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[jalview.git] / src / jalview / commands / EditCommand.java

2023-11-03	James Procter	JAL-4090 JAL-1551 spotlessApply	blob \| commitdiff
2023-08-10	Ben Soares	JAL-629 Change all stdout and stderr output to use...	blob \| commitdiff \| diff to current
2022-03-08	Jim Procter	JAL-3438 spotless for 2.11.2.0	blob \| commitdiff \| diff to current
2021-09-21	Ben Soares	JAL-3691 automatic insertion of Locale.ROOT to toUpperC...	blob \| commitdiff \| diff to current
2019-07-16	gmungoc	JAL-3210 Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-06-18	Jim Procter	Merge branch 'bug/JAL-2830_editManglesDatasetSequence...	blob \| commitdiff \| diff to current
2019-03-13	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-03-01	gmungoc	Merge branch 'feature/JAL-1244stretchStatusMsg' into...	blob \| commitdiff \| diff to current
2019-03-01	gmungoc	JAL-3140 update for change to SequenceI api	blob \| commitdiff \| diff to current
2019-01-17	gmungoc	Merge branch 'develop' into Jalview-BH/JAL-3026-JAL...	blob \| commitdiff \| diff to current
2018-12-17	Jim Procter	JAL-2830 reinstate toUppercase for new dataset sequence...	blob \| commitdiff \| diff to current
2018-10-05	gmungoc	JAL-1244 improved status message for insert/delete gap	blob \| commitdiff \| diff to current
2018-06-22	gmungoc	JAL-3032 avoid assignments on the same line as synchronized	blob \| commitdiff \| diff to current
2018-01-18	gmungoc	JAL-2830 removed toUpperCase() from edited dataset...	blob \| commitdiff \| diff to current
2018-01-18	gmungoc	JAL-2541 cutWithFeatures_exhaustive test including...	blob \| commitdiff \| diff to current
2017-11-16	Jim Procter	JAL-2822 rejig new dataset after edit computation so...	blob \| commitdiff \| diff to current
2017-11-16	Jim Procter	JAL-2822 stash start/end before setSequence (which...	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	JAL-2830 failing test added for Replace	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	Merge branch 'bug/JAL-2829deleteCharsWithGaps' into	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	JAL-2541 add new dataset sequence to alignment dataset	blob \| commitdiff \| diff to current
2017-11-07	Jim Procter	JAL-2684 JAL-2822 avoid out of bounds exception if...	blob \| commitdiff \| diff to current
2017-11-07	Jim Procter	JAL-2822 JAL-2684 only create dataset seq for an edit...	blob \| commitdiff \| diff to current
2017-10-24	Jim Procter	JAL-2541 remove second unnecessary if	blob \| commitdiff \| diff to current
2017-10-24	Jim Procter	JAL-2541 only need to shift features for ‘internal...	blob \| commitdiff \| diff to current
2017-10-24	Jim Procter	JAL-2541 Cut ops always stash the old dataset sequence...	blob \| commitdiff \| diff to current
2017-10-24	Jim Procter	JAL-2541 don’t need to trash the sequence features...	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 test with seq start > 1 (and fix Undo bug...	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 it works!! it works!!!	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 clean unit test of cut/undo (ungapped sequence)	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 save/Undo only 'diffs' for features with Cut...	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 adjust end of contact feature spanning cut...	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 clearer comments (redo of lost commit f7967ad)	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 working Cut/Undo with feature relocation	blob \| commitdiff \| diff to current
2017-09-14	gmungoc	JAL-2541 revised cut with features (work in progress)	blob \| commitdiff \| diff to current
2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-06-01	gmungoc	JAL-2526 zapCursor() renamed sequenceChanged()	blob \| commitdiff \| diff to current
2017-05-30	gmungoc	JAL-2526 first draft of findIndex/findPosition with...	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2557 removal of Sequence.sequenceFeatures	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2050 make SequenceFeature.score final, adjust const...	blob \| commitdiff \| diff to current
2017-05-24	gmungoc	Merge branch 'bug/JAL-2541cutWithFeatures' into feature...	blob \| commitdiff \| diff to current
2017-05-24	gmungoc	JAL-2505 delete and readd modified feature after Cut...	blob \| commitdiff \| diff to current
2016-10-25	Jim Procter	JAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch	blob \| commitdiff \| diff to current
2015-10-16	Jim Procter	JAL-1925 update source version in license Release_2_9_0b2	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	blob \| commitdiff \| diff to current
2015-09-22	Jim Procter	Merge branch 'develop' into Release_2_9_0b1_Branch	blob \| commitdiff \| diff to current
2015-09-14	gmungoc	JAL-1880 handle sequence offsets properly when mapping...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...	blob \| commitdiff \| diff to current
2015-09-10	Jim Procter	JAL-1645 source formatting and organise imports	blob \| commitdiff \| diff to current
