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JAL-3933 remove obsolete Castor logging configuration
[jalview.git] / src / jalview / datamodel /
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_1_4 tree | commitdiff
2021-06-09 Jim Procterfixes JAL-3840 tree | commitdiff
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows tree | commitdiff
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc... tree | commitdiff
2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop... tree | commitdiff
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests tree | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... tree | commitdiff
2020-10-22 gmungocJAL-3763 failsafe check for null tree | commitdiff
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual... tree | commitdiff
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2 tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 fix compilation error tree | commitdiff
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally... tree | commitdiff
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 preserve sequence IDs from original alignment... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return... tree | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq... tree | commitdiff
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true... tree | commitdiff
2020-09-16 Jim ProcterMerge branch 'failingTest/JAL-3748_reconstructCDSafterP... tree | commitdiff
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands tree | commitdiff
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching... tree | commitdiff
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement... tree | commitdiff
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL... tree | commitdiff
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490 tree | commitdiff
2020-07-27 gmungocJAL-3621 corrected sequence feature sort and test tree | commitdiff
2020-07-27 gmungocJAL-3621 update to intervalstore v1.1 tree | commitdiff
2020-05-01 gmungocJAL-3613 check sequence overlap when matching search... tree | commitdiff
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files tree | commitdiff
2020-04-21 Jim ProcterJAL-3567 translated rather than imputed peptide tree | commitdiff
2020-04-17 gmungocJAL-3567 unit tests for linked feature tooltips tree | commitdiff
2020-04-16 gmungocJAL-3567 adjust layout of linked feature report, unit... tree | commitdiff
2020-04-16 gmungocJAL-3567 added 'imputed by Jalview' to protein conseque... tree | commitdiff
2020-04-16 gmungocJAL-3567 report mapped location for virtual features... tree | commitdiff
2020-02-27 Jim ProcterMerge branch 'bug/JAL-3296changeStartInvalidateCursor... tree | commitdiff
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into... tree | commitdiff
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files tree | commitdiff
2019-09-26 gmungocJAL-2481 remove code duplication left by merge tree | commitdiff
2019-08-22 gmungocMerge branch 'develop' into feature/JAL-3121gffAttributeMap tree | commitdiff
2019-08-22 gmungocJAL-3187 case-insensitive codon variant calculation tree | commitdiff
2019-08-22 gmungocJAL-3121 round trip GFF attributes including map-valued... tree | commitdiff
2019-08-21 gmungocJAL-3187 minor code tidying, todo removal tree | commitdiff
2019-08-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-07-30 gmungocJAL-3198 more efficient Sequence.getDisplayId() tree | commitdiff
2019-07-26 gmungocMerge branch 'features/JAL-3375vcfValidation' into tree | commitdiff
2019-07-25 gmungocJAL-3375 ignore '.' values for VCF data tree | commitdiff
2019-07-08 gmungocJAL-3187 derived peptide variants tweaks and tests tree | commitdiff
2019-07-05 gmungocJAL-3187 initial refactoring towards peptide variant... tree | commitdiff
2019-06-17 gmungocJAL-2792 JAL-3187 linked features (if shown) in Feature... tree | commitdiff
2019-06-17 gmungocJAL-3187 add sequence to feature details table (and... tree | commitdiff
2019-06-13 gmungocJAL-3303 ignore deletions when computing peptide variants tree | commitdiff
2019-06-11 gmungocJAL-3187 CDS has same dataset sequence as transcript tree | commitdiff
2019-06-10 gmungocJAL-3296 ensure sequence cursor reset when sequence... bug/JAL-3296changeStartInvalidateCursor tree | commitdiff
