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Merge branch 'develop' into releases/Release_2_11_3_Branch
[jalview.git] / src / jalview /
2023-11-15 James ProcterMerge branch 'bug/JAL-4334_unknownstartenduniprotfeatur... tree | commitdiff
2023-11-15 James ProcterMerge branch 'patch/JAL-4222_100s_timeout_on_imagexport... tree | commitdiff
2023-11-15 James ProcterJAL-4273 actually pass startSeq etc on to rendering... tree | commitdiff
2023-11-15 James ProcterJAL-4222 bail if we wait too long for Jmol to save... patch/JAL-4222_100s_timeout_on_imagexport tree | commitdiff
2023-11-15 James ProcterJAL-4090 blocker patch JAL-3772 tidy up groovy console... tree | commitdiff
2023-11-15 James ProcterJAL-4090 JAL-4334 position status when start, end or... bug/JAL-4334_unknownstartenduniprotfeatures tree | commitdiff
2023-11-13 James ProcterJAL-4090 JAL-1551 source license tree | commitdiff
2023-11-13 James ProcterJAL-4236 don’t look for headers in JalviewJS tree | commitdiff
2023-11-13 James ProcterJAL-4336 set preferred dimensions for JTextBox workarou... tree | commitdiff
2023-11-13 James ProcterJAL-4090 fix JAL-4236 - just put the name of the class... tree | commitdiff
2023-11-13 James ProcterJAL-4331 construct and pass on overview title before... tree | commitdiff
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-11-02 James ProcterJAL-4169 fix up urls to faq and documentation tree | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3921_jmol_session... tree | commitdiff
2023-11-02 James ProcterJAL-4217 wrap progress bar creation in an invokeLater... tree | commitdiff
2023-11-02 James ProcterJAL-1551 formatting tree | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3088_finalbraceno... tree | commitdiff
2023-11-02 James ProcterJAL-4289 JAL-4253 lower end of group boundary vertical... tree | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4281_idwidthandannotHeight_in_p... tree | commitdiff
2023-11-01 James ProcterMerge branch 'feature/JAL-4315_fc_draganddrop' into... tree | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4317_enablefeaturewhenadjusting... tree | commitdiff
2023-11-01 James ProcterMerge branch 'develop' into patch/JAL-4281_idwidthandan... tree | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4260_fix_up_select_via_ruler_in... tree | commitdiff
2023-11-01 James ProcterJAL-4260 encapsulate logic for resolving nearest column... patch/JAL-4260_fix_up_select_via_ruler_in_wrapped tree | commitdiff
2023-11-01 James ProcterJAL-4260 reinstate annotation auto-id-width for wrapped... tree | commitdiff
2023-10-31 James ProcterJAL-4260 fix up click/drags on ruler area in wrapped... tree | commitdiff
2023-10-31 James ProcterJAL-4260 right align the annotation labels regardless... tree | commitdiff
2023-10-31 James ProcterJAL-244 noticed NPE exception was possible when visibil... tree | commitdiff
2023-10-31 James ProcterJAL-244 knock on - make sure alignPanel is laid out... tree | commitdiff
2023-10-30 James ProcterJAL-4317 enable display of feature when showing its... patch/JAL-4317_enablefeaturewhenadjustingstyle tree | commitdiff
2023-10-30 James ProcterHandle feature settings files loaded via drag and drop... feature/JAL-4315_fc_draganddrop tree | commitdiff
2023-10-30 James ProcterJAL-4315 allow feature settings to be loaded from a... tree | commitdiff
2023-10-30 James ProcterJAL-4315 identify feature settings file from its xml... tree | commitdiff
2023-10-26 James ProcterMerge branch 'bug/JAL-4313_cme_in_tests' into patch... tree | commitdiff
2023-10-25 Ben SoaresMerge branch 'develop' into bug/JAL-4289_group_boundary... bug/JAL-4289_group_boundary_not_drawn_properly_in_fastpaint_or_paint tree | commitdiff
2023-10-25 James ProcterJAL-4312 defend against ConcurrentModificationException bug/JAL-4313_cme_in_tests tree | commitdiff
2023-10-25 James ProcterJAL-4312 call AlignFrame.setAnnotationsVisibility on... tree | commitdiff
2023-10-23 James ProcterJAL-4311 fix ranking so models with like scores are... improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews tree | commitdiff
2023-10-23 James ProcterJAL-4311 failing test case for 3d-beacons epas1_human... tree | commitdiff
2023-10-23 James ProcterJAL-4310 let the user know when model pages are not... tree | commitdiff
2023-10-23 James ProcterMerge branch 'develop' into improvement/JAL-4124_dont_d... tree | commitdiff
2023-10-23 James ProcterMerge branch 'feature/JAL-4307_hetatm_showhide' into... tree | commitdiff
2023-10-23 James ProcterJAL-4090 defensive check for featureSettings redraws... improvement/JAL-4308_smalleridtooltip tree | commitdiff
2023-10-23 James ProcterJAL-4308 reduce number of refs to 5, always have canoni... tree | commitdiff
2023-10-22 James ProcterJAL-1551 errant tab and import tree | commitdiff
2023-10-22 James ProcterMerge branch 'patch/JAL-4298_synchronize_consoledoc... tree | commitdiff
