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[jalview.git] / src / jalview / datamodel / Sequence.java

2017-08-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList	blob \| commitdiff
2017-08-16	Jim Procter	JAL-2418 source formatting	blob \| commitdiff \| diff to current
2017-06-24	gmungoc	JAL-2547 fix case of gap followed by enclosing contact...	blob \| commitdiff \| diff to current
2017-06-22	gmungoc	JAL-2481 JAL-2593 JAL-2526 further optimisation of...	blob \| commitdiff \| diff to current
2017-06-20	gmungoc	JAL-2526 don't retain lastColumnPosition from an invali...	blob \| commitdiff \| diff to current
2017-06-14	gmungoc	JAL-2598 Sequence.getSequence return a copy of the...	blob \| commitdiff \| diff to current
2017-06-08	gmungoc	JAL-2526 correct boundary conditions for sequence left...	blob \| commitdiff \| diff to current
2017-06-08	gmungoc	JAL-2526 cache first/last residue column positions...	blob \| commitdiff \| diff to current
2017-06-06	gmungoc	JAL-2526 less stringent test for invalid cursor	blob \| commitdiff \| diff to current
2017-06-05	gmungoc	Merge branch 'features/JAL-2526sequenceCursor' into	blob \| commitdiff \| diff to current
2017-06-05	gmungoc	Merge branch 'features/JAL-2446NCList' into	blob \| commitdiff \| diff to current
2017-06-05	gmungoc	Merge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor	blob \| commitdiff \| diff to current
2017-06-05	gmungoc	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-06-04	Jim Procter	JAL-2291 bug fix - BitSet.set is [start,end+1)	blob \| commitdiff \| diff to current
2017-06-04	Jim Procter	JAL-2291 SequenceI.getInsertionsAsBits for convenient...	blob \| commitdiff \| diff to current
2017-06-02	gmungoc	JAL-2526 additional tests for findPosition with/without...	blob \| commitdiff \| diff to current
2017-06-01	gmungoc	JAL-2526 additional calls to sequenceChanged() after...	blob \| commitdiff \| diff to current
2017-06-01	gmungoc	JAL-2526 zapCursor() renamed sequenceChanged()	blob \| commitdiff \| diff to current
2017-06-01	gmungoc	JAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn	blob \| commitdiff \| diff to current
2017-05-30	gmungoc	JAL-2526 first draft of findIndex/findPosition with...	blob \| commitdiff \| diff to current
2017-05-29	gmungoc	JAL-2526 Sequence.findPositions to get residue position...	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2557 removal of Sequence.sequenceFeatures	blob \| commitdiff \| diff to current
2017-05-24	gmungoc	Merge branch 'bug/JAL-2541cutWithFeatures' into feature...	blob \| commitdiff \| diff to current
2017-05-18	gmungoc	JAL-2541 fix to initSeqFrom (and minor code tidy);...	blob \| commitdiff \| diff to current
2017-05-09	gmungoc	JAL-2480 include sequenceFeatureStore in createDatasetS...	blob \| commitdiff \| diff to current
2017-04-27	gmungoc	JAL-2480 don't allow null type in SequenceFeature	blob \| commitdiff \| diff to current
2017-04-26	gmungoc	JAL-2490 findFeaturesAtRes with performant feature...	blob \| commitdiff \| diff to current
2017-04-19	gmungoc	JAL-2483 use SequenceFeatures to look up groups, types...	blob \| commitdiff \| diff to current
2017-04-18	gmungoc	JAL-2480 SequenceFeaturesI encapsulates features api	blob \| commitdiff \| diff to current
2017-04-17	gmungoc	JAL-2446 add call to SequenceFeatures.delete(); use...	blob \| commitdiff \| diff to current
2017-03-21	gmungoc	Merge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport	blob \| commitdiff \| diff to current
2017-03-20	gmungoc	JAL-2446 FeatureStore with NCList - work in progress	blob \| commitdiff \| diff to current
2016-11-14	gmungoc	JAL-2296 report whether SequenceFeature actually added...	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
2016-10-06	Jim Procter	JAL-2089 Merge branch releases/Release_2_10_Branch...	blob \| commitdiff \| diff to current
2016-10-05	Jim Procter	JAL-2189 source formatting	blob \| commitdiff \| diff to current
2016-10-03	gmungoc	JAL-2110 additional tests for setDatasetSequence, javad...	blob \| commitdiff \| diff to current
2016-09-28	Jim Procter	JAL-2235 raise exceptions if self reference or referenc...	blob \| commitdiff \| diff to current
2016-09-28	Jim Procter	JAL-2210 instrument setDBRefs to call ensurePrimaries	blob \| commitdiff \| diff to current
2016-09-27	Jim Procter	JAL-2210 promote direct dbrefs from verified sources...	blob \| commitdiff \| diff to current
2016-09-27	Jim Procter	JAL-2210 resolve todo - addDBRef adds to dataset sequen...	blob \| commitdiff \| diff to current
2016-09-16	gmungoc	JAL-2157 JAL-1803 refactored Sequence.updatePDBIds...	blob \| commitdiff \| diff to current
2016-09-07	Jim Procter	JAL-1803 first pass at updatePDBEntry	blob \| commitdiff \| diff to current
2016-09-06	gmungoc	JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...	blob \| commitdiff \| diff to current
2016-09-05	gmungoc	JAL-2106 increased coverage for testGetPrimaryDbRefs	blob \| commitdiff \| diff to current
