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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git] / src / jalview / datamodel / Alignment.java
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin... commit | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports commit | commitdiff
2015-07-30 tcofoegbuJAL-1443 modified exception notifications commit | commitdiff
2015-07-21 tcofoegbuJAL-1443 bugfix to prevent loading of unidentifiable... commit | commitdiff
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe... commit | commitdiff
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch commit | commitdiff
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in... commit | commitdiff
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e... commit | commitdiff
2015-01-09 Jim ProcterMerge branch 'JAL-1372_referenceseq' into feature_29... commit | commitdiff
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7 commit | commitdiff
2014-12-15 Jim ProcterJAL-1620 version bump and release notes commit | commitdiff
2014-11-28 gmungocJAL-1610 check reference annotations against alignment... commit | commitdiff
2014-11-17 Jim Procterformatting commit | commitdiff
2014-11-17 Jim ProcterJAL-1587 JAL-407 instrument setDataset to add dataset... commit | commitdiff
2014-10-10 gmungocJAL-1264 reverted (removed added method) commit | commitdiff
2014-10-08 gmungocMerge branch 'Release_2_8_2_Branch' into commit | commitdiff
2014-10-07 gmungocJAL-1264 wip commit | commitdiff
2014-09-27 darolmarJAL-1355 commit | commitdiff
2014-09-23 darolmarJAL-1355 commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 source formatting commit | commitdiff
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2 commit | commitdiff
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2 commit | commitdiff
2014-05-22 Jim ProcterJAL-1503 update version in GPL header commit | commitdiff
2014-05-02 Jim ProcterMerge branch 'Release_2_8_1_Branch' into JAL-1372_refer... commit | commitdiff
2014-05-01 Jim ProcterJAL-1492 JAL-1397 make AnnotatedCollectionI context... commit | commitdiff
2014-01-29 Jim ProcterJAL-1432 updated copyright notices commit | commitdiff
2013-10-11 Jim ProcterJAL-1114 promote start/end attributes to gettable field... commit | commitdiff
2013-08-30 Jim ProcterJAL-1367 promote the existing representative sequence... commit | commitdiff
2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal Alignm... commit | commitdiff
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE commit | commitdiff
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE commit | commitdiff
2012-10-22 jprocterJalview 2.8 Source Header commit | commitdiff
2012-10-03 jprocterformatting commit | commitdiff
2012-07-03 jprocterJAL-961 allow calcId to be specified independently... commit | commitdiff
2012-06-13 jprocterjavatidy commit | commitdiff
2012-06-12 jprocterJAL-1115 refactor reordering code operating directly... commit | commitdiff
2012-06-12 jprocterJAL-1115 refactor base collection for Alignment from... commit | commitdiff
2012-05-30 jprocterJAL-1114 - refactor methods handling Vectors and Hashta... commit | commitdiff
2012-05-23 jprocterJAL-961 - annotatable datamodel objects can be queried... commit | commitdiff
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065... commit | commitdiff
2011-10-10 jprocterupdate author list in license for (JAL-826) commit | commitdiff
2011-10-04 jprocterMerge remote-tracking branch 'remotes/origin/2_5_1_rna_... commit | commitdiff
2011-09-27 jprocterapply version 2.7 copyright commit | commitdiff
2011-08-15 janengelhardtJAL-891; Sorting of Structure logo implemented; bug... commit | commitdiff
2011-08-11 janengelhardtJAL-885; hasRNAStructure method was introduced to Align... commit | commitdiff
2011-04-21 jprocterallow an alignment annotation row to be removed and... commit | commitdiff
2010-11-12 jprocterpatch for JAL-700 commit | commitdiff
2010-09-23 jprocterapply jalview code style commit | commitdiff
2010-09-23 jprocterJalview 2.6 source licence commit | commitdiff
2010-04-30 jprocterjalview 2.5 release banner commit | commitdiff
