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Merge branch 'develop' into bug/JAL-2314
[jalview.git]
/
src
/
jalview
/
datamodel
/
Alignment.java
2017-03-31
gmungoc
JAL-2405 additional checks for circular reference in...
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commitdiff
2017-03-17
kiramt
JAL-2437 Synchronization corrections and unit tests
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2017-03-10
kiramt
JAL-2437 Fixed reordering of sequences when hiding...
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2017-03-07
kiramt
JAL-2388 Missed commit
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2017-03-03
kiramt
JAL-2388 Initial removal of hidden cols/seqs out of...
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2017-01-06
gmungoc
Merge branch 'develop' into features/JAL-2360colourSche...
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2017-01-05
gmungoc
JAL-2374 fix popup out by one and multiple groups bugs
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2016-12-14
gmungoc
JAL-2360 added check for null annotations array
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2016-12-12
gmungoc
JAL-2360 simplify nucleotide flag, remove setter
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2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
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2016-10-28
Jim Procter
JAL-966 JAL-1738 JAL-345 interfaces for SearchResults...
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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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2016-10-04
gmungoc
JAL-2232 JAL-2154 update dbrefs to newly created datase...
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2016-09-22
gmungoc
JAL-2216 finalize() refactored so not called programmat...
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2016-08-30
gmungoc
Merge branch 'develop' into features/filetypeEnum
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2016-08-22
Jim Procter
JAL-2154 always check dataset sequence for sequence...
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2016-08-19
Jim Procter
JAL-2154 refactor setSequenceAt to replaceSequenceAt...
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2016-08-07
Jim Procter
JAL-2154 add in missing class for createDatasetAlignmen...
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2016-08-04
Jim Procter
JAL-2154 make sure all sequences referenced via DBRefEn...
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2016-07-18
Jim Procter
JAL-2121 cleanup TODO
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2016-07-14
Jim Procter
JAL-1115 change implementation to avoid possibility...
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2016-07-14
Jim Procter
JAL-1270 test coverage TODO Alignment.append(AlignmentI)
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2016-07-12
Jim Procter
JAL-2110 javadoc and TODO re shortcomings of implementation
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2016-07-06
gmungoc
JAL-2110 ensuring mapped dbrefs between protein and cds
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2016-07-04
gmungoc
JAL-2110 unused method removed
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2016-06-20
Jim Procter
JAL-2110 copy alcodonframes only if copy constructor...
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2016-06-19
Jim Procter
JAL-2110 JAL-2131 JAL-1765 remove reference to jalview...
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2016-06-16
Jim Procter
JAL-2110 todo - select mappings involving sequences...
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2016-05-31
gmungoc
JAL-2023 adjustments to mappings added for split frame...
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2016-04-11
tcofoegbu
JAL-2054 Renamed getStartEnd in AlignFrame to getVisibl...
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2016-04-01
gmungoc
JAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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2015-12-22
gmungoc
JAL-653 realise virtual mappings and align when adding...
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2015-12-03
gmungoc
JAL-653 mappings always reside on the dataset alignment...
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2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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2015-10-08
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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2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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2015-07-30
tcofoegbu
JAL-1443 modified exception notifications
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2015-07-21
tcofoegbu
JAL-1443 bugfix to prevent loading of unidentifiable...
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2015-04-13
gmungoc
JAL-1693 make exon alignment for get-xref splitframe...
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2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
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2015-01-09
Jim Procter
Merge branch 'JAL-1372_referenceseq' into feature_29...
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2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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2014-11-28
gmungoc
JAL-1610 check reference annotations against alignment...
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2014-11-17
Jim Procter
formatting
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2014-11-17
Jim Procter
JAL-1587 JAL-407 instrument setDataset to add dataset...
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2014-10-10
gmungoc
JAL-1264 reverted (removed added method)
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2014-10-08
gmungoc
Merge branch 'Release_2_8_2_Branch' into
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2014-10-07
gmungoc
JAL-1264 wip
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2014-09-27
darolmar
JAL-1355
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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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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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2014-05-22
Jim Procter
JAL-1503 update version in GPL header
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2014-05-02
Jim Procter
Merge branch 'Release_2_8_1_Branch' into JAL-1372_refer...
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2014-05-01
Jim Procter
JAL-1492 JAL-1397 make AnnotatedCollectionI context...
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2014-01-29
Jim Procter
JAL-1432 updated copyright notices
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2013-10-11
Jim Procter
JAL-1114 promote start/end attributes to gettable field...
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2013-08-30
Jim Procter
JAL-1367 promote the existing representative sequence...
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2013-06-23
Jim Procter
JAL-1230 proxy method for synchronising internal Alignm...
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2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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diff to current
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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diff to current
2012-10-22
jprocter
Jalview 2.8 Source Header
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2012-10-03
jprocter
formatting
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2012-07-03
jprocter
JAL-961 allow calcId to be specified independently...
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2012-06-13
jprocter
javatidy
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2012-06-12
jprocter
JAL-1115 refactor reordering code operating directly...
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2012-06-12
jprocter
JAL-1115 refactor base collection for Alignment from...
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2012-05-30
jprocter
JAL-1114 - refactor methods handling Vectors and Hashta...
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2012-05-23
jprocter
JAL-961 - annotatable datamodel objects can be queried...
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2012-05-22
jprocter
Merge remote-tracking branch 'origin/Tcoffee_JAL-1065...
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2011-10-10
jprocter
update author list in license for (JAL-826)
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2011-10-04
jprocter
Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...
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2011-09-27
jprocter
apply version 2.7 copyright
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2011-08-15
janengelhardt
JAL-891; Sorting of Structure logo implemented; bug...
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2011-08-11
janengelhardt
JAL-885; hasRNAStructure method was introduced to Align...
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2011-04-21
jprocter
allow an alignment annotation row to be removed and...
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2010-11-12
jprocter
patch for JAL-700
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2010-09-23
jprocter
apply jalview code style
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2010-09-23
jprocter
Jalview 2.6 source licence
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2010-04-30
jprocter
jalview 2.5 release banner
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2010-04-29
jprocter
isAligned assertion (bug 0008144)
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2010-04-28
jprocter
group/annotation association housekeeping
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2009-07-24
jprocter
implement new insert annotation row method and ensure...
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2009-06-08
jprocter
apply gpl development license
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2008-12-19
jprocter
left and right justify method
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2008-12-05
jprocter
support for multiple accession retrieval from a databas...
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2008-11-12
jprocter
javadoc and new method to get alignment sequence index...
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2008-09-04
jprocter
merge from 2_4_Release branch
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2008-07-18
jprocter
allow findSeq to begin *after* a given sequence in...
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diff to current
2007-11-30
jprocter
case invariant matching of seqeunce feature to sequence...
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2007-08-30
jprocter
moved dataset sequence creation onto sequence method
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2007-08-24
jprocter
dataset alignments have a reference count which must...
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diff to current
2007-07-13
jprocter
mapping bug fixes
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2007-06-17
jprocter
AlignedCodonFrame holds mapping information between...
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