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JAL-629 example files from nf-core
[jalview.git]
/
src
/
jalview
/
datamodel
/
2023-01-11
Ben Soares
JAL-629 refactoring TFType. Remove i18n identification...
tree
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commitdiff
2022-12-05
Ben Soares
JAL-629 implementation of --tempfac options
tree
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commitdiff
2022-10-29
Jim Procter
Merge branch 'features/JAL-4061_and_JAL-4062_findselect...
tree
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commitdiff
2022-10-28
Jim Procter
JAL-2349 allow contact matrix to provide labels for...
tree
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commitdiff
2022-10-21
Jim Procter
JAL-4033 - heuristic threshold for pAE matrix - mark...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 formatting/pick correct exception
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 JAL-3855 off by one and daft return
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 JAL-3855 ContactListI.getPosition() to recover...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 JAL-3855 experimenting with filtering columns...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-3855 JAL-2349 AlignmentI.getContactList takes care...
tree
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commitdiff
2022-10-20
Jim Procter
JAL-2349 adjusted range calculation to be inclusive...
tree
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 column selection highlighting
tree
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commitdiff
2022-10-17
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-10-17
Jim Procter
JAL-2349 JAL-3855 Integrate pAE retrieval in StructureF...
tree
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commitdiff
2022-10-15
Jim Procter
JAL-2349 reusable contact map holder for SequenceI...
tree
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commitdiff
2022-10-14
Jim Procter
Merge branch 'features/JAL-3895_alphafoldcolours' into...
tree
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commitdiff
2022-10-06
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-10-06
Jim Procter
JAL-3895 alphafold colours via pluggable annotation...
tree
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commitdiff
2022-09-15
Jim Procter
JAL-4062 avc operation and model method for copying...
tree
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commitdiff
2022-06-10
Jim Procter
JAL-4027 getter for contact matrices on the Alignment.
tree
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commitdiff
2022-06-10
Jim Procter
JAL-1551 formatting
tree
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commitdiff
2022-06-10
Jim Procter
Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL...
tree
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commitdiff
2022-06-06
Jim Procter
JAL-4023 store distances as doubles
tree
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commitdiff
2022-04-16
Jim Procter
JAL-3365 expand range of allowed DSSP secondary structu...
tree
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commitdiff
2022-03-25
Jim Procter
JAL-3980 JAL-3979 TODOs
bug/JAL-3980_JAL-3981_tooltips_sequence_details
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3746 apply copyright to source
tree
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commitdiff
2022-03-08
Jim Procter
JAL-3438 spotless for 2.11.2.0
tree
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commitdiff
2022-02-16
Jim Procter
Merge branch 'develop' into features/r2_11_2_alphafold...
tree
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commitdiff
2022-02-14
Jim Procter
JAL-3956 - PDBEntry objects constructed from 3D-Beacons...
tree
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commitdiff
2022-02-04
Jim Procter
Merge branch 'bug/JAL-3806_mappingCoversSequence_for211...
bug/JAL-3806_without_shared_DS_for_2_11_2
tree
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commitdiff
2022-02-04
Jim Procter
JAL-3806 require mapping extent covers both sequence...
tree
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commitdiff
2022-01-28
Jim Procter
Merge branch 'merge/develop_JAL-3725' into develop
tree
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commitdiff
2022-01-26
Jim Procter
Merge branch 'task/JAL-3763_newDatasetForCds' into...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3806 (2.11.2 version) more lax allowance (3 positio...
tree
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commitdiff
2022-01-26
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2021-12-13
Jim Procter
JAL-3829 isCanonical should by default be false - ensur...
tree
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commitdiff
2021-11-05
Jim Procter
JAL-3919 use model format field to ensure we get the...
tree
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commitdiff
2021-10-01
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
tree
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commitdiff
2021-09-21
Jim Procter
JAL-3829 ignore the fake ID generated when a PDB format...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 ensure nulls are not wildcards when retrieving...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 store 3db metadata on PDBEntry so it can be...
tree
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commitdiff
2021-09-20
Jim Procter
JAL-3829 allow PDBEntry with file and ID with mismatchi...
tree
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commitdiff
2021-09-17
Jim Procter
JAL-2226 new method to search for annotation matching...
tree
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom/To revised with tests; unused...
tree
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commitdiff
2021-09-03
Jim Procter
JAL-3863 promote non-canonical version of dbref to...
tree
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commitdiff
2021-09-03
Jim Procter
JAL-3863 passing test to verify a uniprot accession...
tree
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commitdiff
2021-08-30
Jim Procter
JAL-3829 generalised Alphafold retrieval mechanism...
