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JAL-3541 removed clover report generation debug flag (utf-8 encoding enforcement...
[jalview.git] / src / jalview / datamodel / SequenceI.java
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi... blob | commitdiff
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL... blob | commitdiff | diff to current
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam... blob | commitdiff | diff to current
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures blob | commitdiff | diff to current
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library blob | commitdiff | diff to current
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect blob | commitdiff | diff to current
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into... blob | commitdiff | diff to current
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence... blob | commitdiff | diff to current
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after... blob | commitdiff | diff to current
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings) blob | commitdiff | diff to current
2017-11-22 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759 blob | commitdiff | diff to current
2017-11-16 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures blob | commitdiff | diff to current
2017-11-16 Jim ProcterMerge branch 'bug/JAL-2829deleteCharsWithGaps' into... blob | commitdiff | diff to current
2017-11-15 gmungocJAL-2835 spike updated with latest blob | commitdiff | diff to current
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF blob | commitdiff | diff to current
2017-11-13 gmungocJAL-2176 removed unused Sequence.index blob | commitdiff | diff to current
2017-11-13 gmungocMerge branch 'bug/JAL-2829deleteCharsWithGaps' into blob | commitdiff | diff to current
2017-11-10 gmungocJAL-2562 updated findPosition javadoc to match behaviour blob | commitdiff | diff to current
2017-11-07 Jim ProcterJAL-2822 JAL-2684 clarified javadoc blob | commitdiff | diff to current
2017-10-20 gmungocPush 1793 latest to spike branch blob | commitdiff | diff to current
2017-10-19 gmungocJAL-2755 add missing Javadoc blob | commitdiff | diff to current
2017-10-03 gmungocJAL-2738 copy to spikes/mungo blob | commitdiff | diff to current
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry blob | commitdiff | diff to current
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI! blob | commitdiff | diff to current
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI blob | commitdiff | diff to current
2017-09-21 kiramtJAL-2674 Rewrote propagateInsertions blob | commitdiff | diff to current
2017-09-14 gmungocJAL-2541 working Cut/Undo with feature relocation blob | commitdiff | diff to current
2017-09-14 gmungocJAL-2541 revised cut with features (work in progress) blob | commitdiff | diff to current
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of... blob | commitdiff | diff to current
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the... blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2446 merged to spike branch blob | commitdiff | diff to current
2017-06-09 gmungocJAL-2480 tidy javadoc blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor blob | commitdiff | diff to current
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient... blob | commitdiff | diff to current
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged() blob | commitdiff | diff to current
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn blob | commitdiff | diff to current
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with... blob | commitdiff | diff to current
2017-05-29 gmungocMerge branch 'develop' into features/JAL-2446NCList blob | commitdiff | diff to current
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position... blob | commitdiff | diff to current
2017-05-27 Jim ProcterJAL-2562 javadoc TODO blob | commitdiff | diff to current
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures blob | commitdiff | diff to current
2017-04-27 gmungocJAL-2480 don't allow null type in SequenceFeature blob | commitdiff | diff to current
2017-04-26 gmungocJAL-2490 findFeaturesAtRes with performant feature... blob | commitdiff | diff to current
2017-04-18 gmungocJAL-2480 SequenceFeaturesI encapsulates features api blob | commitdiff | diff to current
2017-03-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport blob | commitdiff | diff to current
2017-03-20 gmungocJAL-2446 FeatureStore with NCList - work in progress blob | commitdiff | diff to current
2016-11-14 gmungocJAL-2296 report whether SequenceFeature actually added... blob | commitdiff | diff to current
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch blob | commitdiff | diff to current
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch... blob | commitdiff | diff to current
2016-10-05 Jim ProcterJAL-2189 source formatting blob | commitdiff | diff to current
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad... blob | commitdiff | diff to current
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries blob | commitdiff | diff to current
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds... blob | commitdiff | diff to current
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry blob | commitdiff | diff to current
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe... blob | commitdiff | diff to current
2016-07-12 Jim ProcterJAL-2110 javadoc blob | commitdiff | diff to current
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method blob | commitdiff | diff to current
2016-05-17 tcofoegbuJAL-2106 JAL-1926 updated source doc for set/getSourceDBRef blob | commitdiff | diff to current
2016-04-05 Jim ProcterJAL-2046 explicit contract for get/set SequenceFeatures... blob | commitdiff | diff to current
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc... blob | commitdiff | diff to current
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2 blob | commitdiff | diff to current
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB... blob | commitdiff | diff to current
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin... blob | commitdiff | diff to current
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... blob | commitdiff | diff to current
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports blob | commitdiff | diff to current
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries... blob | commitdiff | diff to current
2015-06-12 tcofoegbuJAL-1641 refactor blob | commitdiff | diff to current
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and... blob | commitdiff | diff to current
2015-06-05 Jim ProcterJAL-653 refactor sequence interface to separate concret... blob | commitdiff | diff to current
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank... blob | commitdiff | diff to current
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... blob | commitdiff | diff to current
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch blob | commitdiff | diff to current
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... blob | commitdiff | diff to current
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... blob | commitdiff | diff to current
2015-02-12 Jim Procterjavadoc blob | commitdiff | diff to current
2015-01-18 Jim ProcterJAL-1628 new method to get a list of insertions in... blob | commitdiff | diff to current
2015-01-18 Jim ProcterJAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence blob | commitdiff | diff to current
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 blob | commitdiff | diff to current
2014-12-15 Jim ProcterJAL-1620 version bump and release notes blob | commitdiff | diff to current
2014-11-28 gmungocJAL-1610 check reference annotations against alignment... blob | commitdiff | diff to current
2014-11-12 Jim Procterjavadoc blob | commitdiff | diff to current
2014-10-21 Jim ProcterJAL-674 JAL-1551 imports dropped during merge blob | commitdiff | diff to current
2014-10-21 Jim ProcterMerge branch 'features/JAL-1264_showHideAnnotations... blob | commitdiff | diff to current
2014-10-21 Jim ProcterJAL-1551 crlf changes blob | commitdiff | diff to current
2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto blob | commitdiff | diff to current
2014-10-15 Jim ProcterJAL-1551 crlf changes due to checkout with text=auto blob | commitdiff | diff to current
2014-10-10 gmungocJAL-1264 added getAlignmentAnnotations(calcId, label) blob | commitdiff | diff to current
2014-10-06 Jim ProcterJAL-654 javadoc createDatasetSequence and transferAnnot... blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 source formatting blob | commitdiff | diff to current
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 blob | commitdiff | diff to current
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch blob | commitdiff | diff to current
2014-05-22 Jim ProcterJAL-1503 update version in GPL header blob | commitdiff | diff to current
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop blob | commitdiff | diff to current
2014-01-29 Jim ProcterJAL-1432 updated copyright notices blob | commitdiff | diff to current
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