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jalview.git
2023-10-19 Ben SoaresJAL-4298 comment markers commit | commitdiff | tree | snapshot
2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff | tree | snapshot
2023-10-19 Ben SoaresJAL-4305 Isolate and unify the Jalview object from... commit | commitdiff | tree | snapshot
2023-10-19 Ben SoaresMerge branch 'improvement/JAL-3783_upgrade_to_groovy... commit | commitdiff | tree | snapshot
2023-10-18 Ben SoaresJAL-629 Run non-alignframe linked groovy scripts. ... commit | commitdiff | tree | snapshot
2023-10-18 Ben SoaresJAL-4262 Fix the nonblockingdialog so that Jalview... commit | commitdiff | tree | snapshot
2023-10-13 Ben SoaresJAL-3783 Updated groovy jars. Requires javaparser... commit | commitdiff | tree | snapshot
2023-10-13 Ben SoaresJAL-3783 Updated build process to allow multiple groovy... commit | commitdiff | tree | snapshot
2023-10-12 Ben SoaresJAL-3772 Fix the logic of prompt to save URL loaded... commit | commitdiff | tree | snapshot
2023-10-12 Ben SoaresJAL-629 null check and neatening code commit | commitdiff | tree | snapshot
2023-10-11 Ben SoaresJAL-629 correct a timeout. Correct passing html flag. commit | commitdiff | tree | snapshot
2023-10-11 Ben SoaresJAL-629 Add a timeout to modal dialogs for command... commit | commitdiff | tree | snapshot
2023-10-11 Ben SoaresJAL-629 Change getdown not to add -open argument commit | commitdiff | tree | snapshot
2023-10-11 Ben SoaresJAL-629 Remove argfiles from the hashset of used argfil... commit | commitdiff | tree | snapshot
2023-10-11 Ben SoaresJAL-3772 Preference to NOT prompt to save remotely... commit | commitdiff | tree | snapshot
2023-10-11 Ben SoaresJAL-4298 Added diagnostics and minor dimension changes... commit | commitdiff | tree | snapshot
2023-10-05 Ben SoaresJAL-4298 Fixed initial log level to see .jalview_proper... commit | commitdiff | tree | snapshot
2023-10-05 James ProcterMerge branch 'doc/JAL-4090_Release_2_11_3_0' into develop commit | commitdiff | tree | snapshot
2023-10-05 James ProcterJAL-4090 JAL-3858 paedocs commit | commitdiff | tree | snapshot
2023-10-03 Ben SoaresJAL-4001 Only use acquireDialogQueue and releaseDialogQ... bug/JAL-4001_fix_About_Jalview_not_appearing commit | commitdiff | tree | snapshot
2023-10-03 James ProcterJAL-4217 move CommandsTest to testTask3 involving struc... commit | commitdiff | tree | snapshot
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... commit | commitdiff | tree | snapshot
2023-10-03 James ProcterJAL-4090 fix up release notes and what’s new (inc remov... commit | commitdiff | tree | snapshot
2023-10-03 James ProcterMerge branch 'develop' into doc/JAL-4090_Release_2_11_3_0 commit | commitdiff | tree | snapshot
2023-10-03 James ProcterJAL-4061 JAL-4062 update find box image and docs in... commit | commitdiff | tree | snapshot
2023-10-03 James ProcterMerge branch 'develop' into doc/JAL-4090_Release_2_11_3_0 commit | commitdiff | tree | snapshot
2023-10-03 James ProcterMerge branch 'bug/JAL-244_interactingpngexportnotwysiwi... commit | commitdiff | tree | snapshot
2023-10-03 James ProcterJAL-4090 tweak pae doc commit | commitdiff | tree | snapshot
2023-10-02 jprocterJAL-4090 more JAL-3858 docs commit | commitdiff | tree | snapshot
2023-10-02 jprocterMerge branch 'develop' into doc/JAL-4090_Release_2_11_3_0 commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-4090 JAL-3855 updated figure and doc.. a little bug/JAL-244_interactingpngexportnotwysiwig commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-244 ensure background is completely filled with... commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-4090 JAL-4291 disable failing test and note as... commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-244 attempt to fix broken test - still needs to... commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-244 export image with full width IDs regardless... commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-244 JAL-4091 allow calculation of label id width... commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-244 JAL-4091 FIXME for JAL-3362 patch testCalculate... commit | commitdiff | tree | snapshot
