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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview
2023-12-04 MorellThomasNew independent jbgui Panel for PaSiMap. Revert the... commit | commitdiff
2023-12-04 MorellThomasNew GPCAPanel button : output pairwise alignments ... commit | commitdiff
2023-12-01 James ProcterMerge branch 'releases/Release_2_11_3_Branch' commit | commitdiff
2023-12-01 MorellThomasApplying adjustablenw_params.patch (JAL-4159) commit | commitdiff
2023-11-30 James ProcterJAL-4342 test and patch checking annotation csv export... patch/JAL-4342_emptyannotationsexport commit | commitdiff
2023-11-30 James ProcterPatch fixes JAL-4165 - added to release notes JAL-4351 commit | commitdiff
2023-11-30 Ben SoaresJAL-4344 careful application of -Djava.awt.headless... commit | commitdiff
2023-11-27 James ProcterMerge branch 'releases/Release_2_11_3_Branch' commit | commitdiff
2023-11-21 James ProcterJAL-4345 patch and release notes patch/JAL-4345_pae_epas1_doubleclick commit | commitdiff
2023-11-20 James ProcterJAL-4343 patch for JAL-4347 uniprot non-pos feature... commit | commitdiff
2023-11-16 James ProcterMerge branch 'releases/Release_2_11_3_Branch' commit | commitdiff
2023-11-15 James ProcterMerge branch 'bug/JAL-4334_unknownstartenduniprotfeatur... commit | commitdiff
2023-11-15 James ProcterMerge branch 'patch/JAL-4222_100s_timeout_on_imagexport... commit | commitdiff
2023-11-15 James ProcterJAL-4273 actually pass startSeq etc on to rendering... commit | commitdiff
2023-11-15 James ProcterJAL-4222 bail if we wait too long for Jmol to save... patch/JAL-4222_100s_timeout_on_imagexport commit | commitdiff
2023-11-15 James ProcterJAL-4090 blocker patch JAL-3772 tidy up groovy console... commit | commitdiff
2023-11-15 James ProcterJAL-4090 JAL-4334 position status when start, end or... bug/JAL-4334_unknownstartenduniprotfeatures commit | commitdiff
2023-11-13 James ProcterJAL-4090 JAL-1551 source license commit | commitdiff
2023-11-13 James ProcterJAL-4236 don’t look for headers in JalviewJS commit | commitdiff
2023-11-13 James ProcterJAL-4336 set preferred dimensions for JTextBox workarou... commit | commitdiff
2023-11-13 James ProcterJAL-4090 fix JAL-4236 - just put the name of the class... 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
2023-11-02 James ProcterJAL-4169 fix up urls to faq and documentation commit | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3921_jmol_session... commit | commitdiff
2023-11-02 James ProcterJAL-4217 wrap progress bar creation in an invokeLater... commit | commitdiff
2023-11-02 James ProcterJAL-1551 formatting commit | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3088_finalbraceno... commit | commitdiff
2023-11-02 James ProcterJAL-4289 JAL-4253 lower end of group boundary vertical... commit | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4281_idwidthandannotHeight_in_p... commit | commitdiff
2023-11-01 James ProcterMerge branch 'feature/JAL-4315_fc_draganddrop' into... commit | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4317_enablefeaturewhenadjusting... commit | commitdiff
2023-11-01 James ProcterMerge branch 'develop' into patch/JAL-4281_idwidthandan... commit | commitdiff
2023-11-01 James ProcterMerge branch 'patch/JAL-4260_fix_up_select_via_ruler_in... commit | commitdiff
2023-11-01 James ProcterJAL-4260 encapsulate logic for resolving nearest column... patch/JAL-4260_fix_up_select_via_ruler_in_wrapped commit | commitdiff
2023-11-01 James ProcterJAL-4260 reinstate annotation auto-id-width for wrapped... commit | commitdiff
2023-10-31 James ProcterJAL-4260 fix up click/drags on ruler area in wrapped... commit | commitdiff
2023-10-31 James ProcterJAL-4260 right align the annotation labels regardless... commit | commitdiff
2023-10-31 James ProcterJAL-244 noticed NPE exception was possible when visibil... commit | commitdiff
2023-10-31 James ProcterJAL-244 knock on - make sure alignPanel is laid out... commit | commitdiff
2023-10-30 James ProcterJAL-4317 enable display of feature when showing its... patch/JAL-4317_enablefeaturewhenadjustingstyle commit | commitdiff
2023-10-30 James ProcterHandle feature settings files loaded via drag and drop... feature/JAL-4315_fc_draganddrop commit | commitdiff
2023-10-30 James ProcterJAL-4315 allow feature settings to be loaded from a... commit | commitdiff
2023-10-30 James ProcterJAL-4315 identify feature settings file from its xml... commit | commitdiff
2023-10-26 James ProcterMerge branch 'bug/JAL-4313_cme_in_tests' into patch... commit | 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 commit | commitdiff
2023-10-25 James ProcterJAL-4312 defend against ConcurrentModificationException bug/JAL-4313_cme_in_tests commit | commitdiff
2023-10-25 James ProcterJAL-4312 call AlignFrame.setAnnotationsVisibility on... commit | commitdiff
