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JAL-2416 remove unused pep, dna alphabets, unused methods, code format
[jalview.git] / src / jalview / structure /
2017-02-13 gmungocJAL-1632 JAL-2416 load score matrices from file, as... tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-22 Jim ProcterMerge branch 'features/JAL-1738_JAL-345_selectionfromhi... tree | commitdiff
2016-11-04 tcofoegbuJAL-2195 JAL-2262 house keeping tree | commitdiff
2016-10-28 Jim ProcterJAL-966 JAL-1738 JAL-345 interfaces for SearchResults... tree | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch tree | commitdiff
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch' tree | commitdiff
2016-10-17 tcofoegbuJAL-2262 JAL-2195 Improvement to set PDBId availability... tree | commitdiff
2016-10-10 tcofoegbuJAL-2262 JAL-2195 bug fix for mapping local structure... tree | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 apply license tree | commitdiff
2016-10-05 Jim ProcterJAL-2189 source formatting tree | commitdiff
2016-09-19 tcofoegbumerge tree | commitdiff
2016-09-16 gmungocJAL-2164 removed unused parameters from JmolParser... tree | commitdiff
2016-09-13 tcofoegbuRevert "JAL-2164 JAL-1919 disabled and removed PDB... tree | commitdiff
2016-09-13 tcofoegbuJAL-2164 JAL-1919 disabled and removed PDB file parser... tree | commitdiff
2016-09-07 Jim ProcterJAL-1803 transfer mapped chain’s PDBEntry to the *datas... tree | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 javadoc for sifts mapping method tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 prevent SIFTS mappings for sequences that... tree | commitdiff
2016-07-26 Jim ProcterJAL-2157 todo: verify parser/file format enums and... tree | commitdiff
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring tree | commitdiff
2016-07-22 tcofoegbuJAL-2148 Bugfix in structureImportSettings string-to... tree | commitdiff
2016-07-21 tcofoegbuResolve merge conflict for StructureImportSettings tree | commitdiff
2016-07-21 tcofoegbuJAL-2148 fix to heuristically determine chain terminati... tree | commitdiff
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop tree | commitdiff
2016-07-20 Jim ProcterJAL-1926 JAL-2106 fix name for flag controlling additio... tree | commitdiff
2016-07-20 Jim ProcterJAL-1926 JAL-2106 don’t use PDB database constant as... tree | commitdiff
2016-07-20 Jim ProcterJAL-1926 JAL-2106 use enum for ‘DEFAULT_STRUCTURE_FORMA... tree | commitdiff
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... tree | commitdiff
2016-07-11 gmungocfile format enum wip changes tree | commitdiff
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... tree | commitdiff
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser... tree | commitdiff
2016-06-28 tcofoegbuJAL-1479 improved SiftsClient test coverage and impleme... tree | commitdiff
2016-06-15 tcofoegbuJAL-2002 disabled 'Best Uniport Coverage' filter. JAL... tree | commitdiff
2016-06-10 tcofoegbuJAL-1479 updated SIFTS FTP download URL, added improvem... tree | commitdiff
2016-06-08 tcofoegbuJAL-1479 JAL- Fix to eradicate duplicate mapping output... tree | commitdiff
2016-03-30 tcofoegbuJAL-2038 bug fix for NPE while setting progress message... tree | commitdiff
2016-03-24 gmungocJAL-2032 structure follow mouseover in a copy of a... tree | commitdiff
2016-03-22 tcofoegbuJAL-1919 code improvement to make PDB sequence fetcher... tree | commitdiff
2016-03-21 tcofoegbuJAL-1919 refactor moved StructureViewerSettings tree | commitdiff
2016-03-21 tcofoegbudevelop merge tree | commitdiff
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API.... tree | commitdiff
2016-02-20 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-02-19 tcofoegbuJAL-2009 Codes to enable storing inserted residues... tree | commitdiff
2016-02-12 gmungocJAL-2010 simple prototype of 'Highlight Selection'... tree | commitdiff
2016-02-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-01-29 tcofoegbuJAL-1979 refactor out duplicated similar block of code... tree | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge tree | commitdiff
2016-01-26 tcofoegbuJAL-1999 JAL-1479 implemented configurable fail-safe... tree | commitdiff
