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Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java
2023-01-30 Jim ProcterMerge branch 'JAL-3878_ws-overhaul-3' into with_ws_over... blob | commitdiff
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2... blob | commitdiff | diff to current
2022-12-13 Jim ProcterMerge branch 'alpha/origin_2022_JAL-3066_Jalview_212_sl... blob | commitdiff | diff to current
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge... blob | commitdiff | diff to current
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 blob | commitdiff | diff to current
2022-03-02 Mateusz WarownyJAL-3878 Add serviceExecutor to AlignmentViewport. blob | commitdiff | diff to current
2021-07-09 Mateusz WarownyJAL-3690 Remove references to old AlignCalcManager. bug/JAL-3849_aacon-parameters blob | commitdiff | diff to current
2020-12-14 Jim ProcterMerge branch 'Jalview-JS/develop' into merge_js_develop blob | commitdiff | diff to current
2020-10-26 Mateusz WaronwyJAL-3690 - introduce shutdown method that cleans up... blob | commitdiff | diff to current
2020-10-21 Mateusz WarownyJAL - 3690 AlignCalc rebuilt - FutureTask-based manager blob | commitdiff | diff to current
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement... blob | commitdiff | diff to current
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop blob | commitdiff | diff to current
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL... blob | commitdiff | diff to current
2020-08-13 gmungocJAL-3597 additional references nulled, bug in test... blob | commitdiff | diff to current
2020-07-14 gmungocJAL-3597 additional references nulled, bug in test... blob | commitdiff | diff to current
2020-06-09 BobHansonJAL-3446 from applet; JAL-3374 blob | commitdiff | diff to current
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... blob | commitdiff | diff to current
2019-12-09 gmungocJAL-3490 pull up getViewAsVisibleContigs to base class... blob | commitdiff | diff to current
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop blob | commitdiff | diff to current
2019-08-13 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into... blob | commitdiff | diff to current
2019-07-03 tvaJAL-2629 can now filter by sequence e-value or bit... blob | commitdiff | diff to current
2019-06-06 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2019-06-05 tvaJAL-3285 delete duplicate variables in AlignmentViewpor... blob | commitdiff | diff to current
2019-06-05 tvaJAL-3285 add unmerged features into AlignmentViewport blob | commitdiff | diff to current
2019-06-04 Jim ProcterMerge branch 'develop' into developtomchmmer blob | commitdiff | diff to current
2019-04-26 gmungocJAL-3226 removal of superseded changes blob | commitdiff | diff to current
2019-04-23 hansonr[JAL-3226] problem that JavaScript (or Java) may consol... blob | commitdiff | diff to current
2019-04-18 hansonrAdds check for gap padding to disallow fast paint upon... blob | commitdiff | diff to current
2019-04-18 hansonrexplicit Hashtable objects blob | commitdiff | diff to current
2019-03-13 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2019-03-11 gmungocMerge branch 'develop' into merge/JAL-3127 blob | commitdiff | diff to current
2019-03-11 gmungocJAL-3201 restore group colours correctly from project feature/JAL-2250colourAllGroups blob | commitdiff | diff to current
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... blob | commitdiff | diff to current
2019-03-01 gmungocMerge branch 'bug/JAL-3158selectionBroadcasts' into... blob | commitdiff | diff to current
2019-02-26 gmungocJAL-3201 group colour schemes distinct instances blob | commitdiff | diff to current
2019-02-18 gmungocJAL-3187 'on top' optional for complementary features blob | commitdiff | diff to current
2019-01-18 gmungocJAL-3187 basic first version for tooltips only (renderi... blob | commitdiff | diff to current
2018-11-28 gmungocJAL-3158 additional calls to reset 'selection changed... bug/JAL-3158selectionBroadcasts blob | commitdiff | diff to current
2018-10-16 Jim ProcterJAL-3127 use AlignViewportI.addGroup() to add group... blob | commitdiff | diff to current
2018-10-16 Jim Procterviewport flag to indicate when structure view needs... blob | commitdiff | diff to current
2018-07-20 gmungocJAL-3048 revised AlignExportSettings dialog with respon... blob | commitdiff | diff to current
2018-06-01 Jim ProcterJAL-1950 JAL-2937 allow copy of sequences from group... blob | commitdiff | diff to current
2018-03-30 gmungocJAL-2939 field/method naming more consistent blob | commitdiff | diff to current
2018-03-30 gmungocJAL-2939 remove commented out code blob | commitdiff | diff to current
2018-03-26 gmungocJAL-2939 pull up set/IsNormalise[HMM]SequenceLogo blob | commitdiff | diff to current
2018-03-26 gmungocJAL-2939 no need to recalc HMM annotation for show... blob | commitdiff | diff to current
2018-03-21 gmungocJAL-2629 tweaks to Information annotation updating blob | commitdiff | diff to current
2018-03-16 gmungocMerge branch 'develop' into trialMerge blob | commitdiff | diff to current
