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JAL-2526 better names for fields
[jalview.git]
/
src
/
jalview
/
datamodel
/
Sequence.java
2017-06-15
gmungoc
JAL-2541 revised cut with features (work in progress)
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2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
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2017-06-08
gmungoc
JAL-2526 correct boundary conditions for sequence left...
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2017-06-08
gmungoc
JAL-2526 cache first/last residue column positions...
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2017-06-06
gmungoc
JAL-2526 less stringent test for invalid cursor
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2017-06-05
gmungoc
Merge branch 'features/JAL-2526sequenceCursor' into
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2017-06-05
gmungoc
Merge branch 'features/JAL-2446NCList' into
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2017-06-05
gmungoc
Merge branch 'features/JAL-2446NCList' into
features/JAL-2526sequenceCursor
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2017-06-05
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
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2017-06-04
Jim Procter
JAL-2291 bug fix - BitSet.set is [start,end+1)
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2017-06-04
Jim Procter
JAL-2291 SequenceI.getInsertionsAsBits for convenient...
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2017-06-02
gmungoc
JAL-2526 additional tests for findPosition with/without...
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2017-06-01
gmungoc
JAL-2526 additional calls to sequenceChanged() after...
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2017-06-01
gmungoc
JAL-2526 zapCursor() renamed sequenceChanged()
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2017-06-01
gmungoc
JAL-2754 Sequence.findFeatures(fromCol, toCol)
features/JAL-2754findFeaturesByColumn
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2017-05-30
gmungoc
JAL-2526 first draft of findIndex/findPosition with...
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2017-05-29
gmungoc
JAL-2526 Sequence.findPositions to get residue position...
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2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
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2017-05-24
gmungoc
Merge branch 'bug/JAL-2541cutWithFeatures' into feature...
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2017-05-18
gmungoc
JAL-2541 fix to initSeqFrom (and minor code tidy);...
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2017-05-09
gmungoc
JAL-2480 include sequenceFeatureStore in createDatasetS...
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2017-04-27
gmungoc
JAL-2480 don't allow null type in SequenceFeature
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2017-04-26
gmungoc
JAL-2490 findFeaturesAtRes with performant feature...
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2017-04-19
gmungoc
JAL-2483 use SequenceFeatures to look up groups, types...
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2017-04-18
gmungoc
JAL-2480 SequenceFeaturesI encapsulates features api
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2017-04-17
gmungoc
JAL-2446 add call to SequenceFeatures.delete(); use...
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2017-03-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-653_JAL-1766_htslib_refseqsupport
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2017-03-20
gmungoc
JAL-2446 FeatureStore with NCList - work in progress
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2016-11-14
gmungoc
JAL-2296 report whether SequenceFeature actually added...
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2016-10-25
Jim Procter
JAL-2089 patch broken merge to master for Release 2...
releases/Release_2_10_0_Branch
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2016-10-06
Jim Procter
JAL-2089 Merge branch releases/Release_2_10_Branch...
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2016-10-05
Jim Procter
JAL-2189 source formatting
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2016-10-03
gmungoc
JAL-2110 additional tests for setDatasetSequence, javad...
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2016-09-28
Jim Procter
JAL-2235 raise exceptions if self reference or referenc...
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2016-09-28
Jim Procter
JAL-2210 instrument setDBRefs to call ensurePrimaries
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2016-09-27
Jim Procter
JAL-2210 promote direct dbrefs from verified sources...
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2016-09-27
Jim Procter
JAL-2210 resolve todo - addDBRef adds to dataset sequen...
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2016-09-16
gmungoc
JAL-2157 JAL-1803 refactored Sequence.updatePDBIds...
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2016-09-07
Jim Procter
JAL-1803 first pass at updatePDBEntry
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2016-09-06
gmungoc
JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandid...
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2016-09-05
gmungoc
JAL-2106 increased coverage for testGetPrimaryDbRefs
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2016-08-31
Jim Procter
JAL-1926 JAL-2106 fix PDB primary DBRef semantics:...
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2016-08-26
Jim Procter
JAL-2106 fix (last one!) remove the Sequence.sourceDBRe...
bug/JAL-2154projectMappings
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2016-08-25
Jim Procter
JAL-2106 tighten DBRefEntry primary seq test for PDB
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2016-08-25
Jim Procter
Merge branch 'refactor/JAL-2106_sourceDbRef_revision...
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2016-08-24
Jim Procter
JAL-2106 removed setSourceDBRef, refactor getSourceDBRe...
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2016-08-24
Jim Procter
JAL-2106 rejig test to minimally verify patch that...
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2016-08-04
Jim Procter
JAL-2046 stack trace for implementation warning
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2016-08-02
Jim Procter
JAL-2046 additional logic to suppress spurious implemen...
