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JAL-2376 copied out patch from Phyre branch
[jalview.git] / src / jalview / io /
2017-04-25 tcofoegbuJAL-2489 bug fix tree | commitdiff
2017-03-13 gmungocJAL-2438 FeatureColourFinder refactored from FeatureRen... tree | commitdiff
2017-03-01 gmungocMerge branch 'features/JAL-2295setChimeraAttributes... tree | commitdiff
2017-01-26 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-26 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-26 gmungocJAL-2344 test fix and code tidy for review comments tree | commitdiff
2017-01-25 gmungocJAL-2344 push Cache.getProperty("LAST_DIRECTORY") insid... tree | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2017-01-17 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-17 gmungocMerge branch 'develop' into features/JAL-2360colourSche... tree | commitdiff
2017-01-12 gmungocJAL-2344 now flagging formats as 'identifiable' instead... tree | commitdiff
2017-01-11 gmungocJAL-2344 separated AlignmentFileI into AlignmentFileRea... tree | commitdiff
2017-01-11 gmungocJAL-2344 FileFormats singleton for formats, FileFormatI... tree | commitdiff
2017-01-11 gmungocJAL-2344 addSequence() method added to support Groovy... tree | commitdiff
2017-01-06 gmungocMerge branch 'features/JAL-2360colourSchemeApplicabilit... tree | commitdiff
2017-01-06 gmungocJAL-2360 findColour() with no args removed from ColourS... tree | commitdiff
2017-01-04 gmungocJAL-2371 CollectionColourScheme wraps ColourSchemeI tree | commitdiff
2016-12-21 gmungocJAL-2360 tidy spelling and file contents order only tree | commitdiff
2016-12-16 Jim ProcterJAL-2360 report line number when threshold cannot be... tree | commitdiff
2016-12-16 gmungocJAL-2360 getColour() renamed to getColourScheme(),... tree | commitdiff
2016-12-16 gmungocJAL-2360 refactoring for JalviewColourScheme enum, tree | commitdiff
2016-12-08 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-12-07 gmungocJAL-2344 handle null format, simplify JalviewFileChoose... tree | commitdiff
2016-11-29 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-29 gmungocJAL-2344 FileFormat.isStructureFile replaces tree | commitdiff
2016-11-28 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-28 tcofoegbuMerge branch 'features/JAL-2326_JOptionPane-refactoring... tree | commitdiff
2016-11-28 gmungocJAL-2344 added FileFormatI.isStructureFile() tree | commitdiff
2016-11-28 gmungocJAL-2345 cache generated ImageIcon per file path tree | commitdiff
2016-11-25 gmungocJAL-2344 dynamically determine recognised extensions... tree | commitdiff
2016-11-25 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2016-11-25 gmungocJAL-2344 override to ignore (obsolete?) JalviewFileView tree | commitdiff
2016-11-25 gmungocJAL-2344 use .equals() to compare FileFormatI objects tree | commitdiff
2016-11-24 gmungocDistinguish text-only output formats and others (.jar... tree | commitdiff
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane tree | commitdiff
2016-11-24 gmungocFurther tweaks to get tests passing tree | commitdiff
2016-11-24 gmungocFileFormatI further tweaks, clean compile tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop tree | commitdiff
2016-11-23 Jim ProcterMerge branch 'documentation/JAL-2325_release2101' into... tree | commitdiff
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-22 Jim ProcterJAL-2197 changed tooltip for Jnet annotation rows to... tree | commitdiff
2016-11-22 tcofoegbuMerge branch 'bug/JAL-2277_refactorPrintUnwrapped'... tree | commitdiff
2016-11-22 tcofoegbuJAL-2322 added runnable interface to HTMLOutput class... tree | commitdiff
2016-11-22 gmungocJAL-2277 refactored AlignmentPanel.printUnwrapped to... tree | commitdiff
2016-11-21 gmungocMerge branch 'develop' into bug/JAL-2323disulfideOverview tree | commitdiff
2016-11-17 gmungocJAL-2327 disulfide bond abstracted to SequenceFeature... tree | commitdiff
2016-11-16 Jim ProcterMerge branch 'features/JAL-1723_sequenceReport' into... tree | commitdiff
2016-11-16 tcofoegbuJAL-2322 JAL-2309 replaced references to isheadless... tree | commitdiff
2016-11-16 gmungocMerge branch 'develop' into features/JAL-2295setChimera... tree | commitdiff
2016-11-14 tcofoegbuJAL-2322 Refactored unified architecture for data ... tree | commitdiff
2016-11-11 tcofoegbuJAL-2277 Refactored out duplicated method - printUnwrap... tree | commitdiff
2016-11-09 gmungocJAL-2295 single constant for "RESNUM" feature name tree | commitdiff
2016-11-02 kiramtMerge remote-tracking branch 'origin/bug/JAL-2282'... tree | commitdiff
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold... tree | commitdiff
2016-11-01 tcofoegbuJAL-2280 refactored and improved structure file identif... tree | commitdiff
2016-11-01 kiramtJAL-2282 Refactor SequenceAnnotationReport to use refac... tree | commitdiff
2016-10-31 gmungocMerge branch 'develop' into features/JAL-1723_sequenceR... tree | commitdiff
2016-10-26 tcofoegbuMerge branch 'features/JAL-2284_export-biojsmsa-via... tree | commitdiff
2016-10-26 tcofoegbuJAL-2284 basic support for exporting BioJS MSA viewer... features/JAL-2284_export-biojsmsa-via-cli tree | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch tree | commitdiff
2016-10-25 tcofoegbuJAL-2277 Improvement to support html+svg export in... bug/JAL-2277_html-output-wrapped-mode 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
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties 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
2016-10-05 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties tree | commitdiff
2016-10-05 gmungocJAL-1191 revert to using SequenceOntologyLite due to... tree | commitdiff
2016-10-05 gmungocJAL-1191 configure full SO for desktop, SOLite for... tree | commitdiff
2016-10-05 gmungocJAL-1191 use full SO in desktop application tree | commitdiff
2016-10-05 gmungocJAL-1191 refined warning message tree | commitdiff
2016-10-05 gmungocJAL-1191 added mRNA isA transcript to SequenceOntologyL... tree | commitdiff
2016-09-29 gmungocJAL-2213 made RESNUM constant private (not used elsewhe... tree | commitdiff
2016-09-23 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-09-23 tcofoegbuJAL-2164 JAL-1919 fixed failed revert commit tree | commitdiff
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176... 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
2016-09-13 gmungocJAL-2196 refactor PDBEntry.getProperty,setProperty... tree | commitdiff
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157 tree | commitdiff
2016-09-07 Jim ProcterJAL-1803 JAL-1919 set type when structure file is parsed tree | commitdiff
2016-09-04 Jim ProcterJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loade... tree | commitdiff
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive... tree | commitdiff
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p... tree | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum tree | commitdiff
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr tree | commitdiff
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR... tree | commitdiff
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... tree | commitdiff
2016-08-24 gmungocJAL-1424 undo i18n of exception message tree | commitdiff
2016-08-22 gmungocJAL-2175 code tidying tree | commitdiff
2016-08-22 gmungocJAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip tree | commitdiff
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering... tree | commitdiff
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring tree | commitdiff
2016-07-25 tcofoegbuJAL-2157 bugfix for regression from commit 82a6c8e2e25b... 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 remove startRes/endRes fields - not... tree | commitdiff
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... tree | commitdiff
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