2023-10-01 James ProcterJAL-4160 update args used in test suite for new CLI... commit | commitdiff | tree | snapshot
2023-09-29 James ProcterMerge branch 'bug/JAL-244_interactingpngexportnotwysiwi... commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-629 JAL-4265 JAL-4286 report the filename for the... commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-4090 JAL-629 FER1+SPIOL -> FER1_SPIOL in command... commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-244 JAL-4090 use current IdWidth when exporting... commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-4090 figures in paematrix doc commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-4288 fix up gradle generated getdown launch jvl... commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-4090 fix url to new cli docs commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-4153 move JvCacheableInputBoxTest to testTask2 commit | commitdiff | tree | snapshot
2023-09-29 James ProcterJAL-3858 fix check annotation row and column positionin... commit | commitdiff | tree | snapshot
2023-09-28 James ProcterJAL-4090 JAL-3855 figure showing PAEs for epas1 homolog... commit | commitdiff | tree | snapshot
2023-09-28 James ProcterJAL-1556 JAL-4090 colour by annotation options on annot... commit | commitdiff | tree | snapshot
2023-09-28 James ProcterJAL-3858 don’t divide if we only had one value to count commit | commitdiff | tree | snapshot
2023-09-28 James ProcterJAL-3858 check annotation row and column positioning... commit | commitdiff | tree | snapshot
2023-09-28 James ProcterJAL-3858 improved contactInterval computation and added... commit | commitdiff | tree | snapshot
2023-09-26 James ProcterJAL-3858 JAL-4090 pae matrix docs. WIP commit | commitdiff | tree | snapshot
2023-09-26 James ProcterJAL-3858 JAL-4090 avoid NPE when given out of bound... commit | commitdiff | tree | snapshot
2023-09-25 James ProcterJAL-3858 JAL-4090 PAE documentation.. commit | commitdiff | tree | snapshot
2023-09-25 James ProcterJAL-3858 minimum value for a range is used to shade... commit | commitdiff | tree | snapshot
2023-09-25 James ProcterJAL-3858 javadoc and slightly revised green linear... commit | commitdiff | tree | snapshot
2023-09-25 James ProcterJAL-3858 report PAE range with sensible precision commit | commitdiff | tree | snapshot
2023-09-25 James ProcterJAL-4090 fix link... commit | commitdiff | tree | snapshot
2023-09-22 James ProcterJAL-4090 smaller associate PDB file panel image in... commit | commitdiff | tree | snapshot
2023-09-21 James ProcterJAL-4090 what’s new and additional help docs for JAL... commit | commitdiff | tree | snapshot
2023-09-21 James ProcterJAL-4090 JAL-4262 JAL-4265 release notes commit | commitdiff | tree | snapshot
2023-09-21 James ProcterJAL-1551 javadoc for mapUtils commit | commitdiff | tree | snapshot
2023-09-21 James ProcterJAL-3855 disable the AlphaFold DB entry in Sequence... commit | commitdiff | tree | snapshot
2023-09-21 James ProcterJAL-3858 JAL-3855 documentation for import and display... commit | commitdiff | tree | snapshot
2023-09-21 James ProcterMerge branch 'merge/JAL-4262+JAL-4265+JAL-4269+JAL... commit | commitdiff | tree | snapshot
2023-09-21 Ben SoaresJAL-4265 Use ColourUtils.parseColourString() for consis... merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 commit | commitdiff | tree | snapshot
