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Merge branch 'releases/Release_2_11_4_Branch'
[jalview.git]
/
src
/
jalview
/ datamodel
2021-11-05
Jim Procter
JAL-3919 use model format field to ensure we get the...
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commitdiff
2021-10-01
gmungoc
JAL-3725 restrict mapped virtual feature location to...
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commitdiff
2021-09-21
Ben Soares
JAL-3691 automatic insertion of Locale.ROOT to toUpperC...
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commitdiff
2021-09-21
Jim Procter
JAL-3829 ignore the fake ID generated when a PDB format...
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commitdiff
2021-09-20
Jim Procter
JAL-3829 ensure nulls are not wildcards when retrieving...
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commitdiff
2021-09-20
Jim Procter
JAL-3829 store 3db metadata on PDBEntry so it can be...
commit
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commitdiff
2021-09-20
Jim Procter
JAL-3829 allow PDBEntry with file and ID with mismatchi...
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commitdiff
2021-09-17
Jim Procter
JAL-2226 new method to search for annotation matching...
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commitdiff
2021-09-16
gmungoc
JAL-3761 locateInFrom/To revised with tests; unused...
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commitdiff
2021-09-03
Jim Procter
JAL-3863 promote non-canonical version of dbref to...
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commitdiff
2021-09-03
Jim Procter
JAL-3863 passing test to verify a uniprot accession...
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commitdiff
2021-08-30
Jim Procter
JAL-3829 generalised Alphafold retrieval mechanism...
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commitdiff
2021-08-30
Jim Procter
JAL-3863 mark first accession retrieved from Uniprot...
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commitdiff
2021-08-30
Jim Procter
Merge branch 'feature/JAL-3855_ebi_alphafold_import...
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commitdiff
2021-08-30
Jim Procter
JAL-3829 3d-beacons structure chooser logic (not yet...
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commitdiff
2021-08-18
Jim Procter
JAL-2349 allow contact map to be associated with a...
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commitdiff
2021-08-11
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into feature...
commit
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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
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commitdiff
2021-06-09
Jim Procter
fixes JAL-3840
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commitdiff
2021-06-09
Jim Procter
JAL-3840 failing test - show that addGaps overflows
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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
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commitdiff
2021-06-09
Jim Procter
fixes JAL-3840
commit
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commitdiff
2021-06-09
Jim Procter
JAL-3840 failing test - show that addGaps overflows
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commitdiff
2021-03-04
Jim Procter
Revert "Merge branch 'bug/JAL-3806_mappingCoversSequenc...
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commitdiff
2021-01-28
gmungoc
JAL-3806 more lax allowance (3 positions) for stop...
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commitdiff
2020-10-28
gmungoc
JAL-3725 restrict mapped virtual feature location to...
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commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
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commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
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commitdiff
2020-10-22
gmungoc
JAL-3763 failsafe check for null
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commitdiff
2020-10-22
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
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commitdiff
2020-10-22
gmungoc
JAL-3700 additions and corrections to unit tests
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commitdiff
2020-10-22
gmungoc
JAL-3763 Javadoc, check for null, additional tests
task/JAL-3763_newDatasetForCds
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commitdiff
2020-10-22
gmungoc
JAL-3763 test coverage for AlignedCodonFrame.markMapped...
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commitdiff
2020-10-15
gmungoc
JAL-3763 unused method removed
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commitdiff
2020-10-08
gmungoc
JAL-3763 failsafe check for null
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commitdiff
2020-10-08
gmungoc
JAL-3763 refactored getCoveringMapping for virtual...
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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
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commitdiff
2020-09-23
Jim Procter
JAL-3748 fix compilation error
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commitdiff
2020-09-23
Jim Procter
JAL-3748 allow AlignedCodonFrame.covers to optionally...
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commitdiff
2020-09-22
Jim Procter
JAL-3748 don’t trash start/end on SequenceI reconstruct...
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commitdiff
2020-09-17
gmungoc
JAL-3700 additions and corrections to unit tests
bug/JAL-3700_mapSequenceSelection
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commitdiff
2020-09-16
Jim Procter
JAL-3748 preserve sequence IDs from original alignment...
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commitdiff
2020-09-16
Jim Procter
JAL-3748 make findAlignedSequence require mapped from...
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commitdiff
2020-09-16
Jim Procter
JAL-3748 pass a list to findAlignedSequence to return...
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commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 use AlignedCodonFrame.covers(seq...
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commitdiff
2020-09-16
Jim Procter
JAL-3700 JAL-3748 AlignedCodonFrame.covers(seq,true...
