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JAL-4059 Converting Pattern/Matcher methods that are possibly incompatible with JS...
[jalview.git]
/
src
/
jalview
/
commands
/
2023-08-10
Ben Soares
JAL-629 Change all stdout and stderr output to use...
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-06-18
Jim Procter
Merge branch 'bug/JAL-2830_editManglesDatasetSequence...
tree
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commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'feature/JAL-1244stretchStatusMsg' into...
tree
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commitdiff
2019-03-01
gmungoc
JAL-3140 update for change to SequenceI api
tree
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commitdiff
2019-01-17
gmungoc
Merge branch 'develop' into Jalview-BH/JAL-3026-JAL...
tree
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commitdiff
2018-12-17
Jim Procter
JAL-2830 reinstate toUppercase for new dataset sequence...
tree
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commitdiff
2018-10-05
gmungoc
JAL-1244 improved status message for insert/delete gap
tree
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commitdiff
2018-06-22
gmungoc
JAL-3032 avoid assignments on the same line as synchronized
tree
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commitdiff
2018-01-18
gmungoc
JAL-2830 removed toUpperCase() from edited dataset...
tree
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commitdiff
2018-01-18
gmungoc
JAL-2541 cutWithFeatures_exhaustive test including...
tree
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commitdiff
2017-11-16
Jim Procter
JAL-2822 rejig new dataset after edit computation so...
tree
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commitdiff
2017-11-16
Jim Procter
JAL-2822 stash start/end before setSequence (which...
tree
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commitdiff
2017-11-13
gmungoc
JAL-2830 failing test added for Replace
tree
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commitdiff
2017-11-13
gmungoc
Merge branch 'bug/JAL-2829deleteCharsWithGaps' into
tree
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commitdiff
2017-11-13
gmungoc
JAL-2541 add new dataset sequence to alignment dataset
tree
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commitdiff
2017-11-07
Jim Procter
JAL-2684 JAL-2822 avoid out of bounds exception if...
tree
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commitdiff
2017-11-07
Jim Procter
JAL-2822 JAL-2684 only create dataset seq for an edit...
tree
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commitdiff
2017-10-24
Jim Procter
JAL-2541 remove second unnecessary if
tree
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commitdiff
2017-10-24
Jim Procter
JAL-2541 only need to shift features for ‘internal...
tree
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commitdiff
2017-10-24
Jim Procter
JAL-2541 Cut ops always stash the old dataset sequence...
tree
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commitdiff
2017-10-24
Jim Procter
JAL-2541 don’t need to trash the sequence features...
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 test with seq start > 1 (and fix Undo bug...
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 it works!! it works!!!
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 clean unit test of cut/undo (ungapped sequence)
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 save/Undo only 'diffs' for features with Cut...
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 adjust end of contact feature spanning cut...
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 clearer comments (redo of lost commit f7967ad)
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 working Cut/Undo with feature relocation
tree
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commitdiff
2017-09-14
gmungoc
JAL-2541 revised cut with features (work in progress)
tree
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commitdiff
2017-09-05
Jim Procter
Merge branch 'master' into portforward/JAL-2675_2102b1t...
tree
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commitdiff
2017-09-04
Jim Procter
JAL-2675 source license
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
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commitdiff
2017-06-01
gmungoc
JAL-2526 zapCursor() renamed sequenceChanged()
tree
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commitdiff
2017-05-30
gmungoc
JAL-2526 first draft of findIndex/findPosition with...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
tree
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
tree
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commitdiff
2017-05-24
gmungoc
Merge branch 'bug/JAL-2541cutWithFeatures' into feature...
tree
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commitdiff
2017-05-24
gmungoc
JAL-2505 delete and readd modified feature after Cut...
tree
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commitdiff
2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
tree
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commitdiff
2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
tree
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commitdiff
2016-10-05
Jim Procter
JAL-2189 source formatting
tree
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commitdiff
2015-10-22
gmungoc
JAL-1932 TrimRegionCommand bug fix, tests and purge...
