JAL-2994 put ‘\’ first in character class clause of regex - otherwise doesn’t compile...
[jalview.git] / src / jalview / datamodel / Sequence.java
2018-05-11 gmungocMerge branch 'develop' into features/mchmmer
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue...
2018-04-16 gmungocJAL-2629 JAL-2937 remove redundant is/setHMMConsensusSe...
2018-03-30 gmungocJAL-2941 'map hmm to RF' removed pending clarifications
2018-03-16 gmungocMerge branch 'develop' into trialMerge
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-28 gmungocJAL-2629 some tidying of Hmmer commands (wip)
2018-02-26 gmungocJAL-2599 test coverage and bug fixes for 'minimal file...
2018-02-22 gmungocJAL-2629 tidy tests, refactor hmmer node mapping slightly
2018-02-22 gmungocJAL-2629 tidy unit tests, constants etc
2018-02-20 gmungocJAL-2629 removed SequenceI.get/setLastPosition and...
2018-02-20 gmungocMerge branch 'develop' into features/mchmmer
2018-01-29 kiramtJAL-2759 Fix unintended type change
2018-01-22 kiramtJAL-2579 Moved locateVisibleStartOfSequence to Sequence...
2018-01-19 kiramtJAL-2759 Changes to getVisibleSequenceStrings after...
2017-11-22 gmungocJAL-2069 spike updated with latest (FeatureTypeSettings)
2017-11-22 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-21 kiramtMerge branch 'develop' into feature/JAL-2759
2017-11-16 Jim ProcterMerge branch 'bug/JAL-2829deleteCharsWithGaps' into...
2017-11-15 gmungocJAL-2835 spike updated with latest
2017-11-13 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-11-13 gmungocJAL-2176 removed unused Sequence.index
2017-11-10 gmungocJAL-2829 fixes and unit tests bug/JAL-2829deleteCharsWithGaps
2017-11-08 kiramtMerge branch 'develop' into feature/JAL-2759
2017-10-27 gmungocJAL-1793 spike branch updated to latest
2017-10-24 gmungocJAL-2738 tidy Javadoc, remove debug logging
2017-10-24 gmungocJAL-2738 update spike branch with latest
2017-10-24 gmungocMerge branch 'develop' into features/JAL-1793VCF; lambd...
2017-10-23 Jim ProcterMerge branch 'bug/JAL-2682parseId' into develop
2017-10-20 gmungocPush 1793 latest to spike branch
2017-10-11 gmungocJAL-2772 check array bounds for sequence access bug/JAL-2772pdbArrayBounds
2017-10-10 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-09 gmungocJAL-2480 use interface type for sequenceFeatureStore
2017-10-03 gmungocJAL-2738 copy to spikes/mungo
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI!
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes
2017-09-21 kiramtJAL-2674 Rewrote propagateInsertions
2017-09-21 gmungocJAL-2738 GeneLoci holds mapping of sequence to chromosome
2017-08-29 osboxesJAL-2629 HMMs dropped on the alignment now map to the...
2017-08-25 TZVanaaltenJAL-2629 add multiple options for running hmmbuild...
2017-08-23 gmungocJAL-2682 non-regex sequence id parsing, and tests added
2017-08-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-2446NCList
2017-08-18 TZVanaaltenMerge branch 'develop' into features/hmmer
2017-08-16 Jim ProcterJAL-2418 source formatting
2017-08-11 TZVanaaltenJAL-2629 add ability to build a HMM from a group
2017-08-10 TZVanaaltenJAL-2629 hmmalign now correctly creates a new frame
2017-08-08 TZVanaaltenJAL-2599 fix for index issue on node lookup
2017-08-04 TZVanaaltenJAL-2629 multiple HMMs can now be dropped onto an alignment
2017-07-27 TZVanaaltenJAL-2629 moved HMM storage location to placeholder...
2017-06-24 gmungocJAL-2547 fix case of gap followed by enclosing contact...
2017-06-22 gmungocJAL-2481 JAL-2593 JAL-2526 further optimisation of...
2017-06-20 gmungocJAL-2526 don't retain lastColumnPosition from an invali...
2017-06-14 gmungocJAL-2598 Sequence.getSequence return a copy of the...
2017-06-09 gmungocJAL-2446 merged to spike branch
2017-06-08 gmungocJAL-2526 correct boundary conditions for sequence left...
2017-06-08 gmungocJAL-2526 cache first/last residue column positions...
2017-06-06 gmungocJAL-2526 less stringent test for invalid cursor
2017-06-05 gmungocMerge branch 'features/JAL-2526sequenceCursor' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into
2017-06-05 gmungocMerge branch 'features/JAL-2446NCList' into features/JAL-2526sequenceCursor
2017-06-05 gmungocMerge branch 'develop' into features/JAL-2446NCList
2017-06-04 Jim ProcterJAL-2291 bug fix - BitSet.set is [start,end+1)
2017-06-04 Jim ProcterJAL-2291 SequenceI.getInsertionsAsBits for convenient...
2017-06-02 gmungocJAL-2526 additional tests for findPosition with/without...
2017-06-01 gmungocJAL-2526 additional calls to sequenceChanged() after...
2017-06-01 gmungocJAL-2526 zapCursor() renamed sequenceChanged()
2017-06-01 gmungocJAL-2754 Sequence.findFeatures(fromCol, toCol) features/JAL-2754findFeaturesByColumn
2017-05-30 gmungocJAL-2526 first draft of findIndex/findPosition with...
2017-05-29 gmungocJAL-2526 Sequence.findPositions to get residue position...
2017-05-25 gmungocJAL-2557 removal of Sequence.sequenceFeatures
2017-05-24 gmungocMerge branch 'bug/JAL-2541cutWithFeatures' into feature...
2017-05-18 gmungocJAL-2541 fix to initSeqFrom (and minor code tidy);...
2017-05-09 gmungocJAL-2480 include sequenceFeatureStore in createDatasetS...
2017-04-27 gmungocJAL-2480 don't allow null type in SequenceFeature
2017-04-26 gmungocJAL-2490 findFeaturesAtRes with performant feature...
2017-04-19 gmungocJAL-2483 use SequenceFeatures to look up groups, types...
2017-04-18 gmungocJAL-2480 SequenceFeaturesI encapsulates features api
2017-04-17 gmungocJAL-2446 add call to SequenceFeatures.delete(); use...
2017-03-21 gmungocMerge branch 'develop' into features/JAL-2446NCList features/JAL-653_JAL-1766_htslib_refseqsupport
2017-03-20 gmungocJAL-2446 FeatureStore with NCList - work in progress
2016-11-14 gmungocJAL-2296 report whether SequenceFeature actually added...
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...
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