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commitdiff
2020-09-16
Jim Procter
Merge branch 'failingTest/JAL-3748_reconstructCDSafterP...
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commitdiff
2020-09-16
gmungoc
JAL-3700 fix for propagation of sort commands
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commitdiff
2020-09-16
gmungoc
JAL-3700 check for 'covering' mapping when matching...
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commitdiff
2020-09-16
Jim Procter
JAL-3748 store an AlignmentView for the complement...
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commitdiff
2020-08-17
Jim Procter
JAL-3490 merged with 2.11.2 develop
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commitdiff
2020-08-17
Jim Procter
Merge branch 'patch/Release_2_11_1_Branch_patch_JAL...
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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
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commitdiff
2020-08-05
gmungoc
JAL-3700 fix for propagation of sort commands
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commitdiff
2020-08-03
gmungoc
JAL-3700 check for 'covering' mapping when matching...
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commitdiff
2020-07-27
gmungoc
JAL-3621 corrected sequence feature sort and test
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commitdiff
2020-07-27
gmungoc
JAL-3621 update to intervalstore v1.1
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commitdiff
2020-05-19
gmungoc
JAL-3621 corrected sequence feature sort and test
commit
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commitdiff
2020-05-19
gmungoc
Merge branch 'develop' into feature/JAL-3551Pymol
commit
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commitdiff
2020-05-18
gmungoc
JAL-3621 update to intervalstore v1.1
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commitdiff
2020-05-18
gmungoc
Merge branch 'Jalview-JS/develop' into develop
commit
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commitdiff
2020-05-01
gmungoc
JAL-3613 check sequence overlap when matching search...
commit
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commitdiff
2020-04-21
Jim Procter
JAL-3407 add GPL license to Jalview source files
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commitdiff
2020-04-21
Jim Procter
JAL-3567 translated rather than imputed peptide
commit
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commitdiff
2020-04-17
gmungoc
JAL-3567 unit tests for linked feature tooltips
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commitdiff
2020-04-16
gmungoc
JAL-3567 adjust layout of linked feature report, unit...
commit
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commitdiff
2020-04-16
gmungoc
JAL-3567 added 'imputed by Jalview' to protein conseque...
commit
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commitdiff
2020-04-16
gmungoc
JAL-3567 report mapped location for virtual features...
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
commit
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commitdiff
2020-02-27
Jim Procter
Merge branch 'bug/JAL-3296changeStartInvalidateCursor...
commit
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commitdiff
2020-01-28
gmungoc
Merge branch 'feature/JAL-3121gffAttributeMap' into...
commit
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commitdiff
2019-11-01
Ben Soares
JAL-3474 removed all .cvsignore files stored in the...
improvement/JAL-3474_lots_of_.cvsignore_files
commit
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
commit
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commitdiff
2019-09-26
gmungoc
JAL-2481 remove code duplication left by merge
commit
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commitdiff
2019-08-22
gmungoc
Merge branch 'develop' into feature/JAL-3121gffAttributeMap
commit
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commitdiff
2019-08-22
gmungoc
JAL-3187 case-insensitive codon variant calculation
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commitdiff
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
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commitdiff
2019-08-21
gmungoc
JAL-3187 minor code tidying, todo removal
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commitdiff
2019-08-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
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commitdiff
2019-07-30
gmungoc
JAL-3198 more efficient Sequence.getDisplayId()
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commitdiff
2019-07-26
gmungoc
Merge branch 'features/JAL-3375vcfValidation' into
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commitdiff
2019-07-25
gmungoc
JAL-3375 ignore '.' values for VCF data
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
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commitdiff
2019-07-08
gmungoc
JAL-3187 derived peptide variants tweaks and tests
commit
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commitdiff
2019-07-05
gmungoc
JAL-3187 initial refactoring towards peptide variant...
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commitdiff
2019-06-18
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into merge...
commit
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commitdiff
2019-06-17
gmungoc
JAL-2792 JAL-3187 linked features (if shown) in Feature...
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commitdiff
2019-06-17
gmungoc
JAL-3187 add sequence to feature details table (and...
commit
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commitdiff
2019-06-13
gmungoc
JAL-3303 ignore deletions when computing peptide variants
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commitdiff
2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
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commitdiff
2019-06-10
gmungoc
JAL-3296 ensure sequence cursor reset when sequence...
bug/JAL-3296changeStartInvalidateCursor
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
commit
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
commit
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commitdiff
2019-04-18
hansonr
minor code clean up
commit
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commitdiff
2019-04-18
hansonr
minor code clean up
commit
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commitdiff
2019-04-03
hansonr
j2sNative clean-up. Fixes problem with second try of...
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
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commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
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