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Merge branch 'releases/Release_2_11_3_Branch'
[jalview.git] / src / jalview / io / AlignFile.java
2023-04-19 Ben SoaresJAL-629 Now showing temp fac and secondary structure... commit | commitdiff
2023-02-03 Ben SoaresJAL-629 Fasta sequence id reading whitespace fix. Flexi... commit | commitdiff
2023-01-11 Ben SoaresJAL-629 refactoring TFType. Remove i18n identification... commit | commitdiff
2022-12-05 Ben SoaresJAL-629 implementation of --tempfac options commit | commitdiff
2022-01-17 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... commit | commitdiff
2022-01-17 Ben Soaresclose filehandles straight after parse, without setting... commit | commitdiff
2022-01-11 Ben SoaresJAL-3703 fix Gff3 shared InputStream with embedded... commit | commitdiff
2022-01-11 Ben Soaresclose filehandles straight after parse, without setting... commit | commitdiff
2018-06-28 hansonrJAL-3032 DND enabled; additional io changes for File... commit | commitdiff
2018-05-07 Jim ProcterJAL-2321 ensure default is ‘parseImmediately=true’ commit | commitdiff
2018-05-07 Jim ProcterJAL-2321 isParseImmediately() allows the parse() method... commit | commitdiff
2017-11-15 gmungocJAL-2835 spike updated with latest commit | commitdiff
2017-11-13 gmungocJAL-2176 removed unused Sequence.index commit | commitdiff
2017-10-03 gmungocJAL-2738 copy to spikes/mungo commit | commitdiff
2017-08-16 Jim ProcterJAL-2418 source formatting commit | commitdiff
2017-01-11 gmungocJAL-2344 separated AlignmentFileI into AlignmentFileRea... commit | commitdiff
2017-01-11 gmungocJAL-2344 addSequence() method added to support Groovy... commit | commitdiff
2016-11-24 gmungocFurther tweaks to get tests passing commit | commitdiff
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch commit | commitdiff
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... commit | commitdiff
2016-08-30 gmungocMerge branch 'develop' into features/filetypeEnum commit | commitdiff
2016-07-18 gmungocfileFormat enum wip changes commit | commitdiff
2016-07-11 gmungocfile format enum wip changes commit | commitdiff
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... commit | commitdiff
2016-02-19 gmungocJAL-1706 reverted setting start position as too confusi... commit | commitdiff
2016-01-21 gmungocJAL-1796 parse ensembl genomic coordinates to set start... commit | commitdiff
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 commit | commitdiff
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-1705_ensembl commit | commitdiff
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-06-28 Jim ProcterJAL-1421 todo: remove java.util.Vector from jalview... commit | commitdiff
2015-06-22 Jim ProcterJAL-1780 JAL-653 Format/AppletFormat import and export... commit | commitdiff
2015-06-19 Jim ProcterJAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfil... commit | commitdiff
2015-06-19 Jim ProcterJAL-1780 JAL-653 organise imports commit | commitdiff
2015-05-13 gmungocJAL-1712 fixes/tests for Castor binding of EMBL XML... commit | commitdiff
2015-05-11 tcofoegbuJAL-1641 cherry-picked changes into develop compatible... commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-10-15 Jim ProcterJAL-674 make transferAnnotation method static commit | commitdiff
2014-10-10 Jim ProcterJAL-674 change jalview.io.AlignFile to allow parsing... commit | commitdiff
2014-09-23 darolmarJAL-1355 commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2013-02-13 jprocterfix merge conflicts for finess on JAL-1140 (introduced... commit | commitdiff
2012-12-07 jprocterproxy commit for Anne Menard <menard.annec@gmail.com... commit | commitdiff
2012-12-04 jprocterJAL-1140 - IO classes should only raise generic IOExcep... commit | commitdiff
2012-11-15 jproctercomment on jalview.io.AlignFile architecture commit | commitdiff
2012-11-15 jprocterMerge branch 'develop' into menard commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-08-14 Anne Menardlast version stay many bugs .. commit | commitdiff
2012-07-10 Anne Menardv2 commit | commitdiff
2012-07-05 Anne MenardAdd support RNAML format commit | commitdiff
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065... commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_... commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2011-07-25 janengelhardt'Update to Covariaton color scheme' merge; JAL-580 commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2008-01-29 jprocterFileParse object can be re-used to read different files... commit | commitdiff
2007-05-08 amwaterhouseaddElement commit | commitdiff
2007-04-30 jprocteralignment properties and embedded newick strings can... commit | commitdiff
2007-04-27 jprocterparsers can generate alignment properties commit | commitdiff
2007-04-20 jprocterannotation and seqs vectors are protected members for... commit | commitdiff
2007-02-07 amwaterhouseFormatting commit | commitdiff
2007-01-30 amwaterhouseAny character non aa or nucleotide is a space commit | commitdiff
2007-01-18 amwaterhouseFile Parsing returns Alignments, not Sequence[] commit | commitdiff
2006-12-05 amwaterhouseSequence is char [] commit | commitdiff
2006-10-10 amwaterhouseaaIndex replaces aaHash commit | commitdiff
2006-08-21 amwaterhouseheader updated commit | commitdiff
2006-07-27 amwaterhouseremove unnecessary constructor commit | commitdiff
2006-02-08 amwaterhouseReport invalid chars commit | commitdiff
2005-12-06 amwaterhouseafter merge commit | commitdiff
2005-06-30 amwaterhouseFormatting changes commit | commitdiff
2005-06-08 amwaterhouseFormatted source commit | commitdiff
2005-06-08 amwaterhouseGPL license added commit | commitdiff
2004-11-02 amwaterhouseJalview Imported Sources start commit | commitdiff