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[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

2018-09-14	gmungoc	JAL-3116 parse EMBL XML with JAXB (todo: update unit...	blob \| commitdiff
2018-09-13	gmungoc	JAL-3116 Uniprot XML unmarshalled using JAXB not Castor	blob \| commitdiff \| diff to current
2018-06-07	gmungoc	JAL-2920 wrap description in <html/> if it includes...	blob \| commitdiff \| diff to current
2018-06-06	Jim Procter	JAL-2920 revised TODO for JAL-3025 bug/JAL-2920_uniprotvariantfeature	blob \| commitdiff \| diff to current
2018-06-06	Jim Procter	JAL-2920 don’t output variant/original sequence as...	blob \| commitdiff \| diff to current
2018-06-06	Jim Procter	JAL-1920 JAL-3017 use newline not <br/> in description...	blob \| commitdiff \| diff to current
2018-06-04	Jim Procter	JAL-3017 parse multiple variant elements for uniprot...	blob \| commitdiff \| diff to current
2018-05-21	gmungoc	JAL-2920 use HGVS notation for protein variant feature	blob \| commitdiff \| diff to current
2018-01-16	gmungoc	JAL-2885 uniprot now https, uniprot/ensembl/pfam/xfam...	blob \| commitdiff \| diff to current
2017-11-22	gmungoc	JAL-2069 spike updated with latest (FeatureTypeSettings)	blob \| commitdiff \| diff to current
2017-11-13	Jim Procter	JAL-2758 remove configurable behaviour - Uniprot sequen...	blob \| commitdiff \| diff to current
2017-11-13	Jim Procter	JAL-2758 typo	blob \| commitdiff \| diff to current
2017-10-06	Jim Procter	JAL-2758 flag and tests for omitting uniprot accession... features/JAL-2758_shorteruniprot	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-29	Jim Procter	JAL-2748 formatting	blob \| commitdiff \| diff to current
2017-09-29	Jim Procter	JAL-2745 JAL-2748 direct download of XML from uniprot.org	blob \| commitdiff \| diff to current
2017-09-29	Jim Procter	JAL-2748 formatting	blob \| commitdiff \| diff to current
2017-09-29	Jim Procter	JAL-2745 JAL-2748 direct download of XML from uniprot.org	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2050 make SequenceFeature.score final, adjust const...	blob \| commitdiff \| diff to current
2017-05-24	gmungoc	JAL-2506 relocate Uniprot binding classes, bind to...	blob \| commitdiff \| diff to current
2017-05-16	gmungoc	JAL-2505 set SequenceFeature group in constructor	blob \| commitdiff \| diff to current
2016-11-30	gmungoc	JAL-2344 use ".cif" for saved mmCIF file (and refactor...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2016-10-24	Jim Procter	Merge branch 'releases/Release_2_10_0_Branch'	blob \| commitdiff \| diff to current
2016-10-06	gmungoc	Merge branch 'develop' into task/JAL-2196pdbeProperties	blob \| commitdiff \| diff to current
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-10-05	gmungoc	Merge branch 'develop' into task/JAL-2196pdbeProperties	blob \| commitdiff \| diff to current
2016-10-03	Jim Procter	JAL-2210 use addDBRef to ensure normalisation (just...	blob \| commitdiff \| diff to current
2016-10-03	Jim Procter	JAL-2210 need to add both transcript and product, and...	blob \| commitdiff \| diff to current
2016-10-03	Jim Procter	JAL-2210 JAL-2232 remove version number from ENACDS...	blob \| commitdiff \| diff to current
2016-10-02	Jim Procter	JAL-2210 remove ENSEMBL from protein DB list:	blob \| commitdiff \| diff to current
2016-09-28	Jim Procter	JAL-2232 extract EMBLCDS refs from EMBL refs on Uniprot...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-05-23	gmungoc	JAL-2113 EBIFetchClient refactor / unit tests / remove...	blob \| commitdiff \| diff to current
2016-03-22	tcofoegbu	JAL-1919 code improvement to make PDB sequence fetcher...	blob \| commitdiff \| diff to current
2016-03-11	gmungoc	JAL-1705 refactoring etc for fetching Ensembl --> Uniprot	blob \| commitdiff \| diff to current
2016-02-12	gmungoc	JAL-1270 remove trailing space + test	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-08	gmungoc	JAL-1705 DbSourceProxy properties converted to methods...	blob \| commitdiff \| diff to current
2015-11-02	tcofoegbu	JAL-1955 Uniprot sequence fetcher refactor	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-653 JAL-1780 reorder imports	blob \| commitdiff \| diff to current
2015-05-12	gmungoc	JAL-1712 fixes/tests for Castor binding and 'show flank...	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1693 make exon alignment for get-xref splitframe...	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-01-18	jprocter	JAL-1238 tier index indicating distance of a source...	blob \| commitdiff \| diff to current
2012-11-08	jprocter	tidy imports	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-04	jprocter	avoid importing the mapping every time we parse a unipr...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-06-19	jprocter	regex validator for uniprot	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-12-19	jprocter	wsdbfetch parameter change again (uniprotkb is dbname...	blob \| commitdiff \| diff to current
2008-12-04	jprocter	minimise exceptions for bad uniprot ids	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-26	jprocter	pdb xrefs added as dbrefs and as PDB file links	blob \| commitdiff \| diff to current
2008-08-15	jprocter	xrefs retrieved from Uniprot	blob \| commitdiff \| diff to current
2008-08-01	jprocter	updated jalview version of dasobert 1.53e client and...	blob \| commitdiff \| diff to current
2008-07-31	jprocter	quick fix for the new uniprot name schema - description...	blob \| commitdiff \| diff to current
2008-05-26	jprocter	Uniprot is not actually a multi-acc capable source...	blob \| commitdiff \| diff to current
2007-12-21	jprocter	uniprotxml format comment (ebi changed service parameter)	blob \| commitdiff \| diff to current
2007-12-21	jprocter	sequence db fetcher and db reference validation/annotat...	blob \| commitdiff \| diff to current
2007-11-16	jprocter	refactored ebi soap client and AbstractSequenceFetcher...	blob \| commitdiff \| diff to current
2007-11-16	jprocter	refactor abstract sequence fetching and DBSource machin...	blob \| commitdiff \| diff to current
2007-09-10	jprocter	ensure dbrefs are added to dataset sequence.	blob \| commitdiff \| diff to current
2007-07-13	jprocter	new DBRef management and generalised source and entry...	blob \| commitdiff \| diff to current

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