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JAL-3989 Code tidying, added JVL_HEADER for older versions of Jalview, allow time...
[jalview.git] / src / jalview / datamodel /
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu... tree | commitdiff
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details tree | commitdiff
2022-03-08 Jim ProcterJAL-3746 apply copyright to source tree | commitdiff
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0 tree | commitdiff
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons... tree | commitdiff
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2 tree | commitdiff
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence... tree | commitdiff
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop tree | commitdiff
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into... tree | commitdiff
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio... tree | commitdiff
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur... tree | commitdiff
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the... tree | commitdiff
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to... tree | commitdiff
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC... tree | commitdiff
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 store 3db metadata on PDBEntry so it can be... tree | commitdiff
2021-09-20 Jim ProcterJAL-3829 allow PDBEntry with file and ID with mismatchi... tree | commitdiff
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching... tree | commitdiff
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused... tree | commitdiff
2021-09-03 Jim ProcterJAL-3863 promote non-canonical version of dbref to... tree | commitdiff
2021-09-03 Jim ProcterJAL-3863 passing test to verify a uniprot accession... tree | commitdiff
2021-08-30 Jim ProcterJAL-3829 generalised Alphafold retrieval mechanism... tree | commitdiff
2021-08-30 Jim ProcterJAL-3863 mark first accession retrieved from Uniprot... tree | commitdiff
2021-08-30 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import... tree | commitdiff
2021-08-30 Jim ProcterJAL-3829 3d-beacons structure chooser logic (not yet... tree | commitdiff
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_2 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
2021-06-09 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
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests task/JAL-3763_newDatasetForCds tree | commitdiff
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped... tree | commitdiff
2020-10-15 gmungocJAL-3763 unused method removed tree | commitdiff
2020-10-08 gmungocJAL-3763 failsafe check for null tree | commitdiff
2020-10-08 gmungocJAL-3763 refactored getCoveringMapping for virtual... 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
2020-09-17 gmungocJAL-3700 additions and corrections to unit tests bug/JAL-3700_mapSequenceSelection 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 ProcterJAL-3490 merged with 2.11.2 develop 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
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands tree | commitdiff
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching... 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
2020-05-19 gmungocJAL-3621 corrected sequence feature sort and test tree | commitdiff
2020-05-19 gmungocMerge branch 'develop' into feature/JAL-3551Pymol tree | commitdiff
2020-05-18 gmungocJAL-3621 update to intervalstore v1.1 tree | commitdiff
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop 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
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop 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
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop 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
2019-07-16 gmungocJAL-3210 Merge branch 'develop' into trialMerge 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
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