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[jalview.git] / src / jalview / structure / StructureSelectionManager.java

2022-03-08	Jim Procter	JAL-3438 spotless for 2.11.2.0	blob \| commitdiff
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
2021-12-13	Jim Procter	JAL-3929 preserve lowercase pdbid in group name for...	blob \| commitdiff \| diff to current
2021-12-08	Jim Procter	JAL-3929 don’t use the url encoded pdbId in feature...	blob \| commitdiff \| diff to current
2021-11-08	Jim Procter	JAL-3855 try harder to ignore DNA/RNA only structures...	blob \| commitdiff \| diff to current
2021-09-08	Jim Procter	JAL-3829 JAL-3868 TODO	blob \| commitdiff \| diff to current
2021-07-27	Jim Procter	JAL-3855 suppress NPE when trying to retrieve SIFTS...	blob \| commitdiff \| diff to current
2020-05-29	gmungoc	Merge branch 'feature/JAL-3551Pymol' into develop	blob \| commitdiff \| diff to current
2020-05-26	gmungoc	JAL-3624 log when SIFTS mapping fails	blob \| commitdiff \| diff to current
2020-05-26	gmungoc	JAL-1761 pattern for structure viewer construction...	blob \| commitdiff \| diff to current
2019-10-08	gmungoc	Merge branch 'develop' into Jalview-JS/develop	blob \| commitdiff \| diff to current
2019-07-16	gmungoc	JAL-3210 Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-06-06	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-05-01	gmungoc	JAL-3244 ignore file path separator when comparing...	blob \| commitdiff \| diff to current
2019-03-21	Ben Soares	JAL-3130 Replaced deprecated Class.newInstance() with...	blob \| commitdiff \| diff to current
2019-02-19	gmungoc	JAL-3187 hacks to get peptide variant in to Jmol hover...	blob \| commitdiff \| diff to current
2018-08-21	hansonr	mc_view references were MCview	blob \| commitdiff \| diff to current
2018-05-07	Jim Procter	JAL-2321 use configured values for structure derived...	blob \| commitdiff \| diff to current
2018-05-07	Jim Procter	JAL-2321 add secondary structure & temp factor if not...	blob \| commitdiff \| diff to current
2018-04-13	gmungoc	Merge branch 'features/JAL-2944_openStructuresInSelecte... features/JAL-2944_openStructuresInSelectedView	blob \| commitdiff \| diff to current
2018-04-12	gmungoc	JAL-2223 don't add duplicate mappings to StructureSelec...	blob \| commitdiff \| diff to current
2018-04-12	gmungoc	JAL-2944 tidies for review comments	blob \| commitdiff \| diff to current
2018-04-11	Jim Procter	JAL-2946 catch unexpected SIFTS mapping exceptions...	blob \| commitdiff \| diff to current
2018-02-13	Jim Procter	JAL-2781 null local siftsClient variable if exception...	blob \| commitdiff \| diff to current
2018-02-13	Jim Procter	JAL-2781 refactor StructureSelectionManager.siftsClient...	blob \| commitdiff \| diff to current
2018-02-13	Jim Procter	JAL-2781 FIXME: value of sourceType parameter always...	blob \| commitdiff \| diff to current
2018-02-13	Jim Procter	JAL-2781 refactor possibly non-functional ‘extract...	blob \| commitdiff \| diff to current
2018-02-13	Jim Procter	JAL-2781 tidy up comments on getMapping/computeMapping	blob \| commitdiff \| diff to current
2018-02-11	Jim Procter	JAL-2781 use SIFTs mapping rather than maxChain AlignSe...	blob \| commitdiff \| diff to current
2017-10-27	gmungoc	JAL-1793 spike branch updated to latest	blob \| commitdiff \| diff to current
2017-10-25	Jim Procter	Merge branch 'bug/JAL-2392_deadlockonpdbdisplay' into...	blob \| commitdiff \| diff to current
2017-10-24	gmungoc	JAL-2495 highlight all mapped sequences from structure...	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
2017-08-27	Jim Procter	JAL-2693 TODO comments	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
2017-05-29	Jim Procter	Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...	blob \| commitdiff \| diff to current
2017-05-09	tcofoegbu	JAL-2465 fix to dynamically specify data source type...	blob \| commitdiff \| diff to current
2017-05-08	tcofoegbu	Merge branch 'develop' of https://source.jalview.org...	blob \| commitdiff \| diff to current
2017-05-05	kiramt	Merge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges	blob \| commitdiff \| diff to current
2017-05-01	tcofoegbu	JAL-2465 bugfix and rerefactor renamed getPdbFile(...	blob \| commitdiff \| diff to current
2017-04-24	kiramt	JAL-2388 Hidden cols separated from column selection...	blob \| commitdiff \| diff to current
2017-03-23	gmungoc	Merge branch 'develop' into features/JAL-2393customMatrices	blob \| commitdiff \| diff to current
2017-03-08	gmungoc	JAL-2430 colour columns hidden in alignment gray on...	blob \| commitdiff \| diff to current
2017-03-07	gmungoc	JAL-2295 status messages for Chimera attributes set...	blob \| commitdiff \| diff to current
2017-02-13	gmungoc	JAL-1632 JAL-2416 load score matrices from file, as...	blob \| commitdiff \| diff to current
