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JAL-4369 invokeAndWait to avoid hang whilst calling getFiles if a Jmol redraw is...
[jalview.git]
/
src
/
jalview
/
2024-01-23
James Procter
JAL-4369 invokeAndWait to avoid hang whilst calling...
tree
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commitdiff
2024-01-23
James Procter
Merge branch 'features/JAL-4366_foldseek_3di_viewing...
tree
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commitdiff
2024-01-23
James Procter
JAL-4371 minimal test and move PDBEntryUtils to correct...
tree
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commitdiff
2024-01-18
James Procter
JAL-34 fix up comparison annotation so it gets shown...
tree
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commitdiff
2024-01-18
James Procter
JAL-34 mouse over ruler in one alignment highlights...
tree
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commitdiff
2024-01-17
James Procter
JAL-34 - quick hack to see how we can do alignment...
tree
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commitdiff
2024-01-16
James Procter
JAL-4366 JAL-728 show 3di-Mat based quality in the...
tree
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commitdiff
2024-01-16
James Procter
JAL-4366 JAL-728 simple hack to use 3di matrix when...
tree
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commitdiff
2024-01-15
James Procter
JAL-4366 JAL-4371 allow cruft after inferred pdb ids...
tree
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commitdiff
2024-01-14
James Procter
JAL-4366 JAL-4371 tighten up detection of chain code...
tree
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commitdiff
2024-01-14
James Procter
JAL-4366 revive broken alignDNAasDNA test
tree
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commitdiff
2024-01-14
James Procter
JAL-4366 JAL-4371 fix imports
tree
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commitdiff
2024-01-14
James Procter
JAL-4366 avoid corrupting map when no complete mapping...
tree
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commitdiff
2024-01-14
James Procter
JAL-4366 JAL-4371 refactor and fix up code inferring...
tree
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commitdiff
2024-01-12
James Procter
JAL-4366 provide options for updating (or not) the...
tree
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commitdiff
2024-01-12
James Procter
JAL-4366 fixed wrinkles in reconstructing peptide align...
tree
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commitdiff
2024-01-11
James Procter
JAL-4366 fix reconstruction of peptide alignment...
tree
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commitdiff
2024-01-11
James Procter
JAL-4366 use dataset sequences for building the mapping
tree
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commitdiff
2024-01-11
James Procter
JAL-4371 make the PDB fetcher use simple naming 1xyzA...
tree
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commitdiff
2024-01-11
James Procter
JAL-3466 higher ‘crummy alignment’ threshold when decid...
tree
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commitdiff
2024-01-11
James Procter
JAL-4366 remove some tortuous repetition in computeMapp...
tree
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commitdiff
2024-01-11
James Procter
JAL-4366 new mapping type for 3di/protein sequence...
tree
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commitdiff
2024-01-11
James Procter
JAL-4366 allow a 3di alignment to be loaded and shown...
tree
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commitdiff
2023-12-16
James Procter
JAL-4366 1:1 mapping requires exact sequence length...
tree
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commitdiff
2023-12-16
James Procter
JAL-789 pairwise alignment via calculations dialog...
tree
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commitdiff
2023-12-16
James Procter
JAL-4366 mat3di score model
tree
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commitdiff
2023-12-15
James Procter
JAL-4366 hacked in a 1:1 mapping
tree
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commitdiff
2023-12-15
James Procter
JAL-4366 compute coverage on each side of the pairwise...
tree
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commitdiff
2023-12-14
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-14
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-14
James Procter
Merge branch 'develop' into bug/JAL-2934proportionalScr...
bug/JAL-2934proportionalScrolling
tree
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commitdiff
2023-12-12
James Procter
JAL-4217 don’t try and export an image when Jmol is...
tree
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commitdiff
2023-12-12
Ben Soares
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-12
James Procter
Merge branch 'develop' into bug/JAL-4353_cannot_output_...
tree
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commitdiff
2023-12-12
James Procter
JAL-4217 close internal frame on the swing thread to...
tree
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commitdiff
2023-12-12
Ben Soares
JAL-4353 helper method and test for primary/secondary...
tree
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commitdiff
2023-12-12
James Procter
Merge branch 'bug/JAL-4353_cannot_output_multiple_diffe...
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 re-used random color code
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 Preserve the user given 'linkedId' with ArgVal...
tree
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commitdiff
2023-12-06
James Procter
Merge branch 'patch/JAL-840_clustalx_docs_fix' into...
tree
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commitdiff
2023-12-06
James Procter
Merge branch 'bug/JAL-2934proportionalScrolling' into...
tree
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commitdiff
2023-12-06
Ben Soares
JAL-4353 Add a 'random' colour to produce a random...
tree
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commitdiff
2023-12-05
Ben Soares
JAL-4353 Add secondary Types for Args, for STRUCTUREIMA...
tree
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commitdiff
2023-11-30
James Procter
JAL-4342 test and patch checking annotation csv export...
patch/JAL-4342_emptyannotationsexport
tree
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commitdiff
2023-11-30
James Procter
Patch fixes JAL-4165 - added to release notes JAL-4351
tree
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commitdiff
2023-11-30
Ben Soares
JAL-4344 careful application of -Djava.awt.headless...
tree
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commitdiff
2023-11-21
James Procter
JAL-4345 patch and release notes
patch/JAL-4345_pae_epas1_doubleclick
tree
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commitdiff
2023-11-20
James Procter
JAL-4343 patch for JAL-4347 uniprot non-pos feature...
tree
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commitdiff
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
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