2015-03-26	gmungoc	Merge develop to Release_2_8_3_Branch	blob \| commitdiff \| diff to current
2015-03-06	Jim Procter	JAL-1683 replace year/version strings with tokens in...	blob \| commitdiff \| diff to current
2014-12-22	Jim Procter	Merge: 497958b 68dcaa7	blob \| commitdiff \| diff to current
2014-12-15	Jim Procter	JAL-1620 version bump and release notes	blob \| commitdiff \| diff to current
2014-11-25	gmungoc	JFAL-1594 fix Undo bug; enum EditCommand.Action; basic...	blob \| commitdiff \| diff to current
2014-10-30	Charles Ofoegbu	JAL-353 updated patch for undo successive remove redund...	blob \| commitdiff \| diff to current
2014-10-29	Charles Ofoegbu	JAL-353 updated patch for undo successive remove redund...	blob \| commitdiff \| diff to current
2014-10-28	Charles Ofoegbu	JAL-353 undo for successive removal of redundant sequen...	blob \| commitdiff \| diff to current
2014-06-06	Jim Procter	JAL-1517 fix copyright for 2.8.2	blob \| commitdiff \| diff to current
2014-06-05	Jim Procter	JAL-1517 update copyright to version 2.8.2	blob \| commitdiff \| diff to current
2014-05-22	Jim Procter	JAL-1503 update version in GPL header	blob \| commitdiff \| diff to current
2014-01-29	Jim Procter	JAL-1432 updated copyright notices	blob \| commitdiff \| diff to current
2012-10-22	jprocter	Jalview 2.8 Source Header	blob \| commitdiff \| diff to current
2012-10-03	jprocter	formatting	blob \| commitdiff \| diff to current
2012-08-05	jprocter	JAL-1131 - todos for later versions	blob \| commitdiff \| diff to current
2012-08-05	jprocter	JAL-1131 ensure new dataset sequence is created if...	blob \| commitdiff \| diff to current
2012-06-13	jprocter	javatidy	blob \| commitdiff \| diff to current
2012-06-12	jprocter	JAL-1115 refactor base collection for Alignment from...	blob \| commitdiff \| diff to current
2011-10-10	jprocter	update author list in license for (JAL-826)	blob \| commitdiff \| diff to current
2011-10-04	jprocter	Merge remote-tracking branch 'remotes/origin/2_5_1_rna_...	blob \| commitdiff \| diff to current
2011-09-27	jprocter	apply version 2.7 copyright	blob \| commitdiff \| diff to current
2011-07-25	janengelhardt	JAL-842; toy example to insert nucleotides in sequences...	blob \| commitdiff \| diff to current
2010-09-23	jprocter	apply jalview code style	blob \| commitdiff \| diff to current
2010-09-23	jprocter	Jalview 2.6 source licence	blob \| commitdiff \| diff to current
2010-04-30	jprocter	jalview 2.5 release banner	blob \| commitdiff \| diff to current
2009-06-08	jprocter	apply gpl development license	blob \| commitdiff \| diff to current
2008-09-04	jprocter	merge from 2_4_Release branch	blob \| commitdiff \| diff to current
2008-08-26	jprocter	bugfix todo for the 'edit sequence' command	blob \| commitdiff \| diff to current
2007-06-17	jprocter	recovery of identical dataset sequence object on undo...	blob \| commitdiff \| diff to current
2007-05-04	amwaterhouse	Annotations do not extend when full alignment is adjusted	blob \| commitdiff \| diff to current
2007-05-02	jprocter	refactored do and undo() method to take array of alignm...	blob \| commitdiff \| diff to current
2007-04-27	jprocter	bugfix for deleted annotation undo	blob \| commitdiff \| diff to current
2007-04-25	jprocter	AlignmentAnnotation: added annotation score attribute...	blob \| commitdiff \| diff to current
2007-04-19	jprocter	ensure edit command gapChar is updated and used for...	blob \| commitdiff \| diff to current
2007-04-19	amwaterhouse	REPLACE added to edit command	blob \| commitdiff \| diff to current
2007-04-18	amwaterhouse	Pad gaps when annotation editing	blob \| commitdiff \| diff to current
2007-04-17	jprocter	paste/cut now adds or removes associated AlignmentAnnot...	blob \| commitdiff \| diff to current
2007-02-07	amwaterhouse	Formatting	blob \| commitdiff \| diff to current
2007-02-05	amwaterhouse	Alignment editing columns 0 and 1 fixed	blob \| commitdiff \| diff to current
2007-02-05	amwaterhouse	Fixed bug in trim right annotation adjust	blob \| commitdiff \| diff to current
2007-02-05	amwaterhouse	Fixed bug in trim right annotation adjust	blob \| commitdiff \| diff to current
2007-02-02	amwaterhouse	check annotation size when cutting	blob \| commitdiff \| diff to current
2007-01-31	amwaterhouse	Adjust features when cutting and pasting	blob \| commitdiff \| diff to current
2007-01-26	amwaterhouse	Adjusts annotations for sequence edits	blob \| commitdiff \| diff to current
2007-01-25	amwaterhouse	Annotation adjustment moved to EditCommand	blob \| commitdiff \| diff to current
2007-01-24	amwaterhouse	This constructor is never called	blob \| commitdiff \| diff to current
2006-12-05	amwaterhouse	Sequence is char []	blob \| commitdiff \| diff to current
2006-11-30	amwaterhouse	char array replaces string for cuts	blob \| commitdiff \| diff to current
2006-11-21	amwaterhouse	Undo cut from end of alignment, padding on	blob \| commitdiff \| diff to current
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