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2016-06-23
Jim Procter
JAL-2110 SequenceI.isProtein method
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2016-05-31
gmungoc
JAL-2110 refactor + tests to allow a dbref version...
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2016-04-05
Jim Procter
JAL-2046 add/delete SequenceFeature operate on dataset...
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2016-04-05
Jim Procter
JAL-2046 setSequenceFeature contract implementation...
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2016-04-05
Jim Procter
JAL-2046 remove javadoc
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2016-04-05
Jim Procter
JAL-2046 simpler deriveSequence - promote to dataset...
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2016-04-05
Jim Procter
JAL-2046 clarify contract for copy constructor and...
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2016-04-05
Jim Procter
JAL-2046 explicitly copy char[] when cloning sequence...
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2016-04-05
Jim Procter
JAL-2046 safer createDatasetSequence manipulates privat...
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2016-03-21
tcofoegbu
develop merge
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2016-03-03
tcofoegbu
JAL-1919 fixed bug causing PDBfile test failure
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2016-03-03
tcofoegbu
JAL-1919 PDBfile and JmolParser refactor
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2016-03-01
gmungoc
JAL-1705 align CDS and peptide products to transcripts
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2016-01-28
gmungoc
Merge branch 'develop' into JAL-1705_trialMerge
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2016-01-23
gmungoc
JAL-1705 todo comment re writing DBRefEntry/SequenceFea...
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2015-11-30
gmungoc
JAL-1421 use generics JAL-1551 @Override annotations...
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2015-11-05
tcofoegbu
JAL-1942 JAL-1479 refactored SequenceI.getDBRef/Sequenc...
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2015-10-29
tcofoegbu
JAL-1926 JAL-1479 updated PDBfile fetcher to add source...
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2015-10-16
Jim Procter
JAL-1925 update source version in license
Release_2_9_0b2
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2015-10-15
tcofoegbu
JAL-1479 refactored SequenceI interface - changed getDB...
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2015-10-14
tcofoegbu
JAL-1926 added supporting model changes to enable savin...
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2015-10-08
Jim Procter
JAL-1894 update year/version in copyright
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2015-09-10
Jim Procter
JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensin...
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diff to current
2015-09-10
Jim Procter
JAL-1645 source formatting and organise imports
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diff to current
2015-08-07
tcofoegbu
JAL-1824 updated caching procedure for pdb entries...
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2015-08-04
tcofoegbu
JAL-1821 updated the reference sequence column of struc...
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2015-07-08
gmungoc
JAL-1759 merge from develop
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2015-07-01
gmungoc
JAL-1802 handle slide sequences edits in split frame...
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2015-06-17
Jim Procter
Merge branch 'develop' into features/JAL-653_gffalignments
features/JAL-653_gffalignments
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2015-06-12
tcofoegbu
JAL-1641 refactor
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diff to current
2015-06-06
Jim Procter
JAL-653 allow a dummy sequence to take on attributes...
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2015-06-05
tcofoegbu
JAL-1760 JAL-1641 Serialisation of Hidden Seqs and...
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diff to current
2015-06-05
Jim Procter
JAL-653 refactor sequence interface to separate concret...
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diff to current
2015-05-12
gmungoc
JAL-1712 fixes/tests for Castor binding and 'show flank...
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2015-04-30
tcofoegbu
JAL-1717 updated the PDBEntry model and updated the...
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2015-04-13
gmungoc
JAL-1693 make exon alignment for get-xref splitframe...
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2015-03-26
gmungoc
Merge develop to Release_2_8_3_Branch
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2015-03-06
Jim Procter
JAL-1683 replace year/version strings with tokens in...
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diff to current
2015-03-06
Jim Procter
Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e...
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2015-02-19
gmungoc
JAL-1665 refactored Sequence.getSequenceFeatures
features/sequenceFeatureRefactor
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2015-01-18
Jim Procter
JAL-1628 new method to get a list of insertions in...
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2015-01-18
Jim Procter
JAL-1372 JAL-1114 JAL-1628 tidy sequenceI/sequence
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2014-12-22
Jim Procter
Merge: 497958b 68dcaa7
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2014-12-15
Jim Procter
JAL-1620 version bump and release notes
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2014-11-28
gmungoc
JAL-1610 check reference annotations against alignment...
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diff to current
2014-11-12
Jim Procter
javadoc
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2014-10-23
gmungoc
JAL-1264 further refactoring and tests
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diff to current
2014-10-10
gmungoc
JAL-1264 added getAlignmentAnnotations(calcId, label)
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2014-10-06
Jim Procter
JAL-654 JAL-1264 sequence associated annotation is...
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diff to current
2014-10-06
Jim Procter
JAL-1115 TODO remove use of java.util.Vector
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diff to current
2014-06-06
Jim Procter
JAL-1517 source formatting
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