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[jalview.git] / src / jalview / io / StockholmFile.java

2018-03-29	gmungoc	JAL-2907 bug fix redone on HMMER branch	blob \| commitdiff
2018-03-28	gmungoc	JAL-1265 output all dbrefs in Stockholm (+tests) (...	blob \| commitdiff \| diff to current
2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-01	TZVanaalten	JAL-2629 manual curation of HMMs via reference annotati...	blob \| commitdiff \| diff to current
2017-08-25	TZVanaalten	JAL-2629 fix issue where Stockholm file would print...	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-18	TZVanaalten	Merge branch 'develop' into features/hmmer	blob \| commitdiff \| diff to current
2017-08-17	TZVanaalten	JAL-2629 add documentation to previous work	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-08-14	TZVanaalten	JAL-2629 remove gap padding, and now has option to...	blob \| commitdiff \| diff to current
2017-08-14	TZVanaalten	JAL-2629 add padding for .sto annotations to fix issues...	blob \| commitdiff \| diff to current
2017-07-27	TZVanaalten	JAL-2629 implement hmmbuild	blob \| commitdiff \| diff to current
2017-06-14	gmungoc	JAL-2598 Sequence.getSequence return a copy of the...	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-2557 removal of Sequence.sequenceFeatures	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2050 make SequenceFeature.score final, adjust const...	blob \| commitdiff \| diff to current
2017-05-15	Jim Procter	JAL-2507 capitalisation for annotation lines generated...	blob \| commitdiff \| diff to current
2017-05-15	Jim Procter	JAL-2507 case insensitive recognition of annotation...	blob \| commitdiff \| diff to current
2017-05-15	Jim Procter	JAL-2535 quick hack to implement posterior probabilitie...	blob \| commitdiff \| diff to current
2017-05-11	Jim Procter	JAL-2509 JAL-2507 allow whitespace in GS annotation...	blob \| commitdiff \| diff to current
2017-05-09	Jim Procter	JAL-2509 extend set of brackets recognised by stockholm...	blob \| commitdiff \| diff to current
2017-05-09	Jim Procter	JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...	blob \| commitdiff \| diff to current
2017-05-09	Jim Procter	JAL-2507 output secondary structure regardless of prese...	blob \| commitdiff \| diff to current
2017-05-04	Jim Procter	fix for JAL-2509 - don’t replace all bracket types...	blob \| commitdiff \| diff to current
2017-05-04	Jim Procter	fix for JAL-2507 - resolve stockholm per residue annota...	blob \| commitdiff \| diff to current
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	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
2016-10-06	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
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	blob \| commitdiff \| diff to current
2016-08-26	gmungoc	Merge branch 'develop' into bug/JAL-1841rnaSecStr	blob \| commitdiff \| diff to current
2016-08-24	gmungoc	JAL-1424 undo i18n of exception message	blob \| commitdiff \| diff to current
2016-08-12	gmungoc	JAL-1841 bug fixes / code tidy for rna SS rendering...	blob \| commitdiff \| diff to current
2016-07-18	gmungoc	fileFormat enum wip changes	blob \| commitdiff \| diff to current
2016-07-11	gmungoc	file format enum wip changes	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
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	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
2015-08-18	tcofoegbu	JAL-1861 bugfix to allow parsing of stockholm files...	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2015-02-19	gmungoc	JAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-12-01	Jim Procter	JAL-1199 JAL-1569 incremental patch allow non-standard...	blob \| commitdiff \| diff to current
2014-11-23	Jim Procter	JAL-1569 consistent handling of sequence and alignment...	blob \| commitdiff \| diff to current
2014-11-23	Jim Procter	JAL-1569 formatting	blob \| commitdiff \| diff to current
2014-11-23	Jim Procter	JAL-1569 preserve input ordering for stockholm files...	blob \| commitdiff \| diff to current
2014-11-21	Jim Procter	JAL-674 add RNA sequence associated annotation to align...	blob \| commitdiff \| diff to current
2014-11-21	Jim Procter	JAL-1569 formatting	blob \| commitdiff \| diff to current
2014-09-23	darolmar	JAL-1355	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 source formatting	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
2014-06-05	Jim Procter	Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-02-18	Jim Procter	Merge branch 'JAL-1445' into develop	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2013-06-07	Jim Procter	Merge branch 'develop' into develop_m2_8_1_2	blob \| commitdiff \| diff to current
2013-06-07	Jim Procter	Merge branch 'JAL-1161_optimisingAnnotationPanel' into...	blob \| commitdiff \| diff to current
2013-02-14	Jim Procter	Merge branch 'JAL-1199-Stk_writing' into rnaml_test	blob \| commitdiff \| diff to current
2013-02-13	Jim Procter	Merge branch 'jims_annotate3d_update' into menard_final...	blob \| commitdiff \| diff to current
2013-02-13	jprocter	fix merge conflicts for finess on JAL-1140 (introduced...	blob \| commitdiff \| diff to current
2013-02-06	jprocter	JAL-1265 basic support for parsing database accessions...	blob \| commitdiff \| diff to current
2013-02-05	jprocter	formatting	blob \| commitdiff \| diff to current
2012-12-12	Natasha	Output accession number for file in stockholm format	blob \| commitdiff \| diff to current
2012-12-07	jprocter	Anne reinstated general stockholm parser code but exten...	blob \| commitdiff \| diff to current
2012-12-07	jprocter	proxy commit for Anne Menard <menard.annec@gmail.com...	blob \| commitdiff \| diff to current
2012-12-04	jprocter	JAL-1140 - handled VARNA specific RNA exceptions within...	blob \| commitdiff \| diff to current
2012-11-23	Natasha	stockholm file output code developed by Natasha Sherstneva	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	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
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-14	Anne Menard	last version stay many bugs ..	blob \| commitdiff \| diff to current
2012-07-10	Anne Menard	v2	blob \| commitdiff \| diff to current
2012-07-05	Anne Menard	Add support RNAML format	blob \| commitdiff \| diff to current
2012-03-02	jprocter	(JAL-1052) make RNA secondary structure string parsing...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	JAL-878; Additional structures with a 'GR' tag in Stock...	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	Start merging of Laurens Code	blob \| commitdiff \| diff to current
2011-07-21	jprocter	ensure contents of hash is extended JAL-876	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-06-14	jprocter	patch for JAL-572	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-20	jprocter	Use 0f rather than NaN to specify non-valued annotation...	blob \| commitdiff \| diff to current
2008-01-29	jprocter	FileParse object can be re-used to read different files...	blob \| commitdiff \| diff to current
2008-01-22	jprocter	more efficient parsing of large files, do not create...	blob \| commitdiff \| diff to current
2008-01-21	jprocter	fix regex for annotation subtype to use non-whitespace...	blob \| commitdiff \| diff to current
2007-10-24	jprocter	add parsed PDB reference to sequences	blob \| commitdiff \| diff to current
2007-06-18	jprocter	1.1 methods	blob \| commitdiff \| diff to current
2007-06-04	jprocter	fix for 'RF' annotation tags and ensured parser is...	blob \| commitdiff \| diff to current
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