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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / structure /
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply tree | commitdiff
2023-11-02 James ProcterMerge branch 'develop' into patch/JAL-3921_jmol_session... tree | commitdiff
2023-10-19 James ProcterJAL-4307 View->Ligands submenu, implementation for... tree | commitdiff
2023-10-03 James ProcterMerge branch 'patch/JAL-4062_sort_and_merge_contiguousr... tree | commitdiff
2023-09-20 James ProcterJAL-4265 JAL-4267 added a ‘restoreSession’ StructureVie... tree | commitdiff
2023-09-20 James ProcterJAL-4265 back out redundant ‘saveState’ and ‘restoreSta... tree | commitdiff
2023-09-20 Ben SoaresJAL-4265 Added saveState and restoreState to interface... tree | commitdiff
2023-09-06 James ProcterJAL-629 javadoc on new setMapping variant for structure... tree | commitdiff
2023-08-21 James ProcterJAL-4062 appendResult(seq,start,end) called by structur... tree | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... tree | commitdiff
2023-05-22 James ProcterJAL-629 javadoc on StructureSelectionManager.computeMapping tree | commitdiff
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... tree | commitdiff
2023-03-17 Jim ProcterJAL-3921 allow Jmol saveState to be executed as evalScr... patch/JAL-3921_jmol_session_save tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Removal of unnecessary methods. Set pLTTD tempf... tree | commitdiff
2023-03-02 Ben SoaresJAL-629 Some refactoring to allow more flexible use... tree | commitdiff
2023-02-24 Ben SoaresJAL-629 add widgets to StructureChooser for tempfac... tree | commitdiff
2023-02-03 James ProcterJAL-1551 remove temp file in src tree | commitdiff
2023-01-23 Ben SoaresJAL-629 Attempts to add PAE to structure. --headless... tree | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... tree | commitdiff
2022-10-28 Jim ProcterJAL-2961 centerViewOn command for structure viewers... tree | commitdiff
2022-10-26 Jim ProcterJAL-4086 quick and dirty mouseovers on ruler highlighti... tree | commitdiff
2022-10-22 Jim ProcterJAL-2349 JAL-3855 highlight residues associated with... tree | commitdiff
2022-06-10 Jim ProcterMerge branch 'features/r2_11_2_alphafold/JAL-2349_JAL... tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-02-16 Jim ProcterMerge branch 'develop' into features/r2_11_2_alphafold... tree | commitdiff
2022-02-15 Jim ProcterJAL-1761 backbone type parameter for configuring which... tree | commitdiff
2022-02-15 Jim ProcterJAL-1761 need to pass molecule type when generating... tree | commitdiff
2022-02-11 Jim ProcterJAL-3949 - refactor logging from jalview.bin.Cache... tree | commitdiff
2022-02-11 Ben SoaresJAL-3949 Complete new abstracted logging framework... tree | commitdiff
2021-12-13 Jim ProcterJAL-3929 preserve lowercase pdbid in group name for... tree | commitdiff
2021-12-08 Jim ProcterJAL-3929 don’t use the url encoded pdbId in feature... tree | commitdiff
2021-11-08 Jim ProcterJAL-3855 try harder to ignore DNA/RNA only structures... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-08 Jim ProcterJAL-3829 JAL-3868 TODO tree | commitdiff
2021-08-13 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import... tree | commitdiff
2021-08-11 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into feature... tree | commitdiff
2021-07-27 Jim ProcterJAL-3855 suppress NPE when trying to retrieve SIFTS... tree | commitdiff
2020-09-10 gmungocJAL-3518 removed unneeded override in ChimeraCommands tree | commitdiff
2020-06-25 gmungocJAL-3518 pull up [get|list]ResidueAttributes to Structu... tree | commitdiff
2020-06-23 gmungocJAL-3518 separation of ChimeraXManager, pull up of... tree | commitdiff
2020-06-23 gmungocJAL-3518 pull up closeViewer() and external viewer... tree | commitdiff
2020-06-01 gmungocJAL-3518 more test coverage for structure commands tree | commitdiff
2020-05-29 gmungocMerge branch 'feature/JAL-3551Pymol' into develop tree | commitdiff
2020-05-26 gmungocJAL-3624 log when SIFTS mapping fails tree | commitdiff
2020-05-26 gmungocJAL-1761 pattern for structure viewer construction... tree | commitdiff
2020-05-21 gmungocJAL-3551 copy Jalview features to Pymol 'p' (with pull... tree | commitdiff
2020-05-19 gmungocMerge branch 'develop' into feature/JAL-3551Pymol tree | commitdiff
2020-05-11 gmungocJAL-3551 concatenate colour by sequence commands for... tree | commitdiff
