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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / gui / AlignFrame.java
2024-09-17 Jim ProcterJAL-4418 JAL-4392 show/hide group associated secondary... commit | commitdiff
2024-09-13 Ben SoaresJAL-4461 Tests for JalviewFileChooser.defaultSaveFileFo... commit | commitdiff
2024-09-13 Ben SoaresJAL-4461 Adding in a number of properties that control... commit | commitdiff
2024-09-12 Jim ProcterJAL-4461 fix up formatting and remove old comment commit | commitdiff
2024-09-12 Ben SoaresJAL-4461 Change labelling of All-known-alignment-files... commit | commitdiff
2024-09-11 Ben SoaresJAL-4460 Update currentFileFormat /after/ new format... commit | commitdiff
2024-08-07 Jim ProcterJAL-4447 standardised title formula for reporting score... commit | commitdiff
2024-08-07 Jim ProcterJAL-4159 JAL-789 report pasimap and pairwise alignment... commit | commitdiff
2024-08-05 Jim ProcterJAL-4446 allow progress bar message to be changed whils... commit | commitdiff
2024-08-05 Jim ProcterJAL-1551 gradle spotlessApply and doc tweaks commit | commitdiff
2024-05-24 Jim ProcterJAL-4257 JAL-4159 JAL-789 tidy up passing of score... commit | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4159_pasimap commit | commitdiff
2024-05-16 Jim ProcterMerge branch 'develop' into feature/JAL-4386_calculate_... commit | commitdiff
2024-05-15 Renia CorreyaJAL-4386 - Implementation of retrieving secondary structure commit | commitdiff
2024-05-13 Jim ProcterMerge branch 'develop' into features/JAL-518_justify_se... commit | commitdiff
2024-04-30 Renia CorreyaJAL-4392 Merging consensus secondary structure commit | commitdiff
2024-04-18 MorellThomasImplemented ProgressBar for PaSiMap commit | commitdiff
2023-12-01 MorellThomasApplying adjustablenw_params.patch (JAL-4159) commit | commitdiff
2023-11-13 James ProcterJAL-4331 construct and pass on overview title before... commit | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-11-01 James ProcterMerge branch 'feature/JAL-4315_fc_draganddrop' into... commit | commitdiff
2023-10-31 James ProcterJAL-244 knock on - make sure alignPanel is laid out... commit | commitdiff
2023-10-30 James ProcterHandle feature settings files loaded via drag and drop... feature/JAL-4315_fc_draganddrop commit | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... commit | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... commit | commitdiff
2023-10-13 Ben SoaresJAL-3783 Updated groovy jars. Requires javaparser... commit | commitdiff
2023-09-11 Ben SoaresJAL-4277 --mkdirs with cautious refusal for paths with .. commit | commitdiff
2023-09-08 MorellThomasProperly integrated endGaps option for AlignSeq.traceAl... commit | commitdiff
2023-09-07 James ProcterJAL-4090 JAL-4160 JAL-4274 image export dimensions... commit | commitdiff
2023-09-01 Ben SoaresMerge branch 'feature/JAL-629_--output_-_means_output_t... commit | commitdiff
2023-09-01 Ben SoaresJAL-629 Fix --structureimage and options commit | commitdiff
2023-08-24 Ben SoaresMerge branch 'bug/JAL-4214_system_freeze_when_opening_f... commit | commitdiff
2023-08-18 Ben SoaresMerge branch 'improvement/JAL-4206_improve_JalviewFileC... commit | commitdiff
2023-08-18 Ben SoaresMerge branch 'feature/JAL-244_Automatically_adjust_left... commit | commitdiff
2023-08-11 Ben SoaresJAL-629 Much better way of dealing with list of filenam... commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-08-09 Ben SoaresJAL-629 Enable output to STDOUT when specifying output... commit | commitdiff
2023-08-02 Ben SoaresJAL-244 Fix buglet with automatic change in id column... commit | commitdiff
2023-07-27 Ben SoaresMerge branch 'develop' into feature/JAL-244_Automatical... commit | commitdiff
2023-07-27 Ben SoaresJAL-244 Allow adjusting Id column width in wrap mode... commit | commitdiff
2023-07-20 James ProcterJAL-3855 tree title for PAE matrix tree is PAE Matrix... patch/JAL-3855_fixup_pae commit | commitdiff
2023-06-29 Ben SoaresJAL-4214 Linux only: Disable menus when internal modal... bug/JAL-4214_system_freeze_when_opening_file_using_gui_in_linux commit | commitdiff
2023-06-13 Ben SoaresJAL-3416 Removed a few more JInternalFrame icons with... commit | commitdiff
2023-06-07 James ProcterJAL-4195 add exception handling for all image output... commit | commitdiff
2023-05-26 James ProcterMerge branch 'develop' into features/JAL-4134_use_annot... commit | commitdiff
2023-05-25 James ProcterJAL-2381 copy and paste sequence also copies contact... commit | commitdiff
2023-05-25 Ben SoaresJAL-4186 Turn JvOptionPane Callable<Void> handlers... commit | commitdiff
2023-05-23 Ben SoaresJAL-629 Added --structureimage code and formatting... commit | commitdiff
