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Merge branch 'develop' into bug/JAL-4059_update_swingJS_for_JalviewJS_2_11_2_and_2_11_3
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
2023-04-19
Ben Soares
JAL-629 Now showing temp fac and secondary structure...
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2023-02-03
Ben Soares
JAL-629 Fasta sequence id reading whitespace fix. Flexi...
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2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
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diff to current
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
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diff to current
2022-01-17
Ben Soares
JAL-3703 fix Gff3 shared InputStream with embedded...
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diff to current
2022-01-17
Ben Soares
close filehandles straight after parse, without setting...
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diff to current
2022-01-11
Ben Soares
JAL-3703 fix Gff3 shared InputStream with embedded...
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diff to current
2022-01-11
Ben Soares
close filehandles straight after parse, without setting...
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diff to current
2018-06-28
hansonr
JAL-3032 DND enabled; additional io changes for File...
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2018-05-07
Jim Procter
JAL-2321 ensure default is ‘parseImmediately=true’
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diff to current
2018-05-07
Jim Procter
JAL-2321 isParseImmediately() allows the parse() method...
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diff to current
2017-11-15
gmungoc
JAL-2835 spike updated with latest
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2017-11-13
gmungoc
JAL-2176 removed unused Sequence.index
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diff to current
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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diff to current
2017-08-16
Jim Procter
JAL-2418 source formatting
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2017-01-11
gmungoc
JAL-2344 separated AlignmentFileI into AlignmentFileRea...
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diff to current
2017-01-11
gmungoc
JAL-2344 addSequence() method added to support Groovy...
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2016-11-24
gmungoc
Further tweaks to get tests passing
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2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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diff to current
2016-08-30
gmungoc
Merge branch 'develop' into features/filetypeEnum
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2016-07-18
gmungoc
fileFormat enum wip changes
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diff to current
2016-07-11
gmungoc
file format enum wip changes
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diff to current
2016-07-08
tcofoegbu
JAL-1919 Fixed failing tests, enabled HETATM processing...
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diff to current
2016-02-19
gmungoc
JAL-1706 reverted setting start position as too confusi...
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2016-01-21
gmungoc
JAL-1796 parse ensembl genomic coordinates to set start...
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2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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2015-10-15
Jim Procter
Merge branch 'develop' into features/JAL-1705_ensembl
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2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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diff to current
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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2015-06-28
Jim Procter
JAL-1421 todo: remove java.util.Vector from jalview...
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2015-06-22
Jim Procter
JAL-1780 JAL-653 Format/AppletFormat import and export...
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2015-06-19
Jim Procter
JAL-653 JAL-1780 refactor getGroups so HTMLfile/JSONfil...
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diff to current
2015-06-19
Jim Procter
JAL-1780 JAL-653 organise imports
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2015-05-13
gmungoc
JAL-1712 fixes/tests for Castor binding of EMBL XML...
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2015-05-11
tcofoegbu
JAL-1641 cherry-picked changes into develop compatible...
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2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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2014-10-15
Jim Procter
JAL-674 make transferAnnotation method static
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2014-10-10
Jim Procter
JAL-674 change jalview.io.AlignFile to allow parsing...
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2014-09-23
darolmar
JAL-1355
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2014-06-06
Jim Procter
JAL-1517 source formatting
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commitdiff
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2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
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2014-06-05
Jim Procter
Merge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
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2014-05-22
Jim Procter
JAL-1503 update version in GPL header
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2014-02-18
Jim Procter
Merge branch 'JAL-1445' into develop
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2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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2013-02-13
jprocter
fix merge conflicts for finess on JAL-1140 (introduced...
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2012-12-07
jprocter
proxy commit for Anne Menard <menard.annec@gmail.com...
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2012-12-04
jprocter
JAL-1140 - IO classes should only raise generic IOExcep...
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2012-11-15
jprocter
comment on jalview.io.AlignFile architecture
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diff to current
2012-11-15
jprocter
Merge branch 'develop' into menard
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2012-10-22
jprocter
Jalview 2.8 Source Header
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2012-10-03
jprocter
formatting
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diff to current
2012-08-14
Anne Menard
last version stay many bugs ..
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2012-07-10
Anne Menard
v2
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2012-07-05
Anne Menard
Add support RNAML format
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diff to current
2012-05-22
jprocter
Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...
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diff to current
2011-10-10
jprocter
update author list in license for (JAL-826)
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diff to current
2011-10-04
jprocter
Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...
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diff to current
2011-09-27
jprocter
apply version 2.7 copyright
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commitdiff
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diff to current
2011-07-25
janengelhardt
'Update to Covariaton color scheme' merge; JAL-580
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commitdiff
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2010-09-23
jprocter
Jalview 2.6 source licence
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commitdiff
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2010-04-30
jprocter
jalview 2.5 release banner
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2009-06-08
jprocter
apply gpl development license
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2008-09-04
jprocter
merge from 2_4_Release branch
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diff to current
2008-01-29
jprocter
FileParse object can be re-used to read different files...
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diff to current
2007-05-08
amwaterhouse
addElement
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diff to current
2007-04-30
jprocter
alignment properties and embedded newick strings can...
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diff to current
2007-04-27
jprocter
parsers can generate alignment properties
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diff to current
2007-04-20
jprocter
annotation and seqs vectors are protected members for...
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diff to current
2007-02-07
amwaterhouse
Formatting
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diff to current
2007-01-30
amwaterhouse
Any character non aa or nucleotide is a space
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diff to current
2007-01-18
amwaterhouse
File Parsing returns Alignments, not Sequence[]
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diff to current
2006-12-05
amwaterhouse
Sequence is char []
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diff to current
2006-10-10
amwaterhouse
aaIndex replaces aaHash
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2006-08-21
amwaterhouse
header updated
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2006-07-27
amwaterhouse
remove unnecessary constructor
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2006-02-08
amwaterhouse
Report invalid chars
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2005-12-06
amwaterhouse
after merge
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commitdiff
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diff to current
2005-06-30
amwaterhouse
Formatting changes
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2005-06-08
amwaterhouse
Formatted source
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diff to current
2005-06-08
amwaterhouse
GPL license added
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2004-11-02
amwaterhouse
Jalview Imported Sources
start
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