2020-03-16 gmungocJAL-3551 tidying, improved commands, fix Jmol model... tree | commitdiff
2020-03-13 gmungocJAL-3551 working proof of concept of Jalview driving... tree | commitdiff
2020-03-03 gmungocJAL-3518 more pull up / test coverage of structure... tree | commitdiff
2020-02-28 gmungocJAL-3518 basic refactoring / pull up of superposeStruct... tree | commitdiff
2020-02-21 gmungocJAL-3518 more extraction of ChimeraX commands as overrides tree | commitdiff
2020-02-20 gmungocJAL-2422 pull-up refactoring of structure commands... tree | commitdiff
2020-01-14 gmungocJAL-2422 proof of concept adaptations for ChimeraX... tree | commitdiff
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop tree | commitdiff
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge tree | commitdiff
2019-06-18 Jim ProcterMerge branch 'features/JAL-2349_matrixvis' into merge... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-05-01 gmungocJAL-3244 ignore file path separator when comparing... tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... tree | commitdiff
2018-08-21 hansonrmc_view references were MCview tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 use configured values for structure derived... tree | commitdiff
2018-05-07 Jim ProcterJAL-2321 add secondary structure & temp factor if not... tree | commitdiff
2018-04-13 gmungocMerge branch 'features/JAL-2944_openStructuresInSelecte... features/JAL-2944_openStructuresInSelectedView tree | commitdiff
2018-04-12 gmungocJAL-2223 don't add duplicate mappings to StructureSelec... tree | commitdiff
2018-04-12 gmungocJAL-2944 tidies for review comments tree | commitdiff
2018-04-11 Jim ProcterJAL-2946 catch unexpected SIFTS mapping exceptions... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 null local siftsClient variable if exception... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor StructureSelectionManager.siftsClient... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 FIXME: value of sourceType parameter always... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 refactor possibly non-functional ‘extract... tree | commitdiff
2018-02-13 Jim ProcterJAL-2781 tidy up comments on getMapping/computeMapping tree | commitdiff
2018-02-11 Jim ProcterJAL-2781 use SIFTs mapping rather than maxChain AlignSe... tree | commitdiff
2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping... tree | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Intege... tree | commitdiff
2018-02-07 Jim ProcterJAL-2780 JAL-2781 fix javadoc in line with behaviour... tree | commitdiff
2017-10-27 gmungocJAL-1793 spike branch updated to latest tree | commitdiff
2017-10-25 Jim ProcterMerge branch 'bug/JAL-2392_deadlockonpdbdisplay' into... tree | commitdiff
2017-10-24 gmungocJAL-2495 highlight all mapped sequences from structure... tree | commitdiff
2017-10-10 Jim ProcterMerge branch 'codereviews/JAL-1990_IProgressIndicator_j... tree | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo tree | commitdiff
2017-08-27 Jim ProcterJAL-2693 TODO comments tree | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting tree | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch tree | commitdiff
2017-06-09 Jim ProcterMerge branch 'develop' into features/JAL-2349_matrixvis tree | commitdiff
2017-05-29 Jim ProcterMerge branch 'features/JAL-2465_No-mapping_Jmol-structu... tree | commitdiff
2017-05-09 tcofoegbuJAL-2465 fix to dynamically specify data source type... tree | commitdiff
2017-05-08 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2017-05-05 kiramtMerge remote-tracking branch 'origin/develop' into features/JAL-2388hiddencolumnschanges tree | commitdiff
2017-05-01 tcofoegbuJAL-2465 bugfix and rerefactor renamed getPdbFile(... tree | commitdiff
2017-04-24 kiramtJAL-2388 Hidden cols separated from column selection... tree | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices tree | commitdiff
2017-03-08 gmungocJAL-2430 colour columns hidden in alignment gray on... tree | commitdiff
2017-03-07 gmungocJAL-2295 status messages for Chimera attributes set... tree | commitdiff
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... tree | commitdiff
2016-12-08 gmungocMerge branch 'bug/JAL-2358phantomChimera' into spikes... tree | commitdiff
2016-12-08 gmungocJAL-2358 ensure mappings removed on close Chimera;... bug/JAL-2358phantomChimera tree | commitdiff
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