Merge branch 'develop' into feature/JAL-3121gffAttributeMap
[jalview.git] / src / jalview / datamodel /
2019-08-22 gmungocMerge branch 'develop' into feature/JAL-3121gffAttributeMap
2019-08-22 gmungocJAL-3187 case-insensitive codon variant calculation
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued...
2019-08-21 gmungocJAL-3187 minor code tidying, todo removal
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId()
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant...
2019-06-17 gmungocJAL-2792 JAL-3187 linked features (if shown) in Feature...
2019-06-17 gmungocJAL-3187 add sequence to feature details table (and...
2019-06-13 gmungocJAL-3303 ignore deletions when computing peptide variants
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
2019-06-06 gmungocMerge branch 'develop' into trialMerge
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with...
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat...
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into...
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi...
2019-03-04 gmungocMerge branch 'bug/JAL-3072scrollThread' into merge...
2019-03-04 gmungocMerge remote-tracking branch 'origin/bug/JAL-3082select...
2019-03-04 gmungocMerge branch 'bug/JAL-3099alignmentVisibleWidth' into...
2019-03-01 gmungocMerge branch 'bug/JAL-3164complementOverview' into...
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL...
2019-03-01 gmungocJAL-3140 reduced coupling to intervalstore.jar feature/intervalStoreJ
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam...
2019-02-24 gmungocJAL-3198 SequenceGroup 'bulk constructor' without dupli...
2019-02-21 gmungocJAL-3187 handle no mapping / complement features withou...
2019-02-20 gmungocJAL-3187 read peptide variant from CSQ:HGVSp if present...
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover...
2019-01-21 gmungocJAL-3187 unit tests updated and errors caught
2019-01-21 gmungocJAL-3187 findFeaturesAtResidue answer in render order...
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct...
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA...
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug...
2018-12-17 Jim ProcterMerge branch 'bug/JAL-2750' into develop
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor...
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library
2018-11-28 gmungocJAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview
2018-11-19 Jim ProcterJAL-3156 JAL-3127 code tidy
2018-11-19 Jim ProcterJAL-3156 javadoc re JAL-3127 and FIXME to make Alignmen...
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit...
2018-09-13 gmungocJAL-3116 Uniprot XML unmarshalled using JAXB not Castor
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch
2018-09-10 gmungocJAL-3099 new method AlignmentI.getVisibleWidth()
2018-08-27 Ben SoaresJAL-3061 / JAL-3053
2018-08-16 gmungocJAL-3082 handle regex error, exclusive threshold, unit...
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene...
2018-08-02 Ben SoaresJAL-3053
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS...
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale...
2018-06-04 Jim ProcterJAL-3017 parse multiple variant elements for uniprot...
2018-06-02 Jim ProcterJAL-3017 parse multiple variant elements for uniprot...
2018-05-31 gmungocJAL-2808 don't capture or report min-max for mixed...
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-05-21 gmungocJAL-2920 use HGVS notation for protein variant feature
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue...
2018-05-10 Jim ProcterMerge branch 'bug/JAL-2920_uniprotvariantfeature' into...
2018-05-10 Jim ProcterJAL-2920 simplified logic and added corner cases for...
2018-05-07 gmungocMerge branch 'releases/Release_2_10_4_Branch' into...
2018-05-07 gmungocJAL-1767 unit test for save and restore PCA features/JAL-1767pcaInProject
2018-05-07 Jim ProcterJAL-2906 apply GPLv3 license source
2018-05-04 gmungocJAL-1767 refactorings to enable faithful restore of...
2018-04-27 gmungocJAL-1767 refactoring and tidying of RotatableCanvas...
2018-04-26 gmungocJAL-2962 code tidying/documentation (non-functional...
2018-04-23 gmungocJAL-2954 more efficient SearchResults.markColumns
2018-03-16 gmungocMerge remote-tracking branch 'origin/releases/Release_2...
2018-03-14 gmungocJAL-2893 include ENSEMBLGENOMES as a 'roundtrip db...
2018-03-13 gmungocJAL-2839 addResult ignores duplicates
2018-03-09 gmungocJAL-2839 Finder refactoring prior to fixing the defect
2018-03-07 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-03-07 gmungocJAL-2925 handle empty annotation when copying group...
2018-02-27 Jim ProcterMerge branch 'feature/JAL-2759' into merge/JAL-2759_2104
2018-02-26 Jim ProcterJAL-2920 parse variation and original elements of the...
2018-02-21 Jim ProcterMerge branch 'bug/JAL-2778again' into releases/Release_...
2018-02-21 kiramtJAL-2778 Revert back to old synchronisation
2018-02-20 Jim ProcterMerge branch 'releases/Release_2_10_4_Branch' into...
2018-02-06 kiramtMerge branch 'develop' into feature/JAL-2759 feature/JAL-2759
2018-02-05 Jim ProcterJAL-2780 JAL-2781 - patch and first test for AlignmentI...
2018-02-05 kiramtJAL-2759 Fix errant RangeElementsIterator (unit tests...
2018-02-05 kiramtJAL-2759 Rename getBoundedStartIterator
2018-02-05 kiramtJAL-2759 Changes to StartRegionIterator after review
2018-02-05 kiramtJAL-2788 possible adjustments to sequence accesses
2018-02-01 kiramtJAL-2759 use right iterator for getVisibleColsIterator
2018-01-31 kiramtJAL-2759 Rationalise VisibleColsIterator and HiddenCols...
2018-01-31 kiramtJAL-2759 Generalised HiddenColsIterator naming
2018-01-31 kiramtJAL-2759 minor refactor to hiding bitsets
2018-01-30 kiramtJAL-2759 Add missing hiddenColumns empty check
2018-01-30 kiramtJAL-2759 updateForDeletedRegion no longer needed
2018-01-30 kiramtJAL-2759 Rationalising hidden cols cursor, and sorting...
2018-01-30 kiramtJAL-2759 comment
2018-01-30 kiramtJAL-2759 Additional tests and tweaks to numColumns...
2018-01-30 kiramtJAL-2759 Keep numColumns up to date
2018-01-29 kiramtJAL-2759 Combine findRegionForColumn code in HiddenColu...
2018-01-29 kiramtJAL-2759 numColumns reset
2018-01-29 kiramtJAL-2759 remove redundant hiddenColumns.clear()
2018-01-29 kiramtJAL-2759 Tidy
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