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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git]
/
src
/
jalview
/ ext
2023-11-03
James Procter
JAL-4090 JAL-1551 spotlessApply
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commitdiff
2023-11-02
James Procter
Merge branch 'develop' into patch/JAL-3921_jmol_session...
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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
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commitdiff
2023-10-20
James Procter
JAL-4307 some models return null for hetatm list
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commitdiff
2023-10-19
James Procter
JAL-4307 View->Ligands submenu, implementation for...
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commitdiff
2023-10-13
James Procter
JAL-4295 concatenate all mouseover highlights into...
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commitdiff
2023-09-20
James Procter
JAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie...
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commitdiff
2023-09-20
James Procter
JAL-4265 back out redundant ‘saveState’ and ‘restoreSta...
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commitdiff
2023-09-20
Ben Soares
JAL-4265 Added saveState and restoreState to interface...
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commitdiff
2023-09-19
Ben Soares
JAL-4265 Change to use JmolCommands
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commitdiff
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
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commitdiff
2023-06-30
James Procter
JAL-4216 compute size of annotation using start/end...
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commitdiff
2023-06-29
James Procter
JAL-4216 compute size of annotation using start/end...
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commitdiff
2023-05-19
James Procter
Merge branch 'develop' into features/JAL-4134_use_annot...
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commitdiff
2023-05-01
James Procter
JAL-3858 report errors when trying to parse JSON to...
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commitdiff
2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
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commitdiff
2023-03-25
Ben Soares
JAL-629 improvements to argparser toString. Improvement...
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commitdiff
2023-03-17
Jim Procter
JAL-3921 allow Jmol saveState to be executed as evalScr...
patch/JAL-3921_jmol_session_save
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commitdiff
2023-03-02
Ben Soares
JAL-629 Removal of unnecessary methods. Set pLTTD tempf...
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commitdiff
2023-03-02
Ben Soares
JAL-629 Some refactoring to allow more flexible use...
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commitdiff
2023-02-22
Ben Soares
Merge branch 'develop' into features/r2_11_2_alphafold...
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commitdiff
2023-02-16
James Procter
Merge branch 'features/r2_11_2_alphafold/JAL-629' into...
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commitdiff
2023-02-03
James Procter
JAL-1551 remove temp file in src
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commitdiff
2023-01-24
James Procter
JAL-629 need to delay call to AlignFile.parse() if...
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commitdiff
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
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commitdiff
2022-10-28
Jim Procter
JAL-4086 commented out attempt to create measurement...
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commitdiff
2022-10-28
Jim Procter
JAL-2961 centerViewOn command for structure viewers...
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commitdiff
2022-10-27
Ben Soares
JAL-4083 don't need globalUseScriptWait after all,...
bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol
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commitdiff
2022-10-27
Ben Soares
JAL-4083 only set globalUseScriptWait if needed
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commitdiff
2022-10-27
Ben Soares
JAL-4083 Use jmolViewer.scriptWait instead of jmolViewe...
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
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commitdiff
2022-10-15
Jim Procter
JAL-3855 import pAE when StructureSelectionManager...
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
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commitdiff
2022-10-07
Jim Procter
Fix for JAL-4075 - don’t write a label in secondary...
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commitdiff
2022-10-06
Jim Procter
JAL-1551 formatting
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commitdiff
2022-10-06
Jim Procter
JAL-3895 alphafold colours via pluggable annotation...
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commitdiff
2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
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commitdiff
2022-06-07
Ben Soares
JAL-4020 class formatting
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commitdiff
2022-06-07
Ben Soares
JAL-4020 added the \Scripts\pymol.exe. to the pathList
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commitdiff
2022-06-06
Ben Soares
JAL-4020 Added the +2 arg for PyMOLWin.exe allowing...
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commitdiff
2022-06-06
Ben Soares
JAL-4020 class reformatting
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commitdiff
2022-06-06
Ben Soares
JAL-4020 Added path search for global installation...
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commitdiff
2022-06-06
Ben Soares
JAL-4020 Added search for PyMOLWinWithConsole.bat ...
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
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commitdiff
2022-03-08
Jim Procter
JAL-3108 updated Ensembl client and model species names
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commitdiff
2022-03-02
Jim Procter
JAL-3619 fix up error messages and try to bail quietly...
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commitdiff
2022-02-16
Jim Procter
JAL-3551 - wrap pair_fit with undo_disable and undo_enable
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commitdiff
2022-02-16
Jim Procter
JAL-3949 report Pymol XMLRPC port via log.info
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commitdiff
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
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commitdiff
2022-02-15
Jim Procter
JAL-1761 backbone type parameter for configuring which...
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commitdiff
2022-02-15
Jim Procter
JAL-1761 need to pass molecule type when generating...
