JAL-2416 remove unused pep, dna alphabets, unused methods, code format
[jalview.git] / src / jalview / ws /
2017-02-18 gmungocJAL-2416 better encapsulated 'constants' for BLOSUM62...
2017-02-17 gmungocJAL-2416 removed DNA and PAM250 matrices from ResiduePr...
2017-02-08 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-01-26 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-26 gmungocJAL-2344 test fix and code tidy for review comments
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2017-01-11 gmungocJAL-2344 FileFormats singleton for formats, FileFormatI...
2017-01-09 kiramtMerge remote-tracking branch 'origin/develop' into...
2017-01-05 gmungocMerge branch 'develop' into features/JAL-2360colourSche...
2016-12-16 gmungocJAL-2356 enhanced unit test to verify reuse (or not...
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum,
2016-12-15 kiramtJAL-2316 Changes following review.
2016-12-14 Jim ProcterMerge branch 'patch/JAL-2197_jpredforjnets' into develop
2016-12-13 kiramtMerge branch 'develop' into features/JAL-2316
2016-12-07 gmungocJAL-2356 use cached Sifts file if not expired
2016-12-07 kiramtJAL-2316 Restructure identifiers.org download
2016-11-30 gmungocJAL-2344 use ".cif" for saved mmCIF file (and refactor...
2016-11-29 gmungocJAL-2344 corrected conversion of Type enum to FileFormat features/JAL-2344FileFormatI
2016-11-28 gmungocMerge branch 'develop' into trialMerge
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane
2016-11-24 gmungocFileFormatI further tweaks, clean compile
2016-11-16 gmungocJAL-2319 corrected reporting of SIFTS mapping
2016-11-08 tcofoegbuJAL-2292 updated method calls
2016-11-04 tcofoegbuJAL-2292 fix for wrong mapping output in sequence mappi...
2016-11-03 tcofoegbuJAL-2312 Bug fix for repeated mapping generation from...
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch'
2016-10-24 Jim ProcterJAL-2197 renamed Jnet to Jared in help, web services...
2016-10-14 gmungocMerge branch 'releases/Release_2_10_Branch' into task... task/JAL-2196pdbeProperties
2016-10-13 gmungocMerge branch 'releases/Release_2_10_Branch' into develop
2016-10-13 gmungocJAL-1479 revise warning message to suit all contexts bug/JAL-2044jmolModelBinding
2016-10-11 gmungocMerge branch 'releases/Release_2_10_Branch' into develop
2016-10-11 gmungocJAL-1479 small tidy of error message when Sifts mapping...
2016-10-06 gmungocJAL-2254 map error text in root node of EMBL XML response
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-06 gmungocJAL-2245 checks for null added (in case EMBL fetch...
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 apply license
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
2016-10-05 Jim ProcterRevert "JAL-2245 Castor mapping and code changes for...
2016-10-04 gmungocMerge branch 'bug/JAL-2245enaXmlChange' into develop
2016-10-04 gmungocJAL-2245 Castor mapping and code changes for change... bug/JAL-2245enaXmlChange
2016-10-03 Jim ProcterJAL-2210 use addDBRef to ensure normalisation (just...
2016-10-03 Jim ProcterJAL-2210 need to add both transcript and product, and...
2016-10-03 Jim ProcterJAL-2210 JAL-2232 remove version number from ENACDS...
2016-10-02 Jim ProcterJAL-2210 remove ENSEMBL from protein DB list:
2016-10-01 Jim ProcterMerge branch 'develop' into bug/JAL-2210_ensembl_unipro...
2016-09-29 gmungocJAL-1856 better warning messages for sequence matching... features/JAL-1856dbRefFetcherMessages
2016-09-29 gmungocJAL-2213 code warnings addressed (typed collections...
2016-09-29 gmungocJAL-2213 removed PDB from db sources list; also code...
2016-09-28 Jim ProcterJAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot...
2016-09-07 Jim ProcterJAL-282 TODO - Sequence name from PDB had redundant...
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...
2016-08-31 Jim ProcterJAL-1926 JAL-2106 source DB refs come from SequenceI...
2016-08-31 Jim ProcterJAL-1926 JAL-2106 resolve source DB refs using canonica...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-26 Jim ProcterJAL-2154 patch regression on DbRefFetcher due to PDB...
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-25 gmungocJAL-2178 remove duplicate Uniprot db source
2016-08-24 Jim ProcterJAL-2106 tidy up and comments for DBRefFetcher
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 gmungocJAL-1355 correct 'thereshold' to 'threshold' in message...
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop
2016-07-20 Jim ProcterJAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMA...
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF...
2016-07-18 Jim ProcterMerge branch 'features/JAL-2068groovyAnnotationWorker...
2016-07-18 gmungocfileFormat enum wip changes
2016-07-12 gmungocFileFormat enum wip changes
2016-07-11 gmungocfile format enum wip changes
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing...
2016-07-01 gmungocJAL-2110 bug fixing and tidying for get cross-refs
2016-06-30 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-29 tcofoegbuJAL-1479 improved Sifts PID calculation for determining...
2016-06-29 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-28 tcofoegbuJAL-1479 minor refactor and housekeeping
2016-06-28 tcofoegbuJAL-1479 improved SiftsClient test coverage and impleme...
2016-06-21 Jim ProcterMerge branch 'features/JAL-2110_crossRefDuplications...
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
2016-06-20 Jim ProcterMerge branch 'develop' into features/JAL-2068groovyAnno... features/JAL-2068groovyAnnotationWorker
2016-06-20 gmungocJAL-1667 updated PDB example query to a valid id (witho...
2016-06-20 Jim ProcterJAL-2110 List now used for AlignCodonFrame references
2016-06-19 Jim ProcterJAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
2016-06-14 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD...
2016-06-10 tcofoegbuJAL-1479 updated SIFTS FTP download URL, added improvem...
2016-06-09 gmungocMerge branch 'develop' into features/JAL-2110_makeSense...
2016-06-08 tcofoegbuJAL-1479 JAL- Fix to eradicate duplicate mapping output...
2016-06-03 gmungocJAL-2110 random stuff
2016-06-02 gmungocMerge branch 'develop' into features/JAL-2110_makeSense...
2016-05-31 Jim ProcterMerge branch 'develop' into features/JAL-2113_emblXml1.2
2016-05-27 gmungocJAL-1942 small tidy (formatting, explict imports, typed...
2016-05-27 gmungocJAL-1911 correct typo in field name
2016-05-26 tcofoegbuJAL-1911 bugfix - do not save i18n text in preference...
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