2023-09-21 Ben SoaresMerge branch 'develop' into merge/JAL-4262+JAL-4265... commit | commitdiff | tree | snapshot
2023-09-20 Ben SoaresJAL-4265 Use ColorUtils.parseColourString() and adjust... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4285 don’t say you are reporting warnings/errors... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4265 JAL-4286 reinstated explicit restoreSession... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4195 JAL-1069 JAL-4160 errors in Cache should go... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterMerge branch 'reviews/merge/JAL-4262+JAL-4265+JAL-4269... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4217 - try to invokeAndWait on Desktop.closeAll... reviews/merge/JAL-4262+JAL-4265+JAL-4269+JAL-4274+JAL-4277+JAL-4285 commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4274 fix test failure message typo commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4265 bail early when attempting to export a view... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4265 JAL-4267 allow injection of custom commands... commit | commitdiff | tree | snapshot
2023-09-20 James ProcterJAL-4265 back out redundant ‘saveState’ and ‘restoreSta... commit | commitdiff | tree | snapshot
2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface... commit | commitdiff | tree | snapshot
2023-09-20 Ben SoaresJAL-629 Explanation of \{m\} in case anyone actually... commit | commitdiff | tree | snapshot
2023-09-20 Ben SoaresJAL-629 Add link and example for BioJS image output commit | commitdiff | tree | snapshot
2023-09-20 Ben SoaresJAL-629 Make arguments appear correctly using all non... commit | commitdiff | tree | snapshot
2023-09-20 Ben SoaresJAL-629 Added/corrected/tidied documentation commit | commitdiff | tree | snapshot
2023-09-19 Ben SoaresJAL-629 JAL-4265 JAL-4269 Updated help Documentation commit | commitdiff | tree | snapshot
2023-09-19 Ben SoaresJAL-629 JAL-4265 JAL-4269 Updated help Documentation commit | commitdiff | tree | snapshot
2023-09-19 Ben SoaresJAL-4265 Change to use JmolCommands commit | commitdiff | tree | snapshot
2023-09-19 Ben SoaresJAL-629 Allow multiple structure images for multiple... commit | commitdiff | tree | snapshot
2023-09-16 Ben SoaresJAL-4250 Fixed blue arrows in drawStemAnnot() commit | commitdiff | tree | snapshot
2023-09-16 Ben SoaresJAL-629 Fix a test and omit an incorrect error message... improvement/JAL-4269_reduce_variants_of_common_subvalue_parameters commit | commitdiff | tree | snapshot
2023-09-16 Ben SoaresJAL-4265 Added --bgcolour for --structureimage output... commit | commitdiff | tree | snapshot
2023-09-16 Ben SoaresJAL-4269 Now using --width, --height, --scale for both... commit | commitdiff | tree | snapshot
2023-09-14 Ben SoaresMerge branch 'develop' into feature/JAL-4274_configurab... commit | commitdiff | tree | snapshot
2023-09-13 Ben SoaresJAL-4274 comments to help follow the tests feature/JAL-4274_configurable_bitmap_export_preferences commit | commitdiff | tree | snapshot
2023-09-13 Ben SoaresJAL-4274 Tests for BIS defaults and overrides commit | commitdiff | tree | snapshot
2023-09-13 Ben SoaresJAL-4274 Use Cache BITMAP_* if no other image restricti... commit | commitdiff | tree | snapshot
2023-09-13 Ben SoaresJAL-4262 Made deprecation warning properly modal bug/JAL-4277_dirname_substitution_always_absolute commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4262 Allow HTML in the dialog box for link to CLI... commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4277 No longer using getCanonicalPath() for parent... commit | commitdiff | tree | snapshot
2023-09-12 Ben SoaresJAL-4285 Better checkFiles processing. Better dialog. commit | commitdiff | tree | snapshot
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