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