Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java
2024-09-17 Jim ProcterJAL-4418 JAL-4392 show/hide group associated secondary...
2024-09-16 Jim ProcterJAL-4392 autohide the secondary structure consensus... patch/JAL-4392_hide_ssconsensus_if_no_data
2024-09-16 Jim ProcterJAL-4392 don't show SS consensus for DNA alignments
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks
2024-05-21 Jim ProcterJAL-4159 connectivity should be computed for the sequen...
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4159_pasimap
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4386_calculate_...
2024-05-15 Renia CorreyaJAL-4386 Added preferences for secondary structure...
2024-05-13 Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se...
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply
2023-09-07 MorellThomasMerge branch 'hardcode'
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use...
2023-07-22 MorellThomasImplement MSA, scoring and counting the connections
2023-07-18 James ProcterJAL-3858 annotation .height is bigger than graphHeight...
2023-05-22 James ProcterJAL-1551 spotless
2023-05-19 James ProcterJAL-1551 spotlessApply
2023-05-19 James ProcterJAL-1551 spotlessApply
2023-02-27 James ProcterJAL-4134 allow tree groups to be stored/recovered on...
2023-02-13 Ben SoaresMerge branch 'merge/JAL-1988_JAL-3772+JAL-3416+JAL...
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold...
2023-01-30 Ben SoaresJAL-1988 Make sensible choices if only the opening... merge/JAL-1988_JAL-3772+JAL-3416+JAL-4054+JAL-4064
2022-11-01 Ben SoaresJAL-1988 JAL-3772 Change default alignmentviewport...
2022-09-26 Ben SoaresJAL-1988 JAL-3772 linked undostack to saved changes...
2022-09-16 Jim ProcterJAL-518 refactored groovy script into main codebase...
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2021-08-11 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into feature...
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement...
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL...
2020-08-13 gmungocJAL-3597 additional references nulled, bug in test...
2020-07-14 gmungocJAL-3597 additional references nulled, bug in test...
2019-12-09 gmungocJAL-3490 pull up getViewAsVisibleContigs to base class...
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop
2019-06-18 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into merge...
2019-06-06 gmungocMerge branch 'develop' into trialMerge
2019-04-26 gmungocJAL-3226 removal of superseded changes
2019-04-23 hansonr[JAL-3226] problem that JavaScript (or Java) may consol...
2019-04-18 hansonrAdds check for gap padding to disallow fast paint upon...
2019-04-18 hansonrexplicit Hashtable objects
2019-03-13 gmungocMerge branch 'develop' into trialMerge
2019-03-11 gmungocMerge branch 'develop' into merge/JAL-3127
2019-03-11 gmungocJAL-3201 restore group colours correctly from project feature/JAL-2250colourAllGroups
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into...
2019-03-01 gmungocMerge branch 'bug/JAL-3158selectionBroadcasts' into...
2019-02-26 gmungocJAL-3201 group colour schemes distinct instances
2019-02-18 gmungocJAL-3187 'on top' optional for complementary features
2019-01-18 gmungocJAL-3187 basic first version for tooltips only (renderi...
2018-11-28 gmungocJAL-3158 additional calls to reset 'selection changed... bug/JAL-3158selectionBroadcasts
2018-10-16 Jim ProcterJAL-3127 use AlignViewportI.addGroup() to add group...
2018-10-16 Jim Procterviewport flag to indicate when structure view needs...
2018-07-20 gmungocJAL-3048 revised AlignExportSettings dialog with respon...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-09 gmungocJAL-2666 fix failure to scroll split alignment of height 1
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after...
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC...
2018-01-15 kiramtJAL-2759 Rename findColumnPosition and adjustForHiddenC...
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-26 Jim ProcterJAL-2488 patch causes of NPE during testStoreAndRecover...
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2727closeAllFreeMemory' into...
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-11 kiramtJAL-2742 removed unused getViewAsCigars
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-14 gmungocJAL-2727 null more fields in AlignmentViewport.dispose...
2017-09-13 gmungocJAL-2727 null additional references on close
2017-09-12 gmungocRevert "JAL-2727 null hconsensus, "
2017-09-12 gmungocJAL-2727 null hconsensus,
2017-09-12 gmungocJAL-2727 ensure ViewportRanges (and gapcounts) are...
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-08 gmungocJAL-2560 alternative fix (reinstate lost line of code)
2017-08-08 gmungocJAL-2649 JAL-2650 wait for Conservation calc to complet...
2017-07-24 gmungocspike branch updated from latest features/JAL-2446
2017-07-06 gmungocJAL-147 unit test for hide/show sequences update Viewpo...
2017-07-05 Jim ProcterMerge branch 'develop' into features/JAL-2349_matrixvis
2017-07-04 gmungocJAL-147 revised update of startSeq, endSeq on unhide...
2017-07-04 gmungocJAL-147 corrected update of ViewportRanges for show...
2017-07-04 gmungocJAL-147 update ViewportRanges height after show/hide...
2017-07-03 gmungocMerge branch 'develop' into bug/JAL-147scrollWrappedView
2017-06-30 gmungocJAL-2602 pulled up identical methods to base class
2017-06-29 gmungocJAL-147 improved wrapped scrolling (including Overview...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-09 Jim ProcterMerge branch 'develop' into features/JAL-2349_matrixvis
2017-06-06 kiramtJAL-2591 Removed getHiddenRegions()==null checks which...
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup
2017-05-15 Jim ProcterJAL-2371 create a default ResidueShader when constructi...
2017-05-12 Jim ProcterMerge branch 'features/JAL-2435splitScreenFont' into...
2017-05-05 gmungocMerge branch 'develop' into features/JAL-2435splitScree...
2017-05-05 kiramtMerge remote-tracking branch
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into
2017-05-03 Jim ProcterJAL-1933 JAL-2501 i18n for all auto calculated descriptions features/JAL-2432_annotbypercent
2017-04-27 Jim ProcterJAL-1933 consensus calculation doesn’t depend on occupa...
2017-04-27 Jim ProcterJAL-1933 only create and add occupancy row to alignment...
2017-04-27 Jim ProcterJAL-1933 occupancy row has a space below it for counts
2017-04-24 kiramtMerge remote-tracking branch
2017-04-24 kiramtJAL-2388 Finished split of hidden columns and selected...
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection...
2017-04-19 kiramtMerge remote-tracking branch 'origin/develop' into
2017-04-03 gmungocMerge branch 'develop' into features/JAL-2435splitScree...
2017-03-31 gmungocMerge branch 'develop' into bug/JAL-2431splitFrameNewView bug/JAL-2431splitFrameNewView
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