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[jalview.git] / src / jalview / gui / AppJmol.java

2023-11-15	James Procter	JAL-4222 bail if we wait too long for Jmol to save... patch/JAL-4222_100s_timeout_on_imagexport	blob \| commitdiff
2023-09-19	Ben Soares	JAL-4265 Change to use JmolCommands	blob \| commitdiff \| diff to current
2023-09-16	Ben Soares	JAL-4265 Added --bgcolour for --structureimage output...	blob \| commitdiff \| diff to current
2023-09-13	Ben Soares	JAL-4274 Use Cache BITMAP_* if no other image restricti...	blob \| commitdiff \| diff to current
2023-08-10	Ben Soares	JAL-629 Change all stdout and stderr output to use...	blob \| commitdiff \| diff to current
2023-07-06	James Procter	JAL-629 make —structure image work again after threadin...	blob \| commitdiff \| diff to current
2023-07-06	James Procter	JAL-4217 wrap imageExport CLI method's call to imageExp...	blob \| commitdiff \| diff to current
2023-07-06	James Procter	JAL-4217 wrap imageExport CLI method's call to imageExp...	blob \| commitdiff \| diff to current
2023-06-07	James Procter	JAL-4195 add exception handling for all image output...	blob \| commitdiff \| diff to current
2023-05-23	Ben Soares	JAL-629 Added --structureimage code and formatting...	blob \| commitdiff \| diff to current
2023-05-22	Ben Soares	JAL-629 --structureimage with formatting args.	blob \| commitdiff \| diff to current
2022-03-08	Jim Procter	JAL-3438 spotless for 2.11.2.0	blob \| commitdiff \| diff to current
2022-02-11	Jim Procter	JAL-3949 - refactor logging from jalview.bin.Cache...	blob \| commitdiff \| diff to current
2022-02-11	Ben Soares	JAL-3949 Complete new abstracted logging framework...	blob \| commitdiff \| diff to current
2021-09-21	Ben Soares	JAL-3691 automatic insertion of Locale.ROOT to toUpperC...	blob \| commitdiff \| diff to current
2021-09-14	Jim Procter	JAL-3829 JAL-3855 moved routing for retrieving structur...	blob \| commitdiff \| diff to current
2021-08-30	Jim Procter	JAL-3829 generalised Alphafold retrieval mechanism...	blob \| commitdiff \| diff to current
2021-07-27	Jim Procter	JAL-3855 check if an alpha fold ID and retrieve using...	blob \| commitdiff \| diff to current
2020-05-26	gmungoc	JAL-1761 pattern for structure viewer construction...	blob \| commitdiff \| diff to current
2020-05-21	gmungoc	JAL-3551 copy Jalview features to Pymol 'p' (with pull...	blob \| commitdiff \| diff to current
2020-05-20	gmungoc	JAL-3626 use Viewer.scriptWait() to send Jmol commands...	blob \| commitdiff \| diff to current
2020-05-19	gmungoc	Merge branch 'develop' into feature/JAL-3551Pymol	blob \| commitdiff \| diff to current
2020-05-15	gmungoc	JAL-3551 pull up Close Viewer dialog to base class	blob \| commitdiff \| diff to current
2020-05-11	gmungoc	JAL-2422 JAL-3551 viewer text/variables generalised...	blob \| commitdiff \| diff to current
2020-04-30	gmungoc	JAL-3551 save structure viewer session refactorings...	blob \| commitdiff \| diff to current
2020-03-13	gmungoc	JAL-3551 working proof of concept of Jalview driving...	blob \| commitdiff \| diff to current
2020-02-21	gmungoc	JAL-2422 tidy of methods and parameters	blob \| commitdiff \| diff to current
2020-02-20	gmungoc	JAL-2422 pull-up refactoring of structure commands...	blob \| commitdiff \| diff to current
2020-02-04	gmungoc	JAL-2422 pull up refactoring in preparation for Chimera...	blob \| commitdiff \| diff to current
2020-01-31	gmungoc	JAL-2422 temporary hacks removed; use hex colours for...	blob \| commitdiff \| diff to current
2019-07-16	gmungoc	JAL-3210 Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-05-02	gmungoc	JAL-3244 renamed Platform method for clarity bug/JAL-3244jmolWindows	blob \| commitdiff \| diff to current
2019-05-01	gmungoc	JAL-3244 ignore file path separator when comparing...	blob \| commitdiff \| diff to current
2018-12-25	hansonr	better Jmol help link	blob \| commitdiff \| diff to current
2018-08-27	hansonr	JAL-3026 Jmol functioning; some issues	blob \| commitdiff \| diff to current
2018-07-23	gmungoc	JAL-3048 all image export (alignment, tree, PCA, Jmol...	blob \| commitdiff \| diff to current
2018-04-12	gmungoc	JAL-1847 minor post-review updates	blob \| commitdiff \| diff to current
2018-04-12	gmungoc	JAL-2944 tidies for review comments	blob \| commitdiff \| diff to current
2018-04-09	Jim Procter	JAL-1847 JAL-2944 make superposition step a configurabl...	blob \| commitdiff \| diff to current
2018-04-05	Jim Procter	JAL-2944 remove modal prompt logic and expose methods...	blob \| commitdiff \| diff to current
2018-04-05	Jim Procter	JAL-2944 pull up structure viewer discovery routine...	blob \| commitdiff \| diff to current
2017-10-27	gmungoc	JAL-1793 spike branch updated to latest	blob \| commitdiff \| diff to current
2017-10-10	Jim Procter	JAL-2392 formatting	blob \| commitdiff \| diff to current