tree
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commitdiff
2021-08-30
Jim Procter
JAL-3863 mark first accession retrieved from Uniprot...
tree
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commitdiff
2021-08-30
Jim Procter
Merge branch 'feature/JAL-3855_ebi_alphafold_import...
tree
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commitdiff
2021-08-30
Jim Procter
JAL-3829 3d-beacons structure chooser logic (not yet...
tree
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commitdiff
2021-08-18
Jim Procter
JAL-2349 allow contact map to be associated with a...
tree
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commitdiff
2021-08-11
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into feature...
tree
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commitdiff
2021-06-09
Jim Procter
JAL-3840 don’t update the modal residue count for gaps
patch/JAL-3840_2_11_2
tree
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commitdiff
2021-06-09
Jim Procter
fixes JAL-3840
tree
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commitdiff
2021-06-09
Jim Procter
JAL-3840 failing test - show that addGaps overflows
tree
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commitdiff
2021-06-09
Jim Procter
JAL-3840 don’t update the modal residue count for gaps
patch/JAL-3840_2_11_1_4
tree
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commitdiff
2021-06-09
Jim Procter
fixes JAL-3840
tree
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commitdiff
2021-06-09
Jim Procter
JAL-3840 failing test - show that addGaps overflows
tree
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commitdiff
2021-03-04
Jim Procter
Revert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
tree
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commitdiff
2021-01-28
gmungoc
JAL-3806 more lax allowance (3 positions) for stop...
tree
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commitdiff
2020-10-28
gmungoc
JAL-3725 restrict mapped virtual feature location to...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 failsafe check for null
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
tree
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commitdiff
2020-10-22
gmungoc
JAL-3700 additions and corrections to unit tests
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
task/JAL-3763_newDatasetForCds
tree
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commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
tree
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commitdiff
2020-10-15
gmungoc
JAL-3763 unused method removed
tree
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commitdiff
2020-10-08
gmungoc
JAL-3763 failsafe check for null
tree
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commitdiff
2020-10-08
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
tree
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commitdiff
2020-09-23
Jim Procter
JAL-3748 not testing for sequence’s containment in...
bug/JAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2
tree
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commitdiff
2020-09-23
Jim Procter
JAL-3748 fix compilation error
tree
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commitdiff
2020-09-23
Jim Procter
JAL-3748 allow AlignedCodonFrame.covers to optionally...
tree
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commitdiff
2020-09-22
Jim Procter
JAL-3748 don’t trash start/end on SequenceI reconstruct...
tree
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commitdiff
2020-09-17
gmungoc
JAL-3700 additions and corrections to unit tests
bug/JAL-3700_mapSequenceSelection
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 preserve sequence IDs from original alignment...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 make findAlignedSequence require mapped from...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 pass a list to findAlignedSequence to return...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
tree
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commitdiff
2020-09-16
Jim Procter
Merge branch 'failingTest/JAL-3748_reconstructCDSafterP...
tree
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commitdiff
2020-09-16
gmungoc
JAL-3700 fix for propagation of sort commands
tree
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commitdiff
2020-09-16
gmungoc
JAL-3700 check for 'covering' mapping when matching...
tree
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commitdiff
2020-09-16
Jim Procter
JAL-3748 store an AlignmentView for the complement...
tree
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commitdiff
2020-08-17
Jim Procter
JAL-3490 merged with 2.11.2 develop
tree
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commitdiff
2020-08-17
Jim Procter
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL...
tree
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commitdiff
2020-08-10
gmungoc
JAL-3490 match count independent of contiguous matches...
patch/Release_2_11_1_Branch_patch_JAL-3490
tree
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commitdiff
2020-08-05
gmungoc
JAL-3700 fix for propagation of sort commands
tree
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commitdiff
2020-08-03
gmungoc
JAL-3700 check for 'covering' mapping when matching...
tree
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commitdiff
2020-07-27
gmungoc
JAL-3621 corrected sequence feature sort and test
tree
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commitdiff
2020-07-27
gmungoc
JAL-3621 update to intervalstore v1.1
tree
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commitdiff
2020-05-19
gmungoc
JAL-3621 corrected sequence feature sort and test
tree
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commitdiff
2020-05-19
gmungoc
Merge branch 'develop' into feature/JAL-3551Pymol
tree
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commitdiff
2020-05-18
gmungoc
JAL-3621 update to intervalstore v1.1
tree
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
tree
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commitdiff
2020-05-01
gmungoc
JAL-3613 check sequence overlap when matching search...
tree
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
tree
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commitdiff
2020-04-21
Jim Procter
JAL-3567 translated rather than imputed peptide
tree
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commitdiff
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