2010-04-29 jprocterisAligned assertion (bug 0008144) commit | commitdiff
2010-04-28 jproctergroup/annotation association housekeeping commit | commitdiff
2009-07-24 jprocterimplement new insert annotation row method and ensure... commit | commitdiff
2009-06-08 jprocterapply gpl development license commit | commitdiff
2008-12-19 jprocterleft and right justify method commit | commitdiff
2008-12-05 jproctersupport for multiple accession retrieval from a databas... commit | commitdiff
2008-11-12 jprocterjavadoc and new method to get alignment sequence index... commit | commitdiff
2008-09-04 jproctermerge from 2_4_Release branch commit | commitdiff
2008-07-18 jprocterallow findSeq to begin *after* a given sequence in... commit | commitdiff
2007-11-30 jproctercase invariant matching of seqeunce feature to sequence... commit | commitdiff
2007-08-30 jproctermoved dataset sequence creation onto sequence method commit | commitdiff
2007-08-24 jprocterdataset alignments have a reference count which must... commit | commitdiff
2007-07-13 jproctermapping bug fixes commit | commitdiff
2007-06-17 jprocterAlignedCodonFrame holds mapping information between... commit | commitdiff
2007-05-10 jprocterfixed array index out of bounds when not removing align... commit | commitdiff
2007-05-07 amwaterhousetIndex prevented deletion of last annotation commit | commitdiff
2007-05-02 jprocterreturn flag indicating if annotations were actually... commit | commitdiff
2007-05-01 jprocterremoveAlignmentAnnotation only removes annotation objec... commit | commitdiff
2007-04-27 jprocterdocumentation and getProperties method commit | commitdiff
2007-04-25 amwaterhousealignmentProperties added commit | commitdiff
2007-04-23 amwaterhouseremove seqref annotations commit | commitdiff
2007-04-17 jproctercopy constructors and AlignmentAnnotation sequenceRef... commit | commitdiff
2007-04-02 amwaterhouseDestroy alignment moved to finalize commit | commitdiff
2007-04-02 amwaterhouseDestroy aligment method added commit | commitdiff
2007-02-07 amwaterhouseFormatting commit | commitdiff
2007-01-26 amwaterhouseOnly set the sequence oncecvs diff datamodel/Alignment... commit | commitdiff
2007-01-25 amwaterhouseAnnotation adjustment moved to EditCommand commit | commitdiff
2007-01-24 amwaterhouseAdjustAnnotations needs position, number and insert commit | commitdiff
2007-01-23 amwaterhouseHidden representatives moved from sequence to viewport commit | commitdiff
2006-12-21 amwaterhouseremove unnecessary import commit | commitdiff
2006-12-05 amwaterhouseSequence is char [] commit | commitdiff
2006-11-23 amwaterhouseDont make groups of hidden sequences commit | commitdiff
2006-11-13 amwaterhouseSequence colour moved to viewport commit | commitdiff
2006-11-08 amwaterhousecurrentSeq and set description in dataset commit | commitdiff
2006-11-03 amwaterhouseConsensus may already have been removed commit | commitdiff
2006-10-27 amwaterhouseNew padgaps works out number of gaps to insert, delete commit | commitdiff
2006-10-25 amwaterhouseWe can delete sequence 0 commit | commitdiff
2006-10-24 amwaterhousemaxIdLength redundant, deleteCols, trimLeft, removeGaps... commit | commitdiff
2006-10-12 amwaterhouseHiddenSequences now array, not hashtable commit | commitdiff
2006-10-09 jprocterfixed getCompactAlignment method to return proper cigar... commit | commitdiff
2006-10-06 amwaterhouseAAFrequency optimized commit | commitdiff
2006-08-21 amwaterhouseheader updated commit | commitdiff
2006-08-21 jprocterremoveGaps method can record changes in alignment colum... commit | commitdiff
2006-08-18 amwaterhousedont remove all representative seqs on delete groups commit | commitdiff
2006-08-18 amwaterhouseremove all representative seqs on delete groups commit | commitdiff
2006-08-15 amwaterhouseMove features to dataset commit | commitdiff
2006-08-14 amwaterhousefindSequenceMatch returns multiple sequences commit | commitdiff
2006-08-09 jprocteralignment from seqCigars will correctly mark deleted... commit | commitdiff
2006-08-04 jprocterrecover original data for tree and pca as alignment... commit | commitdiff
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