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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / structure / StructureSelectionManager.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... commit | commitdiff
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure... commit | commitdiff
2023-08-21 James ProcterJAL-4062 appendResult(seq,start,end) called by structur... commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-05-22 James ProcterJAL-629 javadoc on StructureSelectionManager.computeMapping commit | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... commit | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... commit | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... commit | commitdiff
2022-10-26 Jim ProcterJAL-4086 quick and dirty mouseovers on ruler highlighti... commit | commitdiff
2022-10-22 Jim ProcterJAL-2349 JAL-3855 highlight residues associated with... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... commit | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... commit | commitdiff
2021-12-13 Jim ProcterJAL-3929 preserve lowercase pdbid in group name for... commit | commitdiff
2021-12-08 Jim ProcterJAL-3929 don’t use the url encoded pdbId in feature... commit | commitdiff
2021-11-08 Jim ProcterJAL-3855 try harder to ignore DNA/RNA only structures... commit | commitdiff
2021-09-08 Jim ProcterJAL-3829 JAL-3868 TODO commit | commitdiff
2021-07-27 Jim ProcterJAL-3855 suppress NPE when trying to retrieve SIFTS... commit | commitdiff
2020-05-29 gmungocMerge branch 'feature/JAL-3551Pymol' into develop commit | commitdiff
2020-05-26 gmungocJAL-3624 log when SIFTS mapping fails commit | commitdiff
2020-05-26 gmungocJAL-1761 pattern for structure viewer construction... commit | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop commit | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge commit | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2019-05-01 gmungocJAL-3244 ignore file path separator when comparing... commit | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... commit | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... commit | commitdiff
2018-08-21 hansonrmc_view references were MCview commit | commitdiff
2018-05-07 Jim ProcterJAL-2321 use configured values for structure derived... commit | commitdiff
2018-05-07 Jim ProcterJAL-2321 add secondary structure & temp factor if not... commit | commitdiff
2018-04-13 gmungocMerge branch 'features/JAL-2944_openStructuresInSelecte... features/JAL-2944_openStructuresInSelectedView commit | commitdiff
2018-04-12 gmungocJAL-2223 don't add duplicate mappings to StructureSelec... commit | commitdiff
2018-04-12 gmungocJAL-2944 tidies for review comments commit | commitdiff
2018-04-11 Jim ProcterJAL-2946 catch unexpected SIFTS mapping exceptions... commit | commitdiff
2018-02-13 Jim ProcterJAL-2781 null local siftsClient variable if exception... commit | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor StructureSelectionManager.siftsClient... commit | commitdiff
2018-02-13 Jim ProcterJAL-2781 FIXME: value of sourceType parameter always... commit | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor possibly non-functional ‘extract... commit | commitdiff
2018-02-13 Jim ProcterJAL-2781 tidy up comments on getMapping/computeMapping commit | commitdiff
2018-02-11 Jim ProcterJAL-2781 use SIFTs mapping rather than maxChain AlignSe... commit | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest commit | commitdiff
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2392_deadlockonpdbdisplay' into... commit | commitdiff
2017-10-24 gmungocJAL-2495 highlight all mapped sequences from structure... commit | commitdiff
2017-10-10 Jim ProcterMerge branch 'codereviews/JAL-1990_IProgressIndicator_j... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-08-27 Jim ProcterJAL-2693 TODO comments commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu... commit | commitdiff
2017-05-09 tcofoegbuJAL-2465 fix to dynamically specify data source type... commit | commitdiff
2017-05-08 tcofoegbuMerge branch 'develop' of https://source.jalview.org... commit | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges commit | commitdiff
2017-05-01 tcofoegbuJAL-2465 bugfix and rerefactor renamed getPdbFile(... commit | commitdiff
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... commit | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff
2017-03-08 gmungocJAL-2430 colour columns hidden in alignment gray on... commit | commitdiff
2017-03-07 gmungocJAL-2295 status messages for Chimera attributes set... commit | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... commit | commitdiff
2016-12-08 gmungocMerge branch 'bug/JAL-2358phantomChimera' into spikes... commit | commitdiff
2016-12-08 gmungocJAL-2358 ensure mappings removed on close Chimera;... bug/JAL-2358phantomChimera commit | commitdiff
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera... commit | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge commit | commitdiff
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera... commit | commitdiff
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi... commit | commitdiff
2016-11-14 gmungocJAL-2296 new code and refactoring for 'copy Chimera... commit | commitdiff
2016-11-04 tcofoegbuJAL-2195 JAL-2262 house keeping commit | commitdiff
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch' commit | commitdiff
2016-10-17 tcofoegbuJAL-2262 JAL-2195 Improvement to set PDBId availability... commit | commitdiff
2016-10-10 tcofoegbuJAL-2262 JAL-2195 bug fix for mapping local structure... commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-09-16 gmungocJAL-2164 removed unused parameters from JmolParser... commit | commitdiff
2016-09-13 tcofoegbuRevert "JAL-2164 JAL-1919 disabled and removed PDB... commit | commitdiff
2016-09-13 tcofoegbuJAL-2164 JAL-1919 disabled and removed PDB file parser... commit | commitdiff
2016-09-07 Jim ProcterJAL-1803 transfer mapped chain’s PDBEntry to the *datas... commit | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 javadoc for sifts mapping method commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 prevent SIFTS mappings for sequences that... commit | commitdiff
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring commit | commitdiff
2016-07-11 gmungocfile format enum wip changes commit | commitdiff
2016-06-15 tcofoegbuJAL-2002 disabled 'Best Uniport Coverage' filter. JAL... commit | commitdiff
2016-06-10 tcofoegbuJAL-1479 updated SIFTS FTP download URL, added improvem... commit | commitdiff
2016-06-08 tcofoegbuJAL-1479 JAL- Fix to eradicate duplicate mapping output... commit | commitdiff
2016-03-30 tcofoegbuJAL-2038 bug fix for NPE while setting progress message... commit | commitdiff
2016-03-24 gmungocJAL-2032 structure follow mouseover in a copy of a... commit | commitdiff
2016-03-22 tcofoegbuJAL-1919 code improvement to make PDB sequence fetcher... commit | commitdiff
2016-03-21 tcofoegbudevelop merge commit | commitdiff
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API.... commit | commitdiff
2016-02-20 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff
2016-02-19 tcofoegbuJAL-2009 Codes to enable storing inserted residues... commit | commitdiff
2016-02-12 gmungocJAL-2010 simple prototype of 'Highlight Selection'... commit | commitdiff
2016-02-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff
2016-01-29 tcofoegbuJAL-1979 refactor out duplicated similar block of code... commit | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge commit | commitdiff
2016-01-26 tcofoegbuJAL-1999 JAL-1479 implemented configurable fail-safe... commit | commitdiff
2016-01-11 tcofoegbuJAL-1990 added a progress indicator for Structure Choos... commit | commitdiff
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list... commit | commitdiff
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