JAL-1632 add score model params to PCAModel and PCA constructors
[jalview.git] / src / jalview / datamodel / Sequence.java
2016-10-25 Jim ProcterJAL-2089 patch broken merge to master for Release 2... releases/Release_2_10_0_Branch
2016-10-06 Jim ProcterJAL-2089 Merge branch releases/Release_2_10_Branch...
2016-10-05 Jim ProcterJAL-2189 source formatting
2016-10-03 gmungocJAL-2110 additional tests for setDatasetSequence, javad...
2016-09-28 Jim ProcterJAL-2235 raise exceptions if self reference or referenc...
2016-09-28 Jim ProcterJAL-2210 instrument setDBRefs to call ensurePrimaries
2016-09-27 Jim ProcterJAL-2210 promote direct dbrefs from verified sources...
2016-09-27 Jim ProcterJAL-2210 resolve todo - addDBRef adds to dataset sequen...
2016-09-16 gmungocJAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
2016-09-07 Jim ProcterJAL-1803 first pass at updatePDBEntry
2016-09-06 gmungocJAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...
2016-09-05 gmungocJAL-2106 increased coverage for testGetPrimaryDbRefs
2016-08-31 Jim ProcterJAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
2016-08-26 Jim ProcterJAL-2106 fix (last one!) remove the Sequence.sourceDBRe... bug/JAL-2154projectMappings
2016-08-25 Jim ProcterJAL-2106 tighten DBRefEntry primary seq test for PDB
2016-08-25 Jim ProcterMerge branch 'refactor/JAL-2106_sourceDbRef_revision...
2016-08-24 Jim ProcterJAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
2016-08-24 Jim ProcterJAL-2106 rejig test to minimally verify patch that...
2016-08-04 Jim ProcterJAL-2046 stack trace for implementation warning
2016-08-02 Jim ProcterJAL-2046 additional logic to suppress spurious implemen...
2016-06-23 Jim ProcterJAL-2110 SequenceI.isProtein method
2016-05-31 gmungocJAL-2110 refactor + tests to allow a dbref version...
2016-04-05 Jim ProcterJAL-2046 add/delete SequenceFeature operate on dataset...
2016-04-05 Jim ProcterJAL-2046 setSequenceFeature contract implementation...
2016-04-05 Jim ProcterJAL-2046 remove javadoc
2016-04-05 Jim ProcterJAL-2046 simpler deriveSequence - promote to dataset...
2016-04-05 Jim ProcterJAL-2046 clarify contract for copy constructor and...
2016-04-05 Jim ProcterJAL-2046 explicitly copy char[] when cloning sequence...
2016-04-05 Jim ProcterJAL-2046 safer createDatasetSequence manipulates privat...
2016-03-21 tcofoegbudevelop merge
2016-03-03 tcofoegbuJAL-1919 fixed bug causing PDBfile test failure
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea...
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations...
2015-11-05 tcofoegbuJAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
2015-10-29 tcofoegbuJAL-1926 JAL-1479 updated PDBfile fetcher to add source...
2015-10-16 Jim ProcterJAL-1925 update source version in license Release_2_9_0b2
2015-10-15 tcofoegbuJAL-1479 refactored SequenceI interface - changed getDB...
2015-10-14 tcofoegbuJAL-1926 added supporting model changes to enable savin...
2015-10-08 Jim ProcterJAL-1894 update year/version in copyright
2015-09-10 Jim ProcterJAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports
2015-08-07 tcofoegbuJAL-1824 updated caching procedure for pdb entries...
2015-08-04 tcofoegbuJAL-1821 updated the reference sequence column of struc...
2015-07-08 gmungocJAL-1759 merge from develop
2015-07-01 gmungocJAL-1802 handle slide sequences edits in split frame...