2016-08-31	Jim Procter	JAL-1926 JAL-2106 fix PDB primary DBRef semantics:...	blob \| commitdiff \| diff to current
2016-08-26	Jim Procter	JAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	JAL-2106 tighten DBRefEntry primary seq test for PDB	blob \| commitdiff \| diff to current
2016-08-25	Jim Procter	Merge branch 'refactor/JAL-2106_sourceDbRef_revision...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-08-24	Jim Procter	JAL-2106 rejig test to minimally verify patch that...	blob \| commitdiff \| diff to current
2016-08-04	Jim Procter	JAL-2046 stack trace for implementation warning	blob \| commitdiff \| diff to current
2016-08-02	Jim Procter	JAL-2046 additional logic to suppress spurious implemen...	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 SequenceI.isProtein method	blob \| commitdiff \| diff to current
2016-05-31	gmungoc	JAL-2110 refactor + tests to allow a dbref version...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 add/delete SequenceFeature operate on dataset...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 setSequenceFeature contract implementation...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 remove javadoc	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 simpler deriveSequence - promote to dataset...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 clarify contract for copy constructor and...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 explicitly copy char[] when cloning sequence...	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 safer createDatasetSequence manipulates privat...	blob \| commitdiff \| diff to current
2016-03-21	tcofoegbu	develop merge	blob \| commitdiff \| diff to current
2016-03-03	tcofoegbu	JAL-1919 fixed bug causing PDBfile test failure	blob \| commitdiff \| diff to current
2016-03-03	tcofoegbu	JAL-1919 PDBfile and JmolParser refactor	blob \| commitdiff \| diff to current
2016-03-01	gmungoc	JAL-1705 align CDS and peptide products to transcripts	blob \| commitdiff \| diff to current
2016-01-28	gmungoc	Merge branch 'develop' into JAL-1705_trialMerge	blob \| commitdiff \| diff to current
2016-01-23	gmungoc	JAL-1705 todo comment re writing DBRefEntry/SequenceFea...	blob \| commitdiff \| diff to current
2015-11-30	gmungoc	JAL-1421 use generics JAL-1551 @Override annotations...	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...	blob \| commitdiff \| diff to current
2015-10-29	tcofoegbu	JAL-1926 JAL-1479 updated PDBfile fetcher to add source...	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
2015-10-15	tcofoegbu	JAL-1479 refactored SequenceI interface - changed getDB...	blob \| commitdiff \| diff to current
2015-10-14	tcofoegbu	JAL-1926 added supporting model changes to enable savin...	blob \| commitdiff \| diff to current
2015-10-08	Jim Procter	JAL-1894 update year/version in copyright	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
2015-08-07	tcofoegbu	JAL-1824 updated caching procedure for pdb entries...	blob \| commitdiff \| diff to current
2015-08-04	tcofoegbu	JAL-1821 updated the reference sequence column of struc...	blob \| commitdiff \| diff to current
2015-07-08	gmungoc	JAL-1759 merge from develop	blob \| commitdiff \| diff to current
2015-07-01	gmungoc	JAL-1802 handle slide sequences edits in split frame...	blob \| commitdiff \| diff to current
2015-06-17	Jim Procter	Merge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments	blob \| commitdiff \| diff to current
2015-06-12	tcofoegbu	JAL-1641 refactor	blob \| commitdiff \| diff to current
2015-06-06	Jim Procter	JAL-653 allow a dummy sequence to take on attributes...	blob \| commitdiff \| diff to current
2015-06-05	tcofoegbu	JAL-1760 JAL-1641 Serialisation of Hidden Seqs and...	blob \| commitdiff \| diff to current
2015-06-05	Jim Procter	JAL-653 refactor sequence interface to separate concret...	blob \| commitdiff \| diff to current
2015-05-12	gmungoc	JAL-1712 fixes/tests for Castor binding and 'show flank...	blob \| commitdiff \| diff to current
2015-04-30	tcofoegbu	JAL-1717 updated the PDBEntry model and updated the...	blob \| commitdiff \| diff to current
2015-04-13	gmungoc	JAL-1693 make exon alignment for get-xref splitframe...	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
2015-03-06	Jim Procter	Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...	blob \| commitdiff \| diff to current
2015-02-19	gmungoc	JAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1628 new method to get a list of insertions in...	blob \| commitdiff \| diff to current
2015-01-18	Jim Procter	JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence	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
2014-11-28	gmungoc	JAL-1610 check reference annotations against alignment...	blob \| commitdiff \| diff to current
2014-11-12	Jim Procter	javadoc	blob \| commitdiff \| diff to current
2014-10-23	gmungoc	JAL-1264 further refactoring and tests	blob \| commitdiff \| diff to current
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