2016-01-11 tcofoegbuJAL-1990 added a progress indicator for Structure Choos... tree | commitdiff
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list... tree | commitdiff
2015-11-17 tcofoegbuJAL-1479 Refactored Sifts configuration preference... tree | commitdiff
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi... tree | commitdiff
2015-11-13 tcofoegbuJAL-1479 added transfer of residue annotation for SIFTS... tree | commitdiff
2015-11-11 tcofoegbuJAL-1957 JAL-1479 Further optimisation of SIFTs Client... features/JAL-1479_SIFTS-mapping tree | commitdiff
2015-11-05 tcofoegbuJAL-1479 SiftClient house keeping tree | commitdiff
2015-10-28 tcofoegbuJAL-1479 added support for SIFTs mapping output viewing... tree | commitdiff
2015-10-28 tcofoegbuJAL-1887 JAL-1479 bugfix for incorrect start/end for... tree | commitdiff
2015-10-22 tcofoegbuJAL-1479 added basic support for SIFTs mapping - more... tree | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 tree | commitdiff
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... tree | commitdiff
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin... tree | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright tree | commitdiff
2015-09-16 gmungocJAL-1859 debug logging removed tree | commitdiff
2015-09-16 gmungocJAL-1859 temporary debug output tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 licencing for new files in src tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports tree | commitdiff
2015-08-27 gmungocJAL-1830 refactored so no jalview.gui references from... tree | commitdiff
2015-08-26 gmungocJAL-1830 dropped reference counts for mappings, instead... tree | commitdiff
2015-08-17 gmungocJAL-1829 JAL-1830 refactoring for correct mapping ... tree | commitdiff
2015-06-22 gmungocJAL-892 tidy Varna panel names; JAL-1789 simplified... tree | commitdiff
2015-06-05 gmungocJAL-1752 structure highlight scoped to only its mapped... tree | commitdiff
2015-06-05 gmungocJAL-1622 code tidy only, no functional change tree | commitdiff
2015-06-04 gmungocJAL-1750 View Mapping scoped to that viewer's mappings... tree | commitdiff
2015-05-06 gmungocJAL-1725 broadcast empty selection (to clear selection) features/JAL-1725chimeraListener tree | commitdiff
2015-05-05 gmungocJAL-1725 first version of Jetty server / chimera select... tree | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch tree | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... tree | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 tree | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes tree | commitdiff
2014-11-27 Jim ProcterJAL-674 unused variable tree | commitdiff
2014-11-18 Jim ProcterJAL-674 make temperature factor, local secondary struct... tree | commitdiff
2014-11-17 gmungocJAL-1528 bug fixes and adjustments to Chimera interface tree | commitdiff
2014-11-13 gmungocmerge tree | commitdiff
2014-11-12 gmungocJAL-1528 bug fixes and adjustments to Chimera interface tree | commitdiff
2014-11-12 Jim ProcterJAL-974 fix class contamination for jalviewLite build tree | commitdiff
2014-11-12 Jim ProcterJAL-674 use the getMapping/transfer to transfer annotat... tree | commitdiff
2014-11-12 Jim ProcterJAL-674 note about broken .transfer method (expect... tree | commitdiff
2014-11-12 Jim ProcterJAL-674 javadoc tree | commitdiff
2014-10-31 Jim ProcterJAL-674 JAL-961 pass row reference to handler to check... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 propagate annotation onto mapped sequence and... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 use PDB ID<>File registry to look up correct... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 flag and proxy method to distinguish setMapping... tree | commitdiff
2014-10-30 Jim ProcterJAL-674 map on StructureSelectionManager to record... tree | commitdiff
2014-10-30 Jim ProcterJAL-1551 format and tidy tree | commitdiff
2014-10-29 Jim ProcterJAL-1264 JAL-674 method to copy annotation on structure... tree | commitdiff
2014-10-21 Jim ProcterJAL-674 don't create multiple secondary structure lines... tree | commitdiff
2014-10-21 Jim ProcterJAL-1551 formatting tree | commitdiff
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