JAL-2994 put ‘\’ first in character class clause of regex - otherwise doesn’t compile...
[jalview.git] / src / jalview / io / StockholmFile.java
2018-03-29 gmungocJAL-2907 bug fix redone on HMMER branch
2018-03-28 gmungocJAL-1265 output all dbrefs in Stockholm (+tests) (...
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-01 TZVanaaltenJAL-2629 manual curation of HMMs via reference annotati...
2017-08-25 TZVanaaltenJAL-2629 fix issue where Stockholm file would print...
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer
2017-08-17 TZVanaaltenJAL-2629 add documentation to previous work
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-14 TZVanaaltenJAL-2629 remove gap padding, and now has option to...
2017-08-14 TZVanaaltenJAL-2629 add padding for .sto annotations to fix issues...
2017-07-27 TZVanaaltenJAL-2629 implement hmmbuild
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-25 gmungocJAL-2050 make SequenceFeature.score final, adjust const...
2017-05-15 Jim ProcterJAL-2507 capitalisation for annotation lines generated...
2017-05-15 Jim ProcterJAL-2507 case insensitive recognition of annotation...
2017-05-15 Jim ProcterJAL-2535 quick hack to implement posterior probabilitie...
2017-05-11 Jim ProcterJAL-2509 JAL-2507 allow whitespace in GS annotation...
2017-05-09 Jim ProcterJAL-2509 extend set of brackets recognised by stockholm...
2017-05-09 Jim ProcterJAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...
2017-05-09 Jim ProcterJAL-2507 output secondary structure regardless of prese...
2017-05-04 Jim Procterfix for JAL-2509 - don’t replace all bracket types...
2017-05-04 Jim Procterfix for JAL-2507 - resolve stockholm per residue annota...
2016-11-25 gmungocMerge branch 'develop' into trialMerge
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum
2016-08-26 gmungocMerge branch 'develop' into bug/JAL-1841rnaSecStr
2016-08-24 gmungocJAL-1424 undo i18n of exception message
2016-08-12 gmungocJAL-1841 bug fixes / code tidy for rna SS rendering...
2016-07-18 gmungocfileFormat enum wip changes
2016-07-11 gmungocfile format enum wip changes
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-08-18 tcofoegbuJAL-1861 bugfix to allow parsing of stockholm files...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-02-19 gmungocJAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-12-01 Jim ProcterJAL-1199 JAL-1569 incremental patch allow non-standard...
2014-11-23 Jim ProcterJAL-1569 consistent handling of sequence and alignment...
2014-11-23 Jim ProcterJAL-1569 formatting
2014-11-23 Jim ProcterJAL-1569 preserve input ordering for stockholm files...
2014-11-21 Jim ProcterJAL-674 add RNA sequence associated annotation to align...
2014-11-21 Jim ProcterJAL-1569 formatting
2014-09-23 darolmarJAL-1355
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-06-07 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2
2013-06-07 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' into...
2013-02-14 Jim ProcterMerge branch 'JAL-1199-Stk_writing' into rnaml_test
2013-02-13 Jim ProcterMerge branch 'jims_annotate3d_update' into menard_final...
2013-02-13 jprocterfix merge conflicts for finess on JAL-1140 (introduced...
2013-02-06 jprocterJAL-1265 basic support for parsing database accessions...
2013-02-05 jprocterformatting
2012-12-12 NatashaOutput accession number for file in stockholm format
2012-12-07 jprocterAnne reinstated general stockholm parser code but exten...
2012-12-07 jprocterproxy commit for Anne Menard <menard.annec@gmail.com...
2012-12-04 jprocterJAL-1140 - handled VARNA specific RNA exceptions within...
2012-11-23 Natashastockholm file output code developed by Natasha Sherstneva
2012-11-15 jprocterMerge branch 'develop' into menard
2012-11-08 jproctertidy imports
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-08-14 Anne Menardlast version stay many bugs ..
2012-07-10 Anne Menardv2
2012-07-05 Anne MenardAdd support RNAML format
2012-03-02 jprocter(JAL-1052) make RNA secondary structure string parsing...
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_...
2011-09-27 jprocterapply version 2.7 copyright
2011-07-25 janengelhardtJAL-878; Additional structures with a 'GR' tag in Stock...
2011-07-25 janengelhardtStart merging of Laurens Code
2011-07-21 jprocterensure contents of hash is extended JAL-876
2010-09-23 jprocterapply jalview code style
2010-09-23 jprocterJalview 2.6 source licence
2010-06-14 jprocterpatch for JAL-572
2010-04-30 jprocterjalview 2.5 release banner
2009-06-08 jprocterapply gpl development license
2008-09-04 jproctermerge from 2_4_Release branch
2008-08-20 jprocterUse 0f rather than NaN to specify non-valued annotation...
2008-01-29 jprocterFileParse object can be re-used to read different files...
2008-01-22 jproctermore efficient parsing of large files, do not create...
2008-01-21 jprocterfix regex for annotation subtype to use non-whitespace...
2007-10-24 jprocteradd parsed PDB reference to sequences
2007-06-18 jprocter1.1 methods
2007-06-04 jprocterfix for 'RF' annotation tags and ensured parser is...
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