Merge branch 'JAL-3878_ws-overhaul-3' into with_ws_overhaul-3
[jalview.git] / src / jalview / datamodel /
2023-01-30 Jim ProcterMerge branch 'JAL-3878_ws-overhaul-3' into with_ws_over...
2022-12-14 Jim ProcterMerge branch 'develop' into update_212_Dec_merge_with_2...
2022-12-13 Jim ProcterMerge branch 'alpha/origin_2022_JAL-3066_Jalview_212_sl...
2022-11-21 Jim ProcterMerge commit 'alpha/update_2_12_for_2_11_2_series_merge...
2022-06-06 Jim ProcterJAL-4023 store distances as doubles
2022-04-16 Jim ProcterJAL-3365 expand range of allowed DSSP secondary structu...
2022-04-05 Mateusz WarownyJAL-3878 Add char[] constructor to Sequence
2022-03-25 Jim ProcterJAL-3980 JAL-3979 TODOs bug/JAL-3980_JAL-3981_tooltips_sequence_details
2022-03-08 Jim ProcterJAL-3746 apply copyright to source
2022-03-08 Jim ProcterJAL-3438 spotless for 2.11.2.0
2022-02-14 Jim ProcterJAL-3956 - PDBEntry objects constructed from 3D-Beacons...
2022-02-04 Jim ProcterMerge branch 'bug/JAL-3806_mappingCoversSequence_for211... bug/JAL-3806_without_shared_DS_for_2_11_2
2022-02-04 Jim ProcterJAL-3806 require mapping extent covers both sequence...
2022-01-28 Jim ProcterMerge branch 'merge/develop_JAL-3725' into develop
2022-01-26 Jim ProcterMerge branch 'task/JAL-3763_newDatasetForCds' into...
2022-01-26 gmungocJAL-3806 (2.11.2 version) more lax allowance (3 positio...
2022-01-26 gmungocJAL-3725 restrict mapped virtual feature location to...
2021-12-13 Jim ProcterJAL-3829 isCanonical should by default be false - ensur...
2021-11-05 Jim ProcterJAL-3919 use model format field to ensure we get the...
2021-10-06 Mateusz WarownyJAL-3899 Update usages of uniquify and deuniquify.
2021-10-01 gmungocJAL-3725 restrict mapped virtual feature location to...
2021-09-21 Ben SoaresJAL-3691 automatic insertion of Locale.ROOT to toUpperC...
2021-09-21 Jim ProcterJAL-3829 ignore the fake ID generated when a PDB format...
2021-09-20 Jim ProcterJAL-3829 ensure nulls are not wildcards when retrieving...
2021-09-20 Jim ProcterJAL-3829 store 3db metadata on PDBEntry so it can be...
2021-09-20 Jim ProcterJAL-3829 allow PDBEntry with file and ID with mismatchi...
2021-09-17 Jim ProcterJAL-2226 new method to search for annotation matching...
2021-09-16 gmungocJAL-3761 locateInFrom/To revised with tests; unused...
2021-09-03 Jim ProcterJAL-3863 promote non-canonical version of dbref to...
2021-09-03 Jim ProcterJAL-3863 passing test to verify a uniprot accession...
2021-08-30 Jim ProcterJAL-3829 generalised Alphafold retrieval mechanism...
2021-08-30 Jim ProcterJAL-3863 mark first accession retrieved from Uniprot...
2021-08-30 Jim ProcterMerge branch 'feature/JAL-3855_ebi_alphafold_import...
2021-08-30 Jim ProcterJAL-3829 3d-beacons structure chooser logic (not yet...
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_2
2021-06-09 Jim Procterfixes JAL-3840
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows
2021-06-09 Jim ProcterJAL-3840 don’t update the modal residue count for gaps patch/JAL-3840_2_11_1_4
2021-06-09 Jim Procterfixes JAL-3840
2021-06-09 Jim ProcterJAL-3840 failing test - show that addGaps overflows
2021-03-04 Jim ProcterRevert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
2021-01-28 gmungocJAL-3806 more lax allowance (3 positions) for stop...
2020-12-14 Jim ProcterMerge branch 'Jalview-JS/develop' into merge_js_develop
2020-10-28 gmungocJAL-3725 restrict mapped virtual feature location to...
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped...
2020-10-22 gmungocJAL-3763 failsafe check for null
2020-10-22 gmungocJAL-3763 refactored getCoveringMapping for virtual...
