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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / ws / sifts / SiftsClient.java
2023-11-03 James ProcterJAL-4090 JAL-1551 spotlessApply commit | commitdiff
2023-08-10 Ben SoaresJAL-629 Change all stdout and stderr output to use... commit | commitdiff
2023-07-17 James ProcterJAL-4119 TRACE level console message reporting download... commit | commitdiff
2023-02-02 James ProcterJAL-4119 use split_xml directories rather than the... commit | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 commit | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... commit | commitdiff
2020-11-06 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... commit | commitdiff
2020-06-15 Ben SoaresJAL-3628 Changed other calls to renameTo to use BackupF... commit | commitdiff
2020-05-19 gmungocJAL-3624 use temp file for SIFT download in JS, correct... feature/JAL-3624siftsInJS commit | commitdiff
2018-08-21 hansonrmc_view references were MCview commit | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 don’t create a mapping if sequence... commit | commitdiff
2018-02-13 Jim ProcterJAL-2780 JAL-2781 only create a mapping entry or write... commit | commitdiff
2018-02-13 Jim ProcterJAL-2781 JAL-2780 include sequence start number when... commit | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 use PDBe numbering to map between... commit | commitdiff
2018-02-11 Jim ProcterJAL-2781 mark aligned positions via StructureMapping... commit | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 include a Mapping object in Structure... commit | commitdiff
2018-02-11 Jim ProcterJAL-2780 JAL-2781 UNASSIGNED positions marked as Intege... commit | commitdiff
2018-02-09 Jim ProcterUse the “PDBe” or “PDB” numbering (starts from 1, corre... commit | commitdiff
2018-02-09 Jim ProcterJAL-2780 JAL-2781 should always ensure SIFTS mappings... commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS" commit | commitdiff
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS" commit | commitdiff
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS commit | commitdiff
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-06-09 gmungocJAL-2446 merged to spike branch commit | commitdiff
2017-05-02 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff
2017-05-01 tcofoegbuJAL-2482 bug fix commit | commitdiff
2017-04-21 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff
2017-04-19 tcofoegbuJAL-2482 added null check commit | commitdiff
2017-04-18 tcofoegbuJAL-2482 Bugfix commit | commitdiff
2017-03-23 gmungocMerge branch 'develop' into features/JAL-2393customMatrices commit | commitdiff
2017-02-20 gmungocJAL-2403 ScoreModelI now DistanceModelI, ScoreMatrix... commit | commitdiff
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62... commit | commitdiff
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr... commit | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2295setChimera... commit | commitdiff
2016-12-16 gmungocJAL-2356 enhanced unit test to verify reuse (or not... commit | commitdiff
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera... commit | commitdiff
2016-12-07 gmungocJAL-2356 use cached Sifts file if not expired commit | commitdiff
2016-11-16 gmungocJAL-2319 corrected reporting of SIFTS mapping commit | commitdiff
2016-11-11 gmungocMerge branch 'develop' into features/JAL-2295setChimera... commit | commitdiff
2016-11-11 gmungocJAL-2295 JAL-2269 JAL-2319 mockable SIFTS file, fix... commit | commitdiff
2016-11-08 tcofoegbuJAL-2292 updated method calls commit | commitdiff
2016-11-04 tcofoegbuJAL-2292 fix for wrong mapping output in sequence mappi... commit | commitdiff
2016-11-03 tcofoegbuJAL-2312 Bug fix for repeated mapping generation from... commit | commitdiff
2016-10-13 gmungocJAL-1479 revise warning message to suit all contexts bug/JAL-2044jmolModelBinding commit | commitdiff
2016-10-11 gmungocJAL-1479 small tidy of error message when Sifts mapping... commit | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting commit | commitdiff
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid... commit | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 source DB refs come from SequenceI... commit | commitdiff
2016-08-31 Jim ProcterJAL-1926 JAL-2106 resolve source DB refs using canonica... commit | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... commit | commitdiff
2016-06-29 tcofoegbuJAL-1479 improved Sifts PID calculation for determining... commit | commitdiff
2016-06-28 tcofoegbuJAL-1479 minor refactor and housekeeping commit | commitdiff
2016-06-28 tcofoegbuJAL-1479 improved SiftsClient test coverage and impleme... 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
2016-03-24 tcofoegbuJAL-1479 Commented out debug sysout's for SiftsClient commit | commitdiff
2016-03-22 tcofoegbuJAL-1919 code improvement to make PDB sequence fetcher... commit | commitdiff
2016-03-03 tcofoegbuJAL-1919 updated unicode mapping symbol commit | commitdiff
2016-03-03 tcofoegbuJAL-1919 updated unicode symbol for mapping commit | commitdiff
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API.... commit | commitdiff
2016-02-19 tcofoegbuJAL-2009 Codes to enable storing inserted residues... commit | commitdiff
2016-01-27 tcofoegbuJAL-1479 fixed off-by-one error in SIFTS mapping output... commit | commitdiff
2016-01-26 tcofoegbudevelop merge commit | commitdiff
2016-01-26 tcofoegbuJAL-1999 JAL-1479 implemented configurable fail-safe... commit | commitdiff
2016-01-21 tcofoegbuJAL-1479 JAL-1979 bugfix to check entire annotation... commit | commitdiff
2016-01-21 tcofoegbuJAL-1479 JAL-1979 updated the modified-aminoacid triple... commit | commitdiff
2016-01-21 tcofoegbuJAL-1919 basic support for importing and viewing mmCIF... commit | commitdiff
2016-01-07 tcofoegbuJAL-1479 implemented timestamp based caching of SIFTS... commit | commitdiff
2015-11-25 tcofoegbuJAL-1479 refactored DBRef fetching code to StructureCho... commit | commitdiff
2015-11-25 tcofoegbuJAL-1479 applet build debug commit | commitdiff
2015-11-25 tcofoegbuJAL-1479 bugfix after decoupling SIFTS preference settings commit | commitdiff
2015-11-23 tcofoegbuJAL-1479 commented out DBRef fetching code from SIFTS... commit | commitdiff
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi... commit | commitdiff
2015-11-13 tcofoegbuJAL-1479 added transfer of residue annotation for SIFTS... commit | commitdiff
2015-11-11 tcofoegbuJAL-1957 JAL-1479 Further optimisation of SIFTs Client... features/JAL-1479_SIFTS-mapping commit | commitdiff
2015-11-05 tcofoegbuJAL-1479 SiftClient house keeping commit | commitdiff
2015-10-29 tcofoegbuJAL-1926 JAL-1479 updated PDBfile fetcher to add source... commit | commitdiff
2015-10-28 tcofoegbuJAL-1479 added support for SIFTs mapping output viewing... commit | commitdiff
2015-10-28 tcofoegbuJAL-1887 JAL-1479 bugfix for incorrect start/end for... commit | commitdiff