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JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog
[jalview.git]
/
src
/
jalview
/
io
/
StockholmFile.java
2020-12-14
Jim Procter
Merge branch 'Jalview-JS/develop' into merge_js_develop
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2020-06-02
BobHanson
JAL-3446 from JAL-3253-applet StockholmFile updated...
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diff to current
2020-06-01
BobHanson
JAL-3626 Regex optimization from JAL-3253-applet; also...
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diff to current
2020-05-18
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
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diff to current
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
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diff to current
2020-04-23
Jim Procter
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_...
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2020-02-18
Jim Procter
JAL-3529 attempt to guess database for a sequence’s...
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diff to current
2020-02-14
Jim Procter
JAL-3532 TODO comment
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diff to current
2020-02-14
Jim Procter
JAL-3529 preferentially output source dbrefs or princip...
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diff to current
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
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diff to current
2019-06-05
tva
JAL-3285 add methods and small changes to StockholmFile...
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diff to current
2019-06-04
Jim Procter
Merge branch 'develop' into developtomchmmer
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diff to current
2019-01-26
hansonr
Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...
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diff to current
2018-08-03
Ben Soares
JAL-3061
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diff to current
2018-08-02
Ben Soares
JAL-3053
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diff to current
2018-07-30
bsoares
Fixed bug ignoring "alpha" extended braces in RNA SS...
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diff to current
2018-03-29
gmungoc
JAL-2907 bug fix redone on HMMER branch
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2018-03-28
gmungoc
JAL-1265 output all dbrefs in Stockholm (+tests) (...
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2018-02-20
gmungoc
Merge branch 'develop' into features/mchmmer
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2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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diff to current
2017-09-01
TZVanaalten
JAL-2629 manual curation of HMMs via reference annotati...
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diff to current
2017-08-25
TZVanaalten
JAL-2629 fix issue where Stockholm file would print...
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2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
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2017-08-18
TZVanaalten
Merge branch 'develop' into features/hmmer
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2017-08-17
TZVanaalten
JAL-2629 add documentation to previous work
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diff to current
2017-08-16
Jim Procter
JAL-2418 source formatting
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diff to current
2017-08-14
TZVanaalten
JAL-2629 remove gap padding, and now has option to...
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diff to current
2017-08-14
TZVanaalten
JAL-2629 add padding for .sto annotations to fix issues...
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2017-07-27
TZVanaalten
JAL-2629 implement hmmbuild
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diff to current
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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2017-06-09
gmungoc
JAL-2446 merged to spike branch
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diff to current
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
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diff to current
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
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diff to current
2017-05-15
Jim Procter
JAL-2507 capitalisation for annotation lines generated...
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commitdiff
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diff to current
2017-05-15
Jim Procter
JAL-2507 case insensitive recognition of annotation...
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diff to current
2017-05-15
Jim Procter
JAL-2535 quick hack to implement posterior probabilitie...
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diff to current
2017-05-11
Jim Procter
JAL-2509 JAL-2507 allow whitespace in GS annotation...
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diff to current
2017-05-09
Jim Procter
JAL-2509 extend set of brackets recognised by stockholm...
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diff to current
2017-05-09
Jim Procter
JAL-2507 unpaired RNA marked as ‘ ‘ in Stockholm SS...
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diff to current
2017-05-09
Jim Procter
JAL-2507 output secondary structure regardless of prese...
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diff to current
2017-05-04
Jim Procter
fix for JAL-2509 - don’t replace all bracket types...
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diff to current
2017-05-04
Jim Procter
fix for JAL-2507 - resolve stockholm per residue annota...
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2016-11-25
gmungoc
Merge branch 'develop' into trialMerge
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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
2016-10-05
Jim Procter
JAL-2189 source formatting
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2016-08-30
gmungoc
Merge branch 'develop' into features/filetypeEnum
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2016-08-26
gmungoc
Merge branch 'develop' into bug/JAL-1841rnaSecStr
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2016-08-24
gmungoc
JAL-1424 undo i18n of exception message
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diff to current
2016-08-12
gmungoc
JAL-1841 bug fixes / code tidy for rna SS rendering...
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commitdiff
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diff to current
2016-07-18
gmungoc
fileFormat enum wip changes
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commitdiff
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diff to current
2016-07-11
gmungoc
file format enum wip changes
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diff to current
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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diff to current
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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diff to current
2015-08-18
tcofoegbu
JAL-1861 bugfix to allow parsing of stockholm files...
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diff to current
2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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diff to current
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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2015-02-19
gmungoc
JAL-1665 refactored Sequence.getSequenceFeatures
features/sequenceFeatureRefactor
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2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
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diff to current
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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2014-12-01
Jim Procter
JAL-1199 JAL-1569 incremental patch allow non-standard...
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diff to current
2014-11-23
Jim Procter
JAL-1569 consistent handling of sequence and alignment...
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commitdiff
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diff to current
2014-11-23
Jim Procter
JAL-1569 formatting
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diff to current
2014-11-23
Jim Procter
JAL-1569 preserve input ordering for stockholm files...
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diff to current
2014-11-21
Jim Procter
JAL-674 add RNA sequence associated annotation to align...
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commitdiff
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diff to current
2014-11-21
Jim Procter
JAL-1569 formatting
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diff to current
2014-09-23
darolmar
JAL-1355
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commitdiff
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diff to current
2014-06-06
Jim Procter
JAL-1517 source formatting
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commitdiff
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diff to current
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
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commitdiff
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diff to current
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
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diff to current
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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2013-06-07
Jim Procter
Merge branch 'develop' into develop_m2_8_1_2
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2013-06-07
Jim Procter
Merge branch 'JAL-1161_optimisingAnnotationPanel' into...
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2013-02-14
Jim Procter
Merge branch 'JAL-1199-Stk_writing' into rnaml_test
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diff to current
2013-02-13
Jim Procter
Merge branch 'jims_annotate3d_update' into menard_final...
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diff to current
2013-02-13
jprocter
fix merge conflicts for finess on JAL-1140 (introduced...
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diff to current
2013-02-06
jprocter
JAL-1265 basic support for parsing database accessions...
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commitdiff
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diff to current
2013-02-05
jprocter
formatting
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diff to current
2012-12-12
Natasha
Output accession number for file in stockholm format
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2012-12-07
jprocter
Anne reinstated general stockholm parser code but exten...
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diff to current
2012-12-07
jprocter
proxy commit for Anne Menard <menard.annec@gmail.com...
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diff to current
2012-12-04
jprocter
JAL-1140 - handled VARNA specific RNA exceptions within...
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2012-11-23
Natasha
stockholm file output code developed by Natasha Sherstneva
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2012-11-15
jprocter
Merge branch 'develop' into menard
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diff to current
2012-11-08
jprocter
tidy imports
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commitdiff
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diff to current
2012-10-22
jprocter
Jalview 2.8 Source Header
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diff to current
2012-10-03
jprocter
formatting
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commitdiff
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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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commitdiff
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diff to current
2012-07-05
Anne Menard
Add support RNAML format
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diff to current
2012-03-02
jprocter
(JAL-1052) make RNA secondary structure string parsing...
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commitdiff
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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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2011-09-27
jprocter
apply version 2.7 copyright
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