2023-10-21 James ProcterJAL-1332 JAL-4298 JAL-3772 rejig the quit handler so... jims/bug/JAL-4298_java_console_causing_hang_at_startup tree | commitdiff
2023-10-20 James ProcterMerge branch 'improvement/JAL-3783_upgrade_to_groovy... tree | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... tree | commitdiff
2023-10-20 James ProcterJAL-4298 reuse existing log level preference method tree | commitdiff
2023-10-20 James ProcterJAL-4307 also report molecule name in tooltip for show... feature/JAL-4307_hetatm_showhide tree | commitdiff
2023-10-20 Ben SoaresJAL-4298 another implicated line bug/JAL-4298_java_console_causing_hang_at_startup tree | commitdiff
2023-10-20 James ProcterMerge branch 'feature/JAL-4307_hetatm_showhide' into... tree | commitdiff
2023-10-20 James ProcterJAL-4307 some models return null for hetatm list tree | commitdiff
2023-10-20 James ProcterJAL-4298 try much harder to avoid modifying console... patch/JAL-4298_synchronize_consoledoc tree | commitdiff
2023-10-19 Ben SoaresMerge branch 'patch/JAL-4298_synchronize_consoledoc... tree | commitdiff
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from prope... tree | commitdiff
2023-10-19 Ben SoaresJAL-4298 comment markers tree | commitdiff
2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy... tree | commitdiff
2023-10-19 James ProcterJAL-4298 avoid deadlock waiting to update doc when... tree | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... tree | commitdiff
2023-10-19 James ProcterJAL-4307 View->Ligands submenu, implementation for... tree | commitdiff
2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy... tree | commitdiff
2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ... tree | commitdiff
2023-10-18 Ben SoaresJAL-4262 Fix the nonblockingdialog so that Jalview... tree | commitdiff
2023-10-17 James ProcterJAL-4134 TODO printNode update for columnTrees tree | commitdiff
2023-10-17 James ProcterJAL-4134 JAL-4302 remove unnecessary casts tree | commitdiff
2023-10-17 James ProcterJAL-4089 selected columns are reported in absolute... tree | commitdiff
2023-10-13 Ben SoaresJAL-3783 Updated groovy jars. Requires javaparser... tree | commitdiff
2023-10-13 James ProcterJAL-4295 concatenate all mouseover highlights into... tree | commitdiff
2023-10-12 Ben SoaresJAL-3772 Fix the logic of prompt to save URL loaded... tree | commitdiff
2023-10-12 Ben SoaresJAL-629 null check and neatening code tree | commitdiff
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. tree | commitdiff
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... tree | commitdiff
2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfil... tree | commitdiff
2023-10-11 Ben SoaresJAL-3772 Preference to NOT prompt to save remotely... tree | commitdiff
2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes... tree | commitdiff
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... tree | commitdiff
2023-10-03 Ben SoaresJAL-4001 Only use acquireDialogQueue and releaseDialogQ... bug/JAL-4001_fix_About_Jalview_not_appearing tree | commitdiff
2023-10-03 Ben SoaresMerge branch 'develop' into bug/JAL-4289_group_boundary... tree | commitdiff
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... tree | commitdiff
2023-10-02 Ben SoaresJAL-4289 In fastPaint(), don't render one more than... tree | commitdiff
2023-10-01 James ProcterJAL-244 ensure background is completely filled with... tree | commitdiff
2023-10-01 James ProcterJAL-244 export image with full width IDs regardless... tree | commitdiff
2023-10-01 James ProcterJAL-244 JAL-4091 allow calculation of label id width... tree | commitdiff
2023-10-01 James ProcterJAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculate... tree | commitdiff
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... tree | commitdiff
2023-09-29 James ProcterJAL-244 JAL-4090 use current IdWidth when exporting... tree | commitdiff
2023-09-29 James ProcterJAL-3858 fix check annotation row and column positionin... tree | commitdiff
2023-09-28 James ProcterJAL-3858 don’t divide if we only had one value to count tree | commitdiff
2023-09-28 James ProcterJAL-3858 check annotation row and column positioning... tree | commitdiff
2023-09-28 James ProcterJAL-3858 improved contactInterval computation and added... tree | commitdiff
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound... tree | commitdiff
2023-09-25 James ProcterJAL-3858 minimum value for a range is used to shade... tree | commitdiff
2023-09-25 James ProcterJAL-3858 javadoc and slightly revised green linear... tree | commitdiff
2023-09-25 James ProcterJAL-3858 report PAE range with sensible precision tree | commitdiff
2023-09-21 James ProcterJAL-1551 javadoc for mapUtils tree | commitdiff
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence... tree | commitdiff
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 tree | commitdiff
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265... tree | commitdiff
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