2020-10-22 gmungocJAL-3700 additions and corrections to unit tests
2020-10-22 gmungocJAL-3763 Javadoc, check for null, additional tests task/JAL-3763_newDatasetForCds
2020-10-22 gmungocJAL-3763 test coverage for AlignedCodonFrame.markMapped...
2020-10-15 gmungocJAL-3763 unused method removed
2020-10-08 gmungocJAL-3763 failsafe check for null
2020-10-08 gmungocJAL-3763 refactored getCoveringMapping for virtual...
2020-09-23 Jim ProcterJAL-3748 not testing for sequence’s containment in... bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
2020-09-23 Jim ProcterJAL-3748 fix compilation error
2020-09-23 Jim ProcterJAL-3748 allow AlignedCodonFrame.covers to optionally...
2020-09-22 Jim ProcterJAL-3748 don’t trash start/end on SequenceI reconstruct...
2020-09-17 gmungocJAL-3700 additions and corrections to unit tests bug/JAL-3700_mapSequenceSelection
2020-09-16 Jim ProcterJAL-3748 preserve sequence IDs from original alignment...
2020-09-16 Jim ProcterJAL-3748 make findAlignedSequence require mapped from...
2020-09-16 Jim ProcterJAL-3748 pass a list to findAlignedSequence to return...
2020-09-16 Jim ProcterJAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
2020-09-16 Jim ProcterJAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
2020-09-16 Jim ProcterMerge branch 'failingTest/JAL-3748_reconstructCDSafterP...
2020-09-16 gmungocJAL-3700 fix for propagation of sort commands
2020-09-16 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-09-16 Jim ProcterJAL-3748 store an AlignmentView for the complement...
2020-08-17 Jim ProcterJAL-3490 merged with 2.11.2 develop
2020-08-17 Jim ProcterMerge branch 'patch/Release_2_11_1_Branch_patch_JAL...
2020-08-10 gmungocJAL-3490 match count independent of contiguous matches... patch/Release_2_11_1_Branch_patch_JAL-3490
2020-08-05 gmungocJAL-3700 fix for propagation of sort commands
2020-08-03 gmungocJAL-3700 check for 'covering' mapping when matching...
2020-07-27 gmungocJAL-3621 corrected sequence feature sort and test
2020-07-27 gmungocJAL-3621 update to intervalstore v1.1
2020-06-30 gmungocJAL-3446 unused imports removed
2020-06-06 BobHansonJAL-3446 adds Jmol viewer embedding.
2020-06-04 gmungocJAL-3446 post-merge unit test fixes, formatting
2020-06-03 BobHansonJAL-3664 support for user.home, user.dir, user
2020-06-03 BobHansonJAL-3446 from JAL-3253 ApplicationSingletonProvider...
2020-06-03 BobHansonJAL-3446 from JAL-3253 ApplicationSingletonProvider
2020-06-03 BobHansonJAL-3446 from JAL-3253 ApplicationSingletonProvider...
2020-05-19 gmungocJAL-3621 corrected sequence feature sort and test
2020-05-19 gmungocMerge branch 'develop' into feature/JAL-3551Pymol
2020-05-18 gmungocJAL-3621 update to intervalstore v1.1
2020-05-18 Jim ProcterMerge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
2020-05-18 gmungocMerge branch 'Jalview-JS/develop' into develop
2020-05-01 gmungocJAL-3613 check sequence overlap when matching search...
2020-04-23 Jim ProcterMerge branch 'develop' into alpha/JAL-3362_Jalview_212_...
2020-04-21 Jim ProcterJAL-3407 add GPL license to Jalview source files
2020-04-21 Jim ProcterJAL-3567 translated rather than imputed peptide
2020-04-17 gmungocJAL-3567 unit tests for linked feature tooltips
2020-04-16 gmungocJAL-3567 adjust layout of linked feature report, unit...
2020-04-16 gmungocJAL-3567 added 'imputed by Jalview' to protein conseque...
2020-04-16 gmungocJAL-3567 report mapped location for virtual features...
2020-03-30 gmungocMerge branch 'develop' into Jalview-JS/develop
2020-02-27 Jim ProcterMerge branch 'bug/JAL-3296changeStartInvalidateCursor...
2020-01-28 gmungocMerge branch 'feature/JAL-3121gffAttributeMap' into...
2019-11-01 Ben SoaresJAL-3474 removed all .cvsignore files stored in the... improvement/JAL-3474_lots_of_.cvsignore_files
2019-10-08 gmungocMerge branch 'develop' into Jalview-JS/develop
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