2017-10-10	Jim Procter	Merge branch 'codereviews/JAL-1990_IProgressIndicator_j...	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-05-01	tcofoegbu	JAL-2465 bugfix and rerefactor renamed getPdbFile(...	blob \| commitdiff \| diff to current
2017-03-02	gmungoc	JAL-2295 make 'Jmol' menu appear; enable/disable Superp...	blob \| commitdiff \| diff to current
2016-12-22	gmungoc	JAL-2360 structure viewers now using ColourMenuHelper...	blob \| commitdiff \| diff to current
2016-12-12	gmungoc	JAL-2361 extract methods to (re-)build colour menu	blob \| commitdiff \| diff to current
2016-12-08	gmungoc	JAL-2358 ensure mappings removed on close Chimera;... bug/JAL-2358phantomChimera	blob \| commitdiff \| diff to current
2016-11-24	tcofoegbu	JAL-2326 updated references of JOptionPane to JvOptionPane	blob \| commitdiff \| diff to current
2016-11-10	tcofoegbu	Bugfix to enable accurate chain extraction/association...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-24	Jim Procter	Merge branch 'releases/Release_2_10_0_Branch'	blob \| commitdiff \| diff to current
2016-10-13	gmungoc	JAL-2044 increase Jmol file load timeout from 5 to...	blob \| commitdiff \| diff to current
2016-10-11	gmungoc	JAL-2233 reverted changes to Jmol logging levels	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-09-29	gmungoc	JAL-2213 corrected wait for files to load in Jmol;...	blob \| commitdiff \| diff to current
2016-09-27	gmungoc	JAL-2233 less verbose logging for Jmol	blob \| commitdiff \| diff to current
2016-02-09	tcofoegbu	JAL-1975 updated image export pipeline to produce more...	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-10-05	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-09-25	gmungoc	JAL-1859 try hoverDelay of 0.1s in Jmol for more respon...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-09-04	Jim Procter	JAL-1847 added AUTOSUPERIMPOSE property which can be...	blob \| commitdiff \| diff to current
2015-08-19	gmungoc	JAL-1742 suppress 'add chain' option for Jmol, pull...	blob \| commitdiff \| diff to current
2015-08-07	tcofoegbu	JAL-1824 updated caching procedure for pdb entries...	blob \| commitdiff \| diff to current
2015-08-05	Jim Procter	JAL-1821 JAL-1759 make sure we wait around until the...	blob \| commitdiff \| diff to current
2015-06-30	gmungoc	JAL-1759 unused JmolPopup removed, code tidy for generics	blob \| commitdiff \| diff to current
2015-06-30	gmungoc	JAL-1759 unused field / methods removed	blob \| commitdiff \| diff to current
2015-06-26	gmungoc	JAL-1759 changed to non-deprecated Viewer.renderScreenI...	blob \| commitdiff \| diff to current
2015-06-26	gmungoc	Merge branch 'develop' into features/JAL-1759jmolUpdate	blob \| commitdiff \| diff to current
2015-06-26	gmungoc	JAL-1759 updates for Jmol 14.2.14_25.06.11	blob \| commitdiff \| diff to current
2015-06-19	tcofoegbu	JAL-1270 JUnit to TestNG refactoring	blob \| commitdiff \| diff to current
2015-06-10	gmungoc	JAL-1764 save Chimera/Jmol state as separate entries...	blob \| commitdiff \| diff to current
2015-06-05	gmungoc	JAL-1622 duplicate assignment removed (no functional...	blob \| commitdiff \| diff to current
2015-06-04	gmungoc	JAL-1750 View Mapping scoped to that viewer's mappings...	blob \| commitdiff \| diff to current
2015-04-30	tcofoegbu	JAL-1717 updated the PDBEntry model and updated the...	blob \| commitdiff \| diff to current
2015-03-30	gmungoc	JAL-1596 refactoring to allow unit tests to start and...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-01-26	gmungoc	Merge branch 'features/JAL-1588saveChimeraSession'...	blob \| commitdiff \| diff to current
2015-01-26	gmungoc	JAL-1588 restoring saved Chimera session(s)	blob \| commitdiff \| diff to current
2015-01-08	gmungoc	JAL-1588 part work save/restore of Chimera session	blob \| commitdiff \| diff to current
2015-01-07	gmungoc	JAL-1588 refactoring to StructureViewerBase and related	blob \| commitdiff \| diff to current
2015-01-06	gmungoc	JAL-1588 refactoring prior to 'save Chimera project'	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-12-05	Charles Ofoegbu	Change the Html export to utilize svg	blob \| commitdiff \| diff to current
2014-11-17	gmungoc	JAL-1528 bug fixes and adjustments to Chimera interface	blob \| commitdiff \| diff to current
2014-11-14	Jim Procter	Merge branch 'develop' into JAL-1483_featureBasedTreeCalc	blob \| commitdiff \| diff to current
2014-11-13	Jim Procter	Merge branch 'features/JAL-1469_svg-output-for-figure...	blob \| commitdiff \| diff to current
2014-11-12	Charles Ofoegbu	Added support for SVG Export	blob \| commitdiff \| diff to current
2014-11-12	gmungoc	JAL-1528 bug fixes and adjustments to Chimera interface	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	blob \| commitdiff \| diff to current
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