2019-06-07 gmungocMerge branch 'develop' into feature/JAL-3187linkedFeatures tree | commitdiff
2019-06-07 gmungocJAL-2738 use GeneLocus extends DBRefEntry to hold chrom... tree | commitdiff
2019-06-06 gmungocMerge branch 'develop' into trialMerge tree | commitdiff
2019-03-21 Ben SoaresJAL-3130 Replaced deprecated Class.newInstance() with... tree | commitdiff
2019-03-20 Ben SoaresJAL-3130 Lots of deprecation fixes. See utils/deprecat... tree | commitdiff
2019-03-11 gmungocMerge branch 'feature/JAL-3127_seqidChainshading' into... tree | commitdiff
2019-03-05 gmungocMerge remote-tracking branch 'origin/bug/JAL-2839findWi... tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3072scrollThread' into merge... tree | commitdiff
2019-03-04 gmungocMerge remote-tracking branch 'origin/bug/JAL-3082select... tree | commitdiff
2019-03-04 gmungocMerge branch 'bug/JAL-3099alignmentVisibleWidth' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'bug/JAL-3164complementOverview' into... tree | commitdiff
2019-03-01 gmungocMerge branch 'feature/intervalStoreJ' into merge/JAL... tree | commitdiff
2019-03-01 gmungocJAL-3140 reduced coupling to intervalstore.jar feature/intervalStoreJ tree | commitdiff
2019-02-28 gmungocJAL-3140 confine intervalstore imports to jalview.datam... tree | commitdiff
2019-02-24 gmungocJAL-3198 SequenceGroup 'bulk constructor' without dupli... tree | commitdiff
2019-02-21 gmungocJAL-3187 handle no mapping / complement features withou... tree | commitdiff
2019-02-20 gmungocJAL-3187 read peptide variant from CSQ:HGVSp if present... tree | commitdiff
2019-02-19 gmungocJAL-3187 hacks to get peptide variant in to Jmol hover... tree | commitdiff
2019-01-21 gmungocJAL-3187 unit tests updated and errors caught tree | commitdiff
2019-01-21 gmungocJAL-3187 findFeaturesAtResidue answer in render order... tree | commitdiff
2019-01-21 gmungocJAL-3187 (hacked up) show complement features on struct... tree | commitdiff
2019-01-16 Jim ProcterMerge branch 'features/pca_jaxb_datasetrefs_JAL-3171_JA... tree | commitdiff
2018-12-19 Jim ProcterMerge branch 'features/JAL-1767pcaInProject' into bug... tree | commitdiff
2018-12-17 Jim ProcterMerge branch 'bug/JAL-2750' into develop tree | commitdiff
2018-12-17 Jim ProcterMerge branch 'develop' into bug/JAL-2541cutRelocateFeatures tree | commitdiff
2018-12-06 Ben SoaresJAL-3130 incorporating feature/JAL-3063jaxbNoCastor... tree | commitdiff
2018-11-29 gmungocJAL-3140 NCList now via IntervalStore library tree | commitdiff
2018-11-28 gmungocJAL-3164 redraw complement overview on hide columns bug/JAL-3164complementOverview tree | commitdiff
2018-11-19 Jim ProcterJAL-3156 JAL-3127 code tidy tree | commitdiff
2018-11-19 Jim ProcterJAL-3156 javadoc re JAL-3127 and FIXME to make Alignmen... tree | commitdiff
2018-09-14 gmungocJAL-3116 parse EMBL XML with JAXB (todo: update unit... tree | commitdiff
2018-09-13 gmungocJAL-3116 Uniprot XML unmarshalled using JAXB not Castor tree | commitdiff
2018-09-11 Jim ProcterMerge branch 'develop' into releases/Release_2_11_Branch tree | commitdiff
2018-09-10 gmungocJAL-3099 new method AlignmentI.getVisibleWidth() tree | commitdiff
2018-08-27 Ben SoaresJAL-3061 / JAL-3053 tree | commitdiff
2018-08-16 gmungocJAL-3082 handle regex error, exclusive threshold, unit... tree | commitdiff
2018-08-10 gmungocJAL-3076 refactor for more efficient scan of 'gene... tree | commitdiff
2018-08-02 Ben SoaresJAL-3053 tree | commitdiff
2018-07-30 bsoaresFixed bug ignoring "alpha" extended braces in RNA SS... tree | commitdiff
2018-07-25 gmungocJAL-3074 don't scroll up/down on drag out of scale... tree | commitdiff
2018-06-04 Jim ProcterJAL-3017 parse multiple variant elements for uniprot... tree | commitdiff
2018-06-02 Jim ProcterJAL-3017 parse multiple variant elements for uniprot... tree | commitdiff
2018-05-31 gmungocJAL-2808 don't capture or report min-max for mixed... tree | commitdiff
2018-05-28 gmungocMerge remote-tracking branch 'origin/releases/Release_2... tree | commitdiff
2018-05-21 gmungocJAL-2920 use HGVS notation for protein variant feature tree | commitdiff
2018-05-11 gmungocJAL-2986 corrected findIndex for out of range residue... tree | commitdiff
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