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commitdiff
2022-02-14
Jim Procter
JAL-3551
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commitdiff
2022-02-11
Jim Procter
JAL-3949 - refactor logging from jalview.bin.Cache...
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commitdiff
2022-02-11
Ben Soares
JAL-3949 Complete new abstracted logging framework...
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commitdiff
2021-12-08
Jim Procter
JAL-3551 JAL-3931 view pymol commands/responses in...
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commitdiff
2021-10-18
Jim Procter
JAL-3905 Fix: wait for response when sending mouseovers...
bug/r2_11_2/JAL-3904_structureviewermenu
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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commitdiff
2021-09-20
Jim Procter
JAL-3829 make sure structure data type reflects actual...
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commitdiff
2021-09-15
Ben Soares
JAL-3818 formatting
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commitdiff
2021-09-15
gmungoc
JAL-3818 process Jmol callbacks in AWT thread
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commitdiff
2021-09-14
Jim Procter
JAL-3855 detect an alphafold model and import its tempe...
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commitdiff
2021-09-13
Ben Soares
Merge branch 'develop' into feature/JAL-2422ChimeraX
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commitdiff
2021-09-02
gmungoc
JAL-1842 adjust code to match changed semantics of...
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commitdiff
2021-09-02
gmungoc
JAL-1842 remove redundant call to FeatureRenderer.featu...
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commitdiff
2021-09-02
gmungoc
JAL-3509 better placement of call to notifyFeaturesChan...
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commitdiff
2021-09-02
gmungoc
JAL-3509 coerce RESNUM to hidden (really) after fetchin...
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commitdiff
2021-08-11
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into feature...
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commitdiff
2021-02-11
gmungoc
JAL-3818 process Jmol callbacks in AWT thread
bug/JAL-3818_jmolDeadlock
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commitdiff
2021-02-04
gmungoc
JAL-2422 a fix and a fudge for two failing ChimeraX...
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commitdiff
2020-09-10
gmungoc
JAL-3518 removed unneeded override in ChimeraCommands
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commitdiff
2020-09-10
gmungoc
JAL-2422 comments updated re ALTLOC handling
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commitdiff
2020-08-31
gmungoc
JAL-3018 Ensembl reviewed REST version updated to 13.0
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commitdiff
2020-08-31
gmungoc
JAL-1191 use Cache.log for logging
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commitdiff
2020-08-31
gmungoc
JAL-1191 reduce logging level for warnings
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commitdiff
2020-08-24
gmungoc
JAL-3018 updated reviewed REST version to 12.0
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commitdiff
2020-07-31
Ben Soares
Merge branch 'releases/Release_2_11_1_Branch' into...
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commitdiff
2020-06-29
gmungoc
JAL-3674 more finessed asynchronous structure commands
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commitdiff
2020-06-29
gmungoc
Merge branch 'develop' of https://source.jalview.org...
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commitdiff
2020-06-28
gmungoc
JAL-3551 PyMOL command constants tidied
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commitdiff
2020-06-28
gmungoc
JAL-3551 fit to window (zoom) command for PyMOL
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commitdiff
2020-06-26
Jim Procter
JAL-3518 fix highlighting in Jalview for selections...
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commitdiff
2020-06-26
Jim Procter
JAL-3672 more efficient when debug not enabled
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commitdiff
2020-06-25
gmungoc
JAL-2010 unused prototype method removed
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commitdiff
2020-06-25
gmungoc
JAL-3518 pull up [get|list]ResidueAttributes to Structu...
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commitdiff
2020-06-23
gmungoc
JAL-3518 separation of ChimeraXManager, pull up of...
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commitdiff
2020-06-23
gmungoc
JAL-3518 pull up closeViewer() and external viewer...
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commitdiff
2020-06-01
gmungoc
JAL-3518 more test coverage for structure commands
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commitdiff
2020-05-29
gmungoc
JAL-3551 null pointer defence while structure files...
feature/JAL-3551Pymol
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commitdiff
2020-05-28
gmungoc
JAL-3551 corrected Pymol open session command
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commitdiff
2020-05-28
gmungoc
JAL-2422 correct ChimeraX save/open session commands...
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commitdiff
2020-05-26
gmungoc
JAL-1761 pattern for structure viewer construction...
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commitdiff
2020-05-21
gmungoc
JAL-3551 copy Jalview features to Pymol 'p' (with pull...
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commitdiff
2020-05-20
gmungoc
JAL-3626 use Viewer.scriptWait() to send Jmol commands...
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commitdiff
2020-05-19
gmungoc
Merge branch 'develop' into feature/JAL-3551Pymol
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2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
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commitdiff
2020-05-15
gmungoc
JAL-3551 pull up Close Viewer dialog to base class
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commitdiff
2020-05-12
gmungoc
JAL-3518 tidy method, remove obsolete comment
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commitdiff
2020-05-12
gmungoc
JAL-3518 failsafe check for null Jmol filename while...
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