tree
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commitdiff
2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
tree
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commitdiff
2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
tree
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commitdiff
2015-09-22
Jim Procter
Merge branch 'develop' into Release_2_9_0b1_Branch
tree
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commitdiff
2015-09-14
gmungoc
JAL-1880 handle sequence offsets properly when mapping...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
tree
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commitdiff
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
tree
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commitdiff
2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
tree
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commitdiff
2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
tree
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commitdiff
2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
tree
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commitdiff
2014-12-15
Jim Procter
JAL-1620 version bump and release notes
tree
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commitdiff
2014-11-25
gmungoc
JFAL-1594 fix Undo bug; enum EditCommand.Action; basic...
tree
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commitdiff
2014-10-30
Charles Ofoegbu
JAL-353 updated patch for undo successive remove redund...
tree
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commitdiff
2014-10-29
Charles Ofoegbu
JAL-353 updated patch for undo successive remove redund...
tree
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commitdiff
2014-10-28
Charles Ofoegbu
JAL-353 undo for successive removal of redundant sequen...
tree
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commitdiff
2014-06-06
Jim Procter
JAL-1517 fix copyright for 2.8.2
tree
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commitdiff
2014-06-05
Jim Procter
JAL-1517 update copyright to version 2.8.2
tree
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commitdiff
2014-05-22
Jim Procter
JAL-1503 update version in GPL header
tree
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commitdiff
2014-01-29
Jim Procter
JAL-1432 updated copyright notices
tree
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commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
tree
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commitdiff
2012-10-03
jprocter
formatting
tree
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commitdiff
2012-08-05
jprocter
JAL-1131 - todos for later versions
tree
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commitdiff
2012-08-05
jprocter
JAL-1131 ensure new dataset sequence is created if...
tree
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commitdiff
2012-06-13
jprocter
javatidy
tree
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commitdiff
2012-06-12
jprocter
JAL-1115 refactor base collection for Alignment from...
tree
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commitdiff
2011-10-10
jprocter
update author list in license for (JAL-826)
tree
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commitdiff
2011-10-04
jprocter
Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...
tree
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commitdiff
2011-09-27
jprocter
apply version 2.7 copyright
tree
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commitdiff
2011-07-25
janengelhardt
JAL-842; toy example to insert nucleotides in sequences...
tree
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commitdiff
2010-09-23
jprocter
apply jalview code style
tree
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commitdiff
2010-09-23
jprocter
Jalview 2.6 source licence
tree
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commitdiff
2010-04-30
jprocter
jalview 2.5 release banner
tree
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commitdiff
2009-06-08
jprocter
apply gpl development license
tree
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commitdiff
2008-09-04
jprocter
merge from 2_4_Release branch
tree
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commitdiff
2008-08-26
jprocter
bugfix todo for the 'edit sequence' command
tree
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commitdiff
2007-06-17
jprocter
recovery of identical dataset sequence object on undo...
tree
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commitdiff
2007-05-04
amwaterhouse
Annotations do not extend when full alignment is adjusted
tree
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commitdiff
2007-05-02
jprocter
refactored do and undo() method to take array of alignm...
tree
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commitdiff
2007-04-27
jprocter
bugfix for deleted annotation undo
tree
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commitdiff
2007-04-25
jprocter
AlignmentAnnotation: added annotation score attribute...
tree
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commitdiff
2007-04-19
jprocter
ensure edit command gapChar is updated and used for...
tree
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commitdiff
2007-04-19
amwaterhouse
REPLACE added to edit command
tree
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commitdiff
2007-04-18
amwaterhouse
Pad gaps when annotation editing
tree
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commitdiff
2007-04-17
jprocter
paste/cut now adds or removes associated AlignmentAnnot...
tree
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commitdiff
2007-02-27
amwaterhouse
jmol added
tree
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commitdiff
2007-02-07
amwaterhouse
Formatting
tree
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commitdiff
2007-02-05
amwaterhouse
Alignment editing columns 0 and 1 fixed
tree
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commitdiff
2007-02-05
amwaterhouse
Fixed bug in trim right annotation adjust
tree
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commitdiff
2007-02-05
amwaterhouse
Fixed bug in trim right annotation adjust
tree
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commitdiff
2007-02-02
amwaterhouse
getWidth -1 for trim right
tree
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commitdiff
2007-02-02
amwaterhouse
check annotation size when cutting
tree
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commitdiff
2007-01-31
amwaterhouse
Adjust features when cutting and pasting
tree
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commitdiff
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