JAL-2629 add hmmbuild validation check which also gets the HMMER version
[jalview.git] / src / jalview / io /
2016-11-24 gmungocDistinguish text-only output formats and others (.jar...
2016-11-24 tcofoegbuJAL-2326 updated references of JOptionPane to JvOptionPane
2016-11-24 gmungocFurther tweaks to get tests passing
2016-11-24 gmungocFileFormatI further tweaks, clean compile
2016-11-23 Jim ProcterMerge branch 'bug/JAL-2323disulfideOverview' into develop
2016-11-23 Jim ProcterMerge branch 'documentation/JAL-2325_release2101' into...
2016-11-23 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-22 Jim ProcterJAL-2197 changed tooltip for Jnet annotation rows to...
2016-11-22 tcofoegbuMerge branch 'bug/JAL-2277_refactorPrintUnwrapped'...
2016-11-22 tcofoegbuJAL-2322 added runnable interface to HTMLOutput class...
2016-11-22 gmungocJAL-2277 refactored AlignmentPanel.printUnwrapped to...
2016-11-21 gmungocMerge branch 'develop' into bug/JAL-2323disulfideOverview
2016-11-17 gmungocJAL-2327 disulfide bond abstracted to SequenceFeature...
2016-11-16 Jim ProcterMerge branch 'features/JAL-1723_sequenceReport' into...
2016-11-16 tcofoegbuJAL-2322 JAL-2309 replaced references to isheadless...
2016-11-16 gmungocMerge branch 'develop' into features/JAL-2295setChimera...
2016-11-14 tcofoegbuJAL-2322 Refactored unified architecture for data ...
2016-11-11 tcofoegbuJAL-2277 Refactored out duplicated method - printUnwrap...
2016-11-09 gmungocJAL-2295 single constant for "RESNUM" feature name
2016-11-02 kiramtMerge remote-tracking branch 'origin/bug/JAL-2282'...
2016-11-02 gmungocJAL-98 JAL-1854 encapsulate 'magic number' threshold...
2016-11-01 tcofoegbuJAL-2280 refactored and improved structure file identif...
2016-11-01 kiramtJAL-2282 Refactor SequenceAnnotationReport to use refac...
2016-10-31 gmungocMerge branch 'develop' into features/JAL-1723_sequenceR...
2016-10-26 tcofoegbuMerge branch 'features/JAL-2284_export-biojsmsa-via...
2016-10-26 tcofoegbuJAL-2284 basic support for exporting BioJS MSA viewer... features/JAL-2284_export-biojsmsa-via-cli
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-25 tcofoegbuJAL-2277 Improvement to support html+svg export in... bug/JAL-2277_html-output-wrapped-mode
2016-10-24 Jim ProcterMerge branch 'releases/Release_2_10_0_Branch'
2016-10-17 tcofoegbuJAL-2262 JAL-2195 Improvement to set PDBId availability...
2016-10-06 gmungocMerge branch 'develop' into task/JAL-2196pdbeProperties
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 gmungocJAL-1191 revert to using SequenceOntologyLite due to...
2016-10-05 gmungocJAL-1191 configure full SO for desktop, SOLite for...
2016-10-05 gmungocJAL-1191 use full SO in desktop application
2016-10-05 gmungocJAL-1191 refined warning message
2016-10-05 gmungocJAL-1191 added mRNA isA transcript to SequenceOntologyL...
2016-09-29 gmungocJAL-2213 made RESNUM constant private (not used elsewhe...
2016-09-23 tcofoegbuMerge branch 'develop' of https://source.jalview.org...
2016-09-23 tcofoegbuJAL-2164 JAL-1919 fixed failed revert commit
2016-09-22 gmungocJAL-1421 typed ResidueProperties.propHash; JAL-2176...
2016-09-16 gmungocJAL-2164 removed unused parameters from JmolParser...
2016-09-13 tcofoegbuRevert "JAL-2164 JAL-1919 disabled and removed PDB...
2016-09-13 tcofoegbuJAL-2164 JAL-1919 disabled and removed PDB file parser...
2016-09-13 gmungocJAL-2196 refactor PDBEntry.getProperty,setProperty...
2016-09-07 Jim ProcterMerge branch 'develop' into bug/JAL-1803_JAL-2157
2016-09-07 Jim ProcterJAL-1803 JAL-1919 set type when structure file is parsed
2016-09-04 Jim ProcterJAL-2148 JAL-1803 JAL-1919 resolve type for mmCIF loade...
2016-09-01 gmungocJAL-1421 add generics to NJTree, refactor recursive...
2016-08-30 Jim ProcterMerge branch 'develop' into merge/develop_bug/JAL-2154p...
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-25 Jim ProcterMerge branch 'develop' into refactor/JAL-2106_sourceDbR...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 gmungocJAL-1424 undo i18n of exception message
2016-08-22 gmungocJAL-2175 code tidying
2016-08-22 gmungocJAL-2175 code/test fixes/tidy for PFAM/MSF/JSON roundtrip
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2016-07-26 tcofoegbuJAL-2157 bugfix for issues from enum refactoring
2016-07-25 tcofoegbuJAL-2157 bugfix for regression from commit 82a6c8e2e25b...
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop
2016-07-20 Jim ProcterJAL-1926 JAL-2106 fix name for flag controlling additio...
2016-07-20 Jim ProcterJAL-1926 JAL-2106 remove startRes/endRes fields - not...
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF...
2016-07-18 gmungocfileFormat enum wip changes
2016-07-14 tcofoegbuJAL-1919 house-keeping
2016-07-12 gmungocFileFormat enum new types
2016-07-12 gmungocFileFormat enum wip changes
2016-07-11 gmungocfile format enum wip changes
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing...
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser...
2016-06-22 gmungocJAL-1982 defensive checks for null annotations array
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into...
2016-06-17 tcofoegbuJAL-1976 clear message if export is cancelled at 'Rende...
2016-06-17 tcofoegbuJAL-1976 improved exception handler.
2016-06-17 tcofoegbuJAL-1976 added an intermediate message between a user...
2016-06-10 tcofoegbuJAL-1479 updated SIFTS FTP download URL, added improvem...
2016-05-26 tcofoegbuJAL-1911 bugfix - do not save i18n text in preference...
2016-05-26 tcofoegbuJAL-1911 bugfix - do not save i18n text in preference...
2016-05-17 tcofoegbuJAL-1270 Fixed anntatedPDBFileInputTest and updated...
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles
2016-05-09 gmungocJAL-2098 identify feature file with "<" in feature...
2016-05-09 gmungocJAL-2018 export graduated feature colours correctly
2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attrib...
2016-04-14 gmungocJAL-2041 clinical_significance shown on sequence featur...
2016-04-14 gmungocJAL-1421 typed map / lists, explicit imports, method...
2016-04-14 gmungocJAL-1270 JAL-653 use 'parse immediately' FeaturesFile...
2016-04-12 gmungocJAL-1723 tooltip dbrefs sorted and limited to two per...
2016-03-24 tcofoegbuJAL-1919 Settings to disable duplicate generation of...
2016-03-24 tcofoegbuJAL-1919 Added ability to generate temprature factor...
2016-03-24 tcofoegbufixed applet build
2016-03-23 tcofoegbuJAL-2009 added programmatic custom feature setting...
2016-03-22 gmungocJAL-1191 isolated SequenceOntology (BioJava wrapper...
2016-03-21 tcofoegbudevelop merge
2016-03-15 tcofoegbuJAL-1919 refined structure view annotation settings...
2016-03-03 tcofoegbuJAL-1919 fixed bug causing PDBfile test failure
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor
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