JAL-2213 removed PDB from db sources list; also code tidy (typed
[jalview.git] / src / jalview / io /
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...
2016-09-07 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...
2016-08-26 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...
2016-07-14 tcofoegbuJAL-1919 house-keeping
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...
2016-03-24 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
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API....
2016-02-25 gmungocJAL-2015 parse/write Jalview feature format pushed...
2016-02-24 gmungocJAL-2015 JAL-1956 rollout of FeatureColourI in place of JAL-1956_featureStyles
2016-02-19 gmungocJAL-1705 JAL-1191 more terms added to hard-coded version
2016-02-19 gmungocJAL-1706 reverted setting start position as too confusi...
2016-02-12 gmungocJAL-1191 additions to SOLite, tweak to test
2016-02-12 gmungocJAL-1705 take feature ID for description if nothing...
2016-02-12 gmungocMerge branch 'develop' into
2016-02-09 tcofoegbumerge develop
2016-02-09 tcofoegbuJAL-1976 catch and handle OOM Error
2016-02-09 tcofoegbuJAL-1976 Added progress indicators for HTML_SVG and...
2016-02-01 gmungocJAL-1705 further unit tests
2016-02-01 gmungocJAL-1191 more terms added to SequenceOntologyLite
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard...
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid...
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence...
2016-01-25 gmungocJAL-1705 EnsemblGene added, and related refactoring
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq...
2016-01-21 gmungocJAL-653 refactor / tidy
2016-01-21 gmungocJAL-653 JAL-1705 set strand for GFF sequence feature
2016-01-21 gmungocJAL-653 comments/javadoc tidy only
2016-01-21 gmungocJAL-1796 parse ensembl genomic coordinates to set start...
2016-01-21 gmungocJAL-1705 include dummy sequences in returned alignment
2016-01-21 gmungocJAL-1705 added isSequenceVariant(), commonly used SO...
2016-01-21 tcofoegbuJAL-1919 basic support for importing and viewing mmCIF...
2016-01-12 gmungocJAL-1191 cache isA (great-)grandparents as well for...
2016-01-11 tcofoegbuJAL-1991 bug fix for some flat-file printers to check...
2016-01-05 gmungocMerge remote-tracking branch 'origin/features/JAL-1705_...
2016-01-05 gmungocJAL-1191 check for obsolete term when descriptions...
2015-12-23 gmungocJAL-1191 zipped SO OBO file added to /resources, more...
2015-12-22 gmungocJAL-1191 and provide the SO OBO file in /resources :-)
2015-12-22 gmungocJAL-1191 SequenceOntology wrapping/caching SO.OBO via...
2015-12-22 gmungocJAL-1191 stub class for a SequenceOntology wrapper
2015-12-22 gmungocJAL-653 set showSequenceFeatures=true on loading a...
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list...
2015-11-30 gmungocJAL-652 further refactoring / tests
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-11-11 tcofoegbumerge
2015-11-10 Jim ProcterJAL-653 added missing pragma string to processing filter
2015-10-30 Jim ProcterJAL-1954 rejigged PFAMFile to split on ‘\t’ if no space...
2015-10-28 tcofoegbuJAL-1887 JAL-1479 bugfix for incorrect start/end for...
2015-10-22 tcofoegbuJAL-1479 added basic support for SIFTs mapping - more...
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-653_JAL-1766_h...
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-1705_ensembl
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
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