAL-1632 one PCA/Tree per panel, closed when panel... blob | commitdiff | diff to current
2017-04-07 gmungocMerge branch 'develop' into features/JAL-2393customMatrices blob | commitdiff | diff to current
2017-04-05 gmungocJAL-2361 simplify constructors, select unsaved but... blob | commitdiff | diff to current
2017-03-31 gmungocMerge branch 'develop' into bug/JAL-2431splitFrameNewView bug/JAL-2431splitFrameNewView blob | commitdiff | diff to current
2017-03-30 gmungocJAL-1608 leave Create Group, Remove Group menu items... blob | commitdiff | diff to current
2017-03-29 gmungocMerge branch 'develop' into bug/JAL-1608createGroups blob | commitdiff | diff to current
2017-03-24 gmungocJAL-1632 TreeChooser renamed CalculationChooser, text... blob | commitdiff | diff to current
2017-03-24 gmungocJAL-838 move two callers off Comparison.PID and depreca... blob | commitdiff | diff to current
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices blob | commitdiff | diff to current
2017-03-16 kiramtJAL-2388 Applied ViewportRanges to code blob | commitdiff | diff to current
2017-03-15 gmungocJAL-2431 show cDNA consensus after New View in split... blob | commitdiff | diff to current
2017-02-27 kiramtJAL-2388 Make startRes,startSeq,endRes,endSeq private... blob | commitdiff | diff to current
2017-02-27 gmungocJAL-1632 similarity options on TreeChooser panel affect... blob | commitdiff | diff to current
2017-02-27 gmungocJAL-1632 refactored NJTree constructor to include Simil... blob | commitdiff | diff to current
2017-02-23 gmungocJAL-2403 JAL-1483 changes to ScoreModelI hierarchy... blob | commitdiff | diff to current
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... blob | commitdiff | diff to current
2017-02-17 gmungocJAL-2423 refactored method to build panel title for... blob | commitdiff | diff to current
2017-02-14 gmungocParsing moved to (new) ScoreMatrixFile, drag and drop... blob | commitdiff | diff to current
2017-02-13 gmungocJAL-1632 first cut of Tree chooser dialog and ScoreMode... blob | commitdiff | diff to current
2017-02-09 gmungocJAL-1608 menu entry text; enable/disable Create/Remove... blob | commitdiff | diff to current
2017-01-31 gmungocJAL-2371 rename global/viewportColourScheme to residueS... blob | commitdiff | diff to current
2017-01-31 gmungocJAL-2385 more tests/bug fixes mostly for gui.SliderPane... blob | commitdiff | diff to current
2017-01-23 gmungocJAL-2386 unit tests for change colour (and minor refact... blob | commitdiff | diff to current
2017-01-23 gmungocJAL-2386 simplify changeColour (doesn't change colour... blob | commitdiff | diff to current
2017-01-20 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... blob | commitdiff | diff to current
2017-01-20 gmungocMerge branch 'develop' into features/JAL-2360colourSche... blob | commitdiff | diff to current
2017-01-19 gmungocJAL-2383 restore PID colour threshold from project... blob | commitdiff | diff to current
2017-01-17 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... blob | commitdiff | diff to current
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2360colourSche... blob | commitdiff | diff to current
2017-01-11 gmungocJAL-2344 FileFormats singleton for formats, FileFormatI... blob | commitdiff | diff to current
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI blob | commitdiff | diff to current
2016-12-22 gmungocJAL-2360 structure viewers now using ColourMenuHelper... blob | commitdiff | diff to current
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