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

2022-12-14	Jim Procter	Merge branch 'develop' into update_212_Dec_merge_with_2...	blob \| commitdiff
2022-11-21	Jim Procter	Merge commit 'alpha/update_2_12_for_2_11_2_series_merge...	blob \| commitdiff \| diff to current
2022-03-08	Jim Procter	JAL-3438 spotless for 2.11.2.0	blob \| commitdiff \| diff to current
2021-09-17	Jim Procter	JAL-2226 new method to search for annotation matching...	blob \| commitdiff \| diff to current
2020-05-18	Jim Procter	Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...	blob \| commitdiff \| diff to current
2019-09-26	Jim Procter	JAL-3070 allow SequenceI.findPositions(0,column+1)...	blob \| commitdiff \| diff to current
2019-06-04	Jim Procter	Merge branch 'develop' into developtomchmmer	blob \| commitdiff \| diff to current
2019-03-13	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2019-03-05	gmungoc	Merge remote-tracking branch 'origin/bug/JAL-2839findWi...	blob \| commitdiff \| diff to current
2019-03-01	gmungoc	Merge branch 'feature/intervalStoreJ' into merge/JAL...	blob \| commitdiff \| diff to current
2019-02-28	gmungoc	JAL-3140 confine intervalstore imports to jalview.datam...	blob \| commitdiff \| diff to current
2019-02-04	hansonr	refactoring for DBMODList	blob \| commitdiff \| diff to current
2019-01-26	hansonr	Jalview.isJS() --> Platform.isJS(), DBRefEntry[] -...	blob \| commitdiff \| diff to current
2018-12-17	Jim Procter	Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures	blob \| commitdiff \| diff to current
2018-11-29	gmungoc	JAL-3140 NCList now via IntervalStore library	blob \| commitdiff \| diff to current
2018-04-16	gmungoc	JAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...	blob \| commitdiff \| diff to current
2018-03-30	gmungoc	JAL-2941 'map hmm to RF' removed pending clarifications	blob \| commitdiff \| diff to current
2018-03-16	gmungoc	Merge branch 'develop' into trialMerge	blob \| commitdiff \| diff to current
2018-03-09	gmungoc	JAL-2839 Finder refactoring prior to fixing the defect	blob \| commitdiff \| diff to current
2018-03-07	Jim Procter	Merge branch 'releases/Release_2_10_4_Branch' into...	blob \| commitdiff \| diff to current
2018-02-28	gmungoc	JAL-2629 some tidying of Hmmer commands (wip)	blob \| commitdiff \| diff to current
2018-02-22	gmungoc	JAL-2629 tidy tests, refactor hmmer node mapping slightly	blob \| commitdiff \| diff to current
2018-02-20	gmungoc	JAL-2629 removed SequenceI.get/setLastPosition and...	blob \| commitdiff \| diff to current
2018-02-20	gmungoc	Merge branch 'develop' into features/mchmmer	blob \| commitdiff \| diff to current
2018-01-22	kiramt	JAL-2579 Moved locateVisibleStartOfSequence to Sequence...	blob \| commitdiff \| diff to current
2018-01-19	kiramt	JAL-2759 Changes to getVisibleSequenceStrings after...	blob \| commitdiff \| diff to current
2017-11-22	gmungoc	JAL-2069 spike updated with latest (FeatureTypeSettings)	blob \| commitdiff \| diff to current
2017-11-22	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	blob \| commitdiff \| diff to current
2017-11-21	kiramt	Merge branch 'develop' into feature/JAL-2759	blob \| commitdiff \| diff to current
2017-11-16	Jim Procter	Merge branch 'develop' into bug/JAL-2541cutRelocateFeatures	blob \| commitdiff \| diff to current
2017-11-16	Jim Procter	Merge branch 'bug/JAL-2829deleteCharsWithGaps' into...	blob \| commitdiff \| diff to current
2017-11-15	gmungoc	JAL-2835 spike updated with latest	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	Merge branch 'develop' into features/JAL-1793VCF	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	JAL-2176 removed unused Sequence.index	blob \| commitdiff \| diff to current