2023-05-22 Ben SoaresJAL-629 --structureimage with formatting args. commit | commitdiff
2023-05-22 James ProcterJAL-4134 only build tree when showing it in the tree... commit | commitdiff
2023-05-19 James ProcterJAL-1551 spotlessApply commit | commitdiff
2023-05-11 Ben SoaresJAL-629 Fix --tempfac. Hide non-working --notempfac... commit | commitdiff
2023-05-02 Ben SoaresJAL-629 Add --renderer arg/subval for vector output... commit | commitdiff
2023-04-22 Ben SoaresJAL-629 Test and fix --annotation --ssannotation args... commit | commitdiff
2023-03-20 James ProcterJAL-4134 propagate column selection changes in tree... commit | commitdiff
2023-03-17 James ProcterJAL-4134 store/restore Newick tree for PAE annotation row commit | commitdiff
2023-02-27 James ProcterJAL-4134 display tree for columns - selecting an intern... commit | commitdiff
2023-02-22 Ben SoaresMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff
2023-02-16 James ProcterMerge branch 'features/r2_11_2_alphafold/JAL-629' into... commit | commitdiff
2023-02-13 James ProcterMerge branch 'develop' into feature/JAL-1713_overviewIn... commit | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... commit | commitdiff
2023-02-03 James ProcterMerge branch 'develop' into features/r2_11_2_alphafold... commit | commitdiff
2023-01-31 James ProcterJAL-1713 update from Jalview 2.11.3 develop commit | commitdiff
2022-11-09 Ben SoaresMerge branch 'improvement/JAL-3416_default_to_LIVE_DRAG... commit | commitdiff
2022-11-09 Ben SoaresJAL-3416 Remove all JFrame/JInternalFrame icons (set... commit | commitdiff
2022-11-04 Ben SoaresJAL-1998 JAL-3772 JAL-3416 Merge conflict resolution... commit | commitdiff
2022-11-03 Ben SoaresJAL-3416 File Chooser iconified, JvOptionPanes iconifie... commit | commitdiff
2022-11-03 Ben SoaresJAL-3416 Start to add JInternalFrame icons (to replace... commit | commitdiff
2022-10-24 Ben SoaresJAL-1988 JAL-3772 Non-blocking modal dialogs for unsave... commit | commitdiff
2022-09-26 Ben SoaresJAL-1988 JAL-3772 linked undostack to saved changes... commit | commitdiff
2022-09-16 Jim ProcterJAL-518 refactored groovy script into main codebase... commit | commitdiff
2022-09-16 Jim ProcterJAL-4062 copy highlighted region docs, new Alignment... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-03-04 Jim ProcterJAL-3746 JAL-3811 document SHOW_JWS2_SERVICES user... commit | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff
2022-02-07 Jim ProcterMerge branch 'feature/JAL-1713_overviewInProject' into... commit | commitdiff
2022-02-07 Jim ProcterJAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTit... bug/JAL-3785autoOverviewTitle commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2021-09-21 Jim ProcterMerge branch 'doc/JAL-3746_Release_2_11_2' into develop commit | commitdiff
2021-09-16 Ben SoaresJAL-3774 combined changes from bug/JAL-3774_splitFrameF... commit | commitdiff
2021-09-15 Jim ProcterJAL-3638 JAL-3680 fix docs for Alt + Arrow LRUD in... commit | commitdiff
2021-02-05 Jim ProcterJAL-3811 document SHOW_JWS2_SERVICES user preference... commit | commitdiff
2020-12-12 gmungocJAL-1713 JAL-3119 JAL-3785 refactored get/set Overview... commit | commitdiff
2020-12-11 gmungocJAL-3785 set full title on automatically opened Overvie... commit | commitdiff
2020-12-11 gmungocJAL-1713 fix typo; overview in project with open overvi... commit | commitdiff
2020-12-10 gmungocJAL-3784 null the right overview reference when it... commit | commitdiff
2020-12-10 gmungocJAL-3119 include view name (if any) in Overview title commit | commitdiff
2020-12-10 gmungocJAL-1713 refactorings to allow save/restore Overview... commit | commitdiff
2020-11-13 Ben SoaresJAL-3775 Eclipse re-formatting commit commit | commitdiff
2020-11-12 Ben SoaresJAL-3633 ensure check both or https:// for urls commit | commitdiff
2020-11-12 Ben SoaresJAL-3628 Error when saving alert box has been moved... commit | commitdiff
2020-11-12 Ben SoaresJAL-3676 Removed BACKUPFILESPRESETENTRY logging for... commit | commitdiff
2020-11-10 Ben SoaresJAL-3628 Fixed oddly worded and non-formatted error... commit | commitdiff
2020-11-10 Ben SoaresJAL-3628 Even more Cache.log.debug statements commit | commitdiff
2020-11-10 Ben SoaresJAL-3628 More Cache.log.debug statements commit | commitdiff
2020-09-23 Ben SoaresJAL-3633 ensure check both or https:// for urls commit | commitdiff
2020-09-21 Jim ProcterMerge branch 'merge_review/JAL-3490_2_11_2_develop... commit | commitdiff
2020-08-31 Jim ProcterJAL-3732 - sequences can be moved up/down in cursor... commit | commitdiff
2020-08-31 Jim ProcterJAL-3732 - sequences can be moved up/down in cursor... commit | commitdiff
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