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

2018-06-28	hansonr	JAL-3032 DND enabled; additional io changes for File...	blob \| commitdiff
2018-05-07	Jim Procter	JAL-2321 ensure default is ‘parseImmediately=true’	blob \| commitdiff \| diff to current
2018-05-07	Jim Procter	JAL-2321 isParseImmediately() allows the parse() method...	blob \| commitdiff \| diff to current
2017-11-15	gmungoc	JAL-2835 spike updated with latest	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	JAL-2176 removed unused Sequence.index	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-01-11	gmungoc	JAL-2344 separated AlignmentFileI into AlignmentFileRea...	blob \| commitdiff \| diff to current
2017-01-11	gmungoc	JAL-2344 addSequence() method added to support Groovy...	blob \| commitdiff \| diff to current
2016-11-24	gmungoc	Further tweaks to get tests passing	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
2016-08-30	gmungoc	Merge branch 'develop' into features/filetypeEnum	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
2016-07-08	tcofoegbu	JAL-1919 Fixed failing tests, enabled HETATM processing...	blob \| commitdiff \| diff to current
2016-02-19	gmungoc	JAL-1706 reverted setting start position as too confusi...	blob \| commitdiff \| diff to current
2016-01-21	gmungoc	JAL-1796 parse ensembl genomic coordinates to set start...	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	Jim Procter	Merge branch 'develop' into features/JAL-1705_ensembl	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
2015-06-28	Jim Procter	JAL-1421 todo: remove java.util.Vector from jalview...	blob \| commitdiff \| diff to current
2015-06-22	Jim Procter	JAL-1780 JAL-653 Format/AppletFormat import and export...	blob \| commitdiff \| diff to current
2015-06-19	Jim Procter	JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfil...	blob \| commitdiff \| diff to current
2015-06-19	Jim Procter	JAL-1780 JAL-653 organise imports	blob \| commitdiff \| diff to current
2015-05-13	gmungoc	JAL-1712 fixes/tests for Castor binding of EMBL XML...	blob \| commitdiff \| diff to current
2015-05-11	tcofoegbu	JAL-1641 cherry-picked changes into develop compatible...	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
2014-10-15	Jim Procter	JAL-674 make transferAnnotation method static	blob \| commitdiff \| diff to current
2014-10-10	Jim Procter	JAL-674 change jalview.io.AlignFile to allow parsing...	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
2013-02-13	jprocter	fix merge conflicts for finess on JAL-1140 (introduced...	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 - IO classes should only raise generic IOExcep...	blob \| commitdiff \| diff to current
2012-11-15	jprocter	comment on jalview.io.AlignFile architecture	blob \| commitdiff \| diff to current
2012-11-15	jprocter	Merge branch 'develop' into menard	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
2012-05-22	jprocter	Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...	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	'Update to Covariaton color scheme' merge; JAL-580	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
2009-06-08	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
2008-01-29	jprocter	FileParse object can be re-used to read different files...	blob \| commitdiff \| diff to current
2007-05-08	amwaterhouse	addElement	blob \| commitdiff \| diff to current
2007-04-30	jprocter	alignment properties and embedded newick strings can...	blob \| commitdiff \| diff to current
2007-04-27	jprocter	parsers can generate alignment properties	blob \| commitdiff \| diff to current
2007-04-20	jprocter	annotation and seqs vectors are protected members for...	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-01-30	amwaterhouse	Any character non aa or nucleotide is a space	blob \| commitdiff \| diff to current
2007-01-18	amwaterhouse	File Parsing returns Alignments, not Sequence[]	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	Sequence is char []	blob \| commitdiff \| diff to current
2006-10-10	amwaterhouse	aaIndex replaces aaHash	blob \| commitdiff \| diff to current
2006-08-21	amwaterhouse	header updated	blob \| commitdiff \| diff to current
2006-07-27	amwaterhouse	remove unnecessary constructor	blob \| commitdiff \| diff to current
2006-02-08	amwaterhouse	Report invalid chars	blob \| commitdiff \| diff to current
2005-12-06	amwaterhouse	after merge	blob \| commitdiff \| diff to current
2005-06-30	amwaterhouse	Formatting changes	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	Formatted source	blob \| commitdiff \| diff to current
2005-06-08	amwaterhouse	GPL license added	blob \| commitdiff \| diff to current
2004-11-02	amwaterhouse	Jalview Imported Sources start	blob \| commitdiff \| diff to current

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