2017-11-13	gmungoc	Merge branch 'bug/JAL-2829deleteCharsWithGaps' into	blob \| commitdiff \| diff to current
2017-11-10	gmungoc	JAL-2562 updated findPosition javadoc to match behaviour	blob \| commitdiff \| diff to current
2017-11-07	Jim Procter	JAL-2822 JAL-2684 clarified javadoc	blob \| commitdiff \| diff to current
2017-10-20	gmungoc	Push 1793 latest to spike branch	blob \| commitdiff \| diff to current
2017-10-19	gmungoc	JAL-2755 add missing Javadoc	blob \| commitdiff \| diff to current
2017-10-03	gmungoc	JAL-2738 copy to spikes/mungo	blob \| commitdiff \| diff to current
2017-09-28	gmungoc	JAL-1796 GeneLociI as distinguished DBRefEntry	blob \| commitdiff \| diff to current
2017-09-26	gmungoc	JAL-2738 promote setGeneLoci to SequenceI!	blob \| commitdiff \| diff to current
2017-09-25	gmungoc	JAL-2738 getGeneLoci promoted to SequenceI	blob \| commitdiff \| diff to current
2017-09-21	kiramt	JAL-2674 Rewrote propagateInsertions	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
2017-08-29	osboxes	JAL-2629 HMMs dropped on the alignment now map to the...	blob \| commitdiff \| diff to current
2017-08-18	TZVanaalten	Merge branch 'develop' into features/hmmer	blob \| commitdiff \| diff to current
2017-08-11	TZVanaalten	JAL-2629 add ability to build a HMM from a group	blob \| commitdiff \| diff to current
2017-08-04	TZVanaalten	JAL-2629 multiple HMMs can now be dropped onto an alignment	blob \| commitdiff \| diff to current
2017-07-27	TZVanaalten	JAL-2629 moved HMM storage location to placeholder...	blob \| commitdiff \| diff to current
2017-06-22	gmungoc	JAL-2481 JAL-2593 JAL-2526 further optimisation of...	blob \| commitdiff \| diff to current
2017-06-14	gmungoc	JAL-2598 Sequence.getSequence return a copy of the...	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2446 merged to spike branch	blob \| commitdiff \| diff to current
2017-06-09	gmungoc	JAL-2480 tidy javadoc	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 SequenceI.getInsertionsAsBits for convenient...	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	Merge branch 'develop' into features/JAL-2446NCList	blob \| commitdiff \| diff to current
2017-05-29	gmungoc	JAL-2526 Sequence.findPositions to get residue position...	blob \| commitdiff \| diff to current
2017-05-27	Jim Procter	JAL-2562 javadoc TODO	blob \| commitdiff \| diff to current
2017-05-25	gmungoc	JAL-2557 removal of Sequence.sequenceFeatures	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
2017-04-18	gmungoc	JAL-2480 SequenceFeaturesI encapsulates features api	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-2210 instrument setDBRefs to call ensurePrimaries	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
2016-08-24	Jim Procter	JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...	blob \| commitdiff \| diff to current
2016-07-12	Jim Procter	JAL-2110 javadoc	blob \| commitdiff \| diff to current
2016-06-23	Jim Procter	JAL-2110 SequenceI.isProtein method	blob \| commitdiff \| diff to current
2016-05-17	tcofoegbu	JAL-2106 JAL-1926 updated source doc for set/getSourceDBRef	blob \| commitdiff \| diff to current
2016-04-05	Jim Procter	JAL-2046 explicit contract for get/set SequenceFeatures...	blob \| commitdiff \| diff to current
2015-11-05	tcofoegbu	JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...	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
2015-06-12	tcofoegbu	JAL-1641 refactor	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
2015-04-13	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
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