2015-06-17 Jim ProcterMerge branch 'develop' into features/JAL-653_gffalignments features/JAL-653_gffalignments
2015-06-12 tcofoegbuJAL-1641 refactor
2015-06-06 Jim ProcterJAL-653 allow a dummy sequence to take on attributes...
2015-06-05 tcofoegbuJAL-1760 JAL-1641 Serialisation of Hidden Seqs and...
2015-06-05 Jim ProcterJAL-653 refactor sequence interface to separate concret...
2015-05-12 gmungocJAL-1712 fixes/tests for Castor binding and 'show flank...
2015-04-30 tcofoegbuJAL-1717 updated the PDBEntry model and updated the...
2015-04-13 gmungocJAL-1693 make exon alignment for get-xref splitframe...
2015-03-26 gmungocMerge develop to Release_2_8_3_Branch
2015-03-06 Jim ProcterJAL-1683 replace year/version strings with tokens in...
2015-03-06 Jim ProcterMerge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
2015-02-19 gmungocJAL-1665 refactored Sequence.getSequenceFeatures features/sequenceFeatureRefactor
2015-01-18 Jim ProcterJAL-1628 new method to get a list of insertions in...
2015-01-18 Jim ProcterJAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
2014-12-22 Jim ProcterMerge: 497958b 68dcaa7
2014-12-15 Jim ProcterJAL-1620 version bump and release notes
2014-11-28 gmungocJAL-1610 check reference annotations against alignment...
2014-11-12 Jim Procterjavadoc
2014-10-23 gmungocJAL-1264 further refactoring and tests
2014-10-10 gmungocJAL-1264 added getAlignmentAnnotations(calcId, label)
2014-10-06 Jim ProcterJAL-654 JAL-1264 sequence associated annotation is...
2014-10-06 Jim ProcterJAL-1115 TODO remove use of java.util.Vector
2014-06-06 Jim ProcterJAL-1517 source formatting
2014-06-06 Jim ProcterJAL-1517 fix copyright for 2.8.2
2014-06-05 Jim ProcterJAL-1517 update copyright to version 2.8.2
2014-06-05 Jim ProcterMerge branch 'docs/2_8_1_Release' into Release_2_8_2_Branch
2014-05-22 Jim ProcterJAL-1503 update version in GPL header
2014-04-25 Jim ProcterMerge branch 'JAL-1177_prop_rnasecstr' into develop
2014-04-25 Jim ProcterJAL-1177 propagate sequence associated annotation to...
2014-02-18 Jim ProcterMerge branch 'JAL-1445' into develop
2014-02-03 Jim ProcterMerge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge
2014-01-29 Jim ProcterJAL-1432 updated copyright notices
2013-10-14 Jim ProcterMerge branch 'develop' into dev_from_2_8_1
2013-10-04 Jim Procterfix for JAL-1380 and efficiency todo for JAL-1381
2012-11-15 jprocterMerge branch 'develop' into menard
2012-10-22 jprocterJalview 2.8 Source Header
2012-10-03 jprocterformatting
2012-08-31 jprocterMerge branch 'develop' into menard
2012-08-28 jprocterjavadoc and note about broken semantics for findIndex
2012-07-10 Anne Menardv2
2012-07-05 Anne MenardAdd support RNAML format
2012-05-24 jprocterensure annotation isn't added twice - note - this could...
2012-05-22 jprocterMerge remote-tracking branch 'origin/Tcoffee_JAL-1065...
2011-10-10 jprocterupdate author list in license for (JAL-826)
2011-09-27 jprocterapply version 2.7 copyright
2011-02-27 jprocterfirst patch for JAL-774 - ensure end is a valid bound...
2010-09-23 jprocterJalview 2.6 source licence
2010-04-30 jprocterjalview 2.5 release banner
2009-06-08 jprocterapply gpl development license
2008-09-04 jproctermerge from 2_4_Release branch
2008-08-06 jproctergetDBRefs now always returns DBRefArray if it exists...
2008-01-22 jprocternew method to get map of sequence positions correspondi...
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