2016-12-08	gmungoc	Merge branch 'bug/JAL-2358phantomChimera' into spikes...	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
2016-11-29	gmungoc	Merge branch 'develop' into features/JAL-2295setChimera...	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2016-11-23	gmungoc	Merge branch 'develop' into features/JAL-2295setChimera...	blob \| commitdiff \| diff to current
2016-11-22	Jim Procter	Merge branch 'features/JAL-1738_JAL-345_selectionfromhi...	blob \| commitdiff \| diff to current
2016-11-14	gmungoc	JAL-2296 new code and refactoring for 'copy Chimera...	blob \| commitdiff \| diff to current
2016-11-04	tcofoegbu	JAL-2195 JAL-2262 house keeping	blob \| commitdiff \| diff to current
2016-10-28	Jim Procter	JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...	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
2016-10-17	tcofoegbu	JAL-2262 JAL-2195 Improvement to set PDBId availability...	blob \| commitdiff \| diff to current
2016-10-10	tcofoegbu	JAL-2262 JAL-2195 bug fix for mapping local structure...	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
2016-09-16	gmungoc	JAL-2164 removed unused parameters from JmolParser...	blob \| commitdiff \| diff to current
2016-09-13	tcofoegbu	Revert "JAL-2164 JAL-1919 disabled and removed PDB...	blob \| commitdiff \| diff to current
2016-09-13	tcofoegbu	JAL-2164 JAL-1919 disabled and removed PDB file parser...	blob \| commitdiff \| diff to current
2016-09-07	Jim Procter	JAL-1803 transfer mapped chain’s PDBEntry to the *datas...	blob \| commitdiff \| diff to current
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 javadoc for sifts mapping method	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 prevent SIFTS mappings for sequences that...	blob \| commitdiff \| diff to current
2016-07-26	tcofoegbu	JAL-2157 bugfix for issues from enum refactoring	blob \| commitdiff \| diff to current
2016-07-11	gmungoc	file format enum wip changes	blob \| commitdiff \| diff to current
2016-06-15	tcofoegbu	JAL-2002 disabled 'Best Uniport Coverage' filter. JAL...	blob \| commitdiff \| diff to current
2016-06-10	tcofoegbu	JAL-1479 updated SIFTS FTP download URL, added improvem...	blob \| commitdiff \| diff to current
2016-06-08	tcofoegbu	JAL-1479 JAL- Fix to eradicate duplicate mapping output...	blob \| commitdiff \| diff to current
2016-03-30	tcofoegbu	JAL-2038 bug fix for NPE while setting progress message...	blob \| commitdiff \| diff to current
2016-03-24	gmungoc	JAL-2032 structure follow mouseover in a copy of a...	blob \| commitdiff \| diff to current
2016-03-22	tcofoegbu	JAL-1919 code improvement to make PDB sequence fetcher...	blob \| commitdiff \| diff to current
2016-03-21	tcofoegbu	develop merge	blob \| commitdiff \| diff to current
2016-02-25	tcofoegbu	JAL-1919 initial support for mmCIF using JMol API....	blob \| commitdiff \| diff to current
2016-02-20	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2016-02-19	tcofoegbu	JAL-2009 Codes to enable storing inserted residues...	blob \| commitdiff \| diff to current
2016-02-12	gmungoc	JAL-2010 simple prototype of 'Highlight Selection'...	blob \| commitdiff \| diff to current
2016-02-01	gmungoc	Merge branch 'develop' into features/JAL-653_JAL-1766_h...	blob \| commitdiff \| diff to current
2016-01-29	tcofoegbu	JAL-1979 refactor out duplicated similar block of code...	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-26	tcofoegbu	JAL-1999 JAL-1479 implemented configurable fail-safe...	blob \| commitdiff \| diff to current
2016-01-11	tcofoegbu	JAL-1990 added a progress indicator for Structure Choos...	blob \| commitdiff \| diff to current
2015-12-22	gmungoc	JAL-653 hold AlignedCodonFrame collections as list...	blob \| commitdiff \| diff to current
2015-11-17	tcofoegbu	JAL-1479 Refactored Sifts configuration preference...	blob \| commitdiff \| diff to current
2015-11-16	tcofoegbu	JAL-1967 JAL-1479 refactored sequence<->structure mappi...	blob \| commitdiff \| diff to current
2015-11-13	tcofoegbu	JAL-1479 added transfer of residue annotation for SIFTS...	blob \| commitdiff \| diff to current
2015-11-11	tcofoegbu	JAL-1957 JAL-1479 Further optimisation of SIFTs Client... features/JAL-1479_SIFTS-mapping	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1479 SiftClient house keeping	blob \| commitdiff \| diff to current
2015-10-28	tcofoegbu	JAL-1479 added support for SIFTs mapping output viewing...	blob \| commitdiff \| diff to current
2015-10-28	tcofoegbu	JAL-1887 JAL-1479 bugfix for incorrect start/end for...	blob \| commitdiff \| diff to current
2015-10-22	tcofoegbu	JAL-1479 added basic support for SIFTs mapping - 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
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-10-14	tcofoegbu	JAL-1926 added supporting model changes to enable savin...	blob \| commitdiff \| diff to current
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