2023-10-23 James ProcterJAL-4311 fix ranking so models with like scores are... improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews commit | commitdiff
2023-10-23 James ProcterJAL-4311 failing test case for 3d-beacons epas1_human... commit | commitdiff
2023-10-23 James ProcterJAL-4310 let the user know when model pages are not... commit | commitdiff
2023-10-23 James ProcterMerge branch 'develop' into improvement/JAL-4124_dont_d... commit | commitdiff
2023-10-23 James ProcterMerge branch 'feature/JAL-4307_hetatm_showhide' into... commit | commitdiff
2023-10-23 James ProcterJAL-4090 defensive check for featureSettings redraws... improvement/JAL-4308_smalleridtooltip commit | commitdiff
2023-10-23 James ProcterJAL-4308 reduce number of refs to 5, always have canoni... commit | commitdiff
2023-10-22 James ProcterJAL-1551 errant tab and import commit | commitdiff
2023-10-22 James ProcterMerge branch 'patch/JAL-4298_synchronize_consoledoc... commit | 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 commit | commitdiff
2023-10-20 James ProcterMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff
2023-10-20 Ben SoaresJAL-4298 Remove a stray return in the processGroovyScri... commit | commitdiff
2023-10-20 James ProcterJAL-4298 reuse existing log level preference method commit | commitdiff
2023-10-20 James ProcterJAL-4307 also report molecule name in tooltip for show... feature/JAL-4307_hetatm_showhide commit | commitdiff
2023-10-20 Ben SoaresJAL-4298 another implicated line bug/JAL-4298_java_console_causing_hang_at_startup commit | commitdiff
2023-10-20 James ProcterMerge branch 'feature/JAL-4307_hetatm_showhide' into... commit | commitdiff
2023-10-20 James ProcterJAL-4307 some models return null for hetatm list commit | commitdiff
2023-10-20 James ProcterJAL-4298 try much harder to avoid modifying console... patch/JAL-4298_synchronize_consoledoc commit | commitdiff
2023-10-19 Ben SoaresMerge branch 'patch/JAL-4298_synchronize_consoledoc... commit | commitdiff
2023-10-19 Ben SoaresJAL-629 Fix --nodebug turning off debug mode from prope... commit | commitdiff
2023-10-19 Ben SoaresJAL-4298 comment markers commit | commitdiff
2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff
2023-10-19 James ProcterJAL-4298 avoid deadlock waiting to update doc when... commit | commitdiff
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... commit | commitdiff
2023-10-19 James ProcterJAL-4307 View->Ligands submenu, implementation for... commit | commitdiff
2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff
2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ... commit | commitdiff
2023-10-18 Ben SoaresJAL-4262 Fix the nonblockingdialog so that Jalview... commit | commitdiff
2023-10-17 James ProcterJAL-4134 TODO printNode update for columnTrees commit | commitdiff
2023-10-17 James ProcterJAL-4134 JAL-4302 remove unnecessary casts commit | commitdiff
2023-10-17 James ProcterJAL-4089 selected columns are reported in absolute... commit | commitdiff
2023-10-13 Ben SoaresJAL-3783 Updated groovy jars. Requires javaparser... commit | commitdiff
2023-10-13 James ProcterJAL-4295 concatenate all mouseover highlights into... commit | commitdiff
2023-10-12 Ben SoaresJAL-3772 Fix the logic of prompt to save URL loaded... commit | commitdiff
2023-10-12 Ben SoaresJAL-629 null check and neatening code commit | commitdiff
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. commit | commitdiff
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... commit | commitdiff
2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfil... commit | commitdiff
2023-10-11 Ben SoaresJAL-3772 Preference to NOT prompt to save remotely... commit | commitdiff
2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes... commit | commitdiff
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... commit | commitdiff
2023-10-03 Ben SoaresJAL-4001 Only use acquireDialogQueue and releaseDialogQ... bug/JAL-4001_fix_About_Jalview_not_appearing commit | commitdiff
2023-10-03 Ben SoaresMerge branch 'develop' into bug/JAL-4289_group_boundary... commit | commitdiff
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... commit | commitdiff
2023-10-02 Ben SoaresJAL-4289 In fastPaint(), don't render one more than... commit | commitdiff
2023-10-01 James ProcterJAL-244 ensure background is completely filled with... commit | commitdiff
2023-10-01 James ProcterJAL-244 export image with full width IDs regardless... commit | commitdiff
2023-10-01 MorellThomasFix Reset Button for PaSiMap and issue with indelfreeAs... commit | commitdiff
2023-10-01 James ProcterJAL-244 JAL-4091 allow calculation of label id width... commit | commitdiff
2023-10-01 James ProcterJAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculate... commit | commitdiff
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... commit | commitdiff
2023-09-29 James ProcterJAL-244 JAL-4090 use current IdWidth when exporting... commit | commitdiff
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