2018-03-07 gmungocJAL-2629 storage and lifecycle of alignment/group HMM... blob | commitdiff | diff to current
2018-03-01 gmungocJAL-2629 revising hmmer annotation updating (wip) blob | commitdiff | diff to current
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip) blob | commitdiff | diff to current
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104 blob | commitdiff | diff to current
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc blob | commitdiff | diff to current
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and... blob | commitdiff | diff to current
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer blob | commitdiff | diff to current
2018-02-09 gmungocJAL-2666 fix failure to scroll split alignment of height 1 blob | commitdiff | diff to current
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after... blob | commitdiff | diff to current
2018-01-16 kiramtJAL-2759 Moved alignment annotation code out of HiddenC... blob | commitdiff | diff to current
2018-01-15 kiramtJAL-2759 Rename findColumnPosition and adjustForHiddenC... blob | commitdiff | diff to current
2017-10-27 gmungocJAL-1793 spike branch updated to latest blob | commitdiff | diff to current
2017-10-26 Jim ProcterJAL-2488 patch causes of NPE during testStoreAndRecover... 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
2017-10-11 kiramtJAL-2742 removed unused getViewAsCigars blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-14 gmungocJAL-2727 null more fields in AlignmentViewport.dispose... blob | commitdiff | diff to current
2017-09-13 gmungocJAL-2727 null additional references on close blob | commitdiff | diff to current
2017-09-12 gmungocRevert "JAL-2727 null hconsensus, " blob | commitdiff | diff to current
2017-09-12 gmungocJAL-2727 null hconsensus, blob | commitdiff | diff to current
2017-09-12 gmungocJAL-2727 ensure ViewportRanges (and gapcounts) are... blob | commitdiff | diff to current
2017-09-01 TZVanaaltenJAL-2629 manual curation of HMMs via reference annotati... blob | commitdiff | diff to current
2017-08-28 tzvanaaltenJAL-2629 add option to set HMM Logo letter height to... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add adjustable parameters to hmmbuild blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 fix for NPE caused by incorrect initiation... blob | commitdiff | diff to current
2017-08-25 TZVanaaltenJAL-2629 add basic parameter adjustment to hmmsearch... blob | commitdiff | diff to current
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer blob | commitdiff | diff to current
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work blob | commitdiff | diff to current
2017-08-16 Jim ProcterJAL-2418 source formatting blob | commitdiff | diff to current
2017-08-15 TZVanaaltenJAL-2629 selected HMM name now shown in HMMER menu blob | commitdiff | diff to current
2017-08-11 TZVanaaltenJAL-2629 add ability to select HMMs blob | commitdiff | diff to current
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame blob | commitdiff | diff to current
2017-08-08 gmungocJAL-2560 alternative fix (reinstate lost line of code) blob | commitdiff | diff to current
2017-08-08 gmungocJAL-2649 JAL-2650 wait for Conservation calc to complet... blob | commitdiff | diff to current
2017-08-07 TZVanaaltenJAL-2629 current hmmer commands are now executed in... blob | commitdiff | diff to current
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment blob | commitdiff | diff to current
2017-08-02 TZVanaaltenJAL-2599 fix for information annotation buttons blob | commitdiff | diff to current
2017-07-24 gmungocspike branch updated from latest features/JAL-2446 blob | commitdiff | diff to current
2017-07-14 TZVanaaltenadd partial button fix to annotation and statistics... features/hmmer_statistics blob | commitdiff | diff to current
2017-07-12 TZVanaaltentest HMM annotaTION blob | commitdiff | diff to current
2017-07-06 gmungocJAL-147 unit test for hide/show sequences update Viewpo... blob | commitdiff | diff to current
2017-07-04 gmungocJAL-147 revised update of startSeq, endSeq on unhide... blob | commitdiff | diff to current
2017-07-04 gmungocJAL-147 corrected update of ViewportRanges for show... blob | commitdiff | diff to current
2017-07-04 gmungocJAL-147 update ViewportRanges height after show/hide... blob | commitdiff | diff to current
2017-07-03 gmungocMerge branch 'develop' into bug/JAL-147scrollWrappedView blob | commitdiff | diff to current
2017-06-30 gmungocJAL-2602 pulled up identical methods to base class blob | commitdiff | diff to current
2017-06-29 gmungocJAL-147 improved wrapped scrolling (including Overview... blob | commitdiff | diff to current
2017-06-29 TZVanaaltentransferred the storage position of the HMM to annotations blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-06-06 kiramtJAL-2591 Removed getHiddenRegions()==null checks which... blob | commitdiff | diff to current
2017-05-24 kiramtJAL-2034 Added isDefined flag to SequenceGroup blob | commitdiff | diff to current
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