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JAL-4366 compute coverage on each side of the pairwise alignment
[jalview.git]
/
src
/
jalview
/
datamodel
/
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
2020-04-17
gmungoc
JAL-3567 unit tests for linked feature tooltips
tree
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commitdiff
2020-04-16
gmungoc
JAL-3567 adjust layout of linked feature report, unit...
tree
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commitdiff
2020-04-16
gmungoc
JAL-3567 added 'imputed by Jalview' to protein conseque...
tree
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commitdiff
2020-04-16
gmungoc
JAL-3567 report mapped location for virtual features...
tree
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commitdiff
2020-03-30
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2020-02-27
Jim Procter
Merge branch 'bug/JAL-3296changeStartInvalidateCursor...
tree
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commitdiff
2020-01-28
gmungoc
Merge branch 'feature/JAL-3121gffAttributeMap' into...
tree
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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
tree
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commitdiff
2019-10-08
gmungoc
Merge branch 'develop' into Jalview-JS/develop
tree
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commitdiff
2019-09-26
gmungoc
JAL-2481 remove code duplication left by merge
tree
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commitdiff
2019-08-22
gmungoc
Merge branch 'develop' into feature/JAL-3121gffAttributeMap
tree
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commitdiff
2019-08-22
gmungoc
JAL-3187 case-insensitive codon variant calculation
tree
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commitdiff
2019-08-22
gmungoc
JAL-3121 round trip GFF attributes including map-valued...
tree
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commitdiff
2019-08-21
gmungoc
JAL-3187 minor code tidying, todo removal
tree
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commitdiff
2019-08-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-07-30
gmungoc
JAL-3198 more efficient Sequence.getDisplayId()
tree
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commitdiff
2019-07-26
gmungoc
Merge branch 'features/JAL-3375vcfValidation' into
tree
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commitdiff
2019-07-25
gmungoc
JAL-3375 ignore '.' values for VCF data
tree
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commitdiff
2019-07-16
gmungoc
JAL-3210 Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-07-08
gmungoc
JAL-3187 derived peptide variants tweaks and tests
tree
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commitdiff
2019-07-05
gmungoc
JAL-3187 initial refactoring towards peptide variant...
tree
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commitdiff
2019-06-18
Jim Procter
Merge branch 'features/JAL-2349_matrixvis' into merge...
tree
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commitdiff
2019-06-17
gmungoc
JAL-2792 JAL-3187 linked features (if shown) in Feature...
tree
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commitdiff
2019-06-17
gmungoc
JAL-3187 add sequence to feature details table (and...
tree
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commitdiff
2019-06-13
gmungoc
JAL-3303 ignore deletions when computing peptide variants
tree
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commitdiff
2019-06-11
gmungoc
JAL-3187 CDS has same dataset sequence as transcript
tree
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commitdiff
2019-06-10
gmungoc
JAL-3296 ensure sequence cursor reset when sequence...
bug/JAL-3296changeStartInvalidateCursor
tree
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commitdiff
2019-06-07
gmungoc
Merge branch 'develop' into feature/JAL-3187linkedFeatures
tree
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commitdiff
2019-06-07
gmungoc
JAL-2738 use GeneLocus extends DBRefEntry to hold chrom...
tree
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commitdiff
2019-06-06
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-04-18
hansonr
minor code clean up
tree
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commitdiff
2019-04-18
hansonr
minor code clean up
tree
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commitdiff
2019-04-03
hansonr
j2sNative clean-up. Fixes problem with second try of...
tree
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commitdiff
2019-03-21
Ben Soares
JAL-3130 Replaced deprecated Class.newInstance() with...
tree
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commitdiff
2019-03-20
Ben Soares
JAL-3130 Lots of deprecation fixes. See utils/deprecat...
tree
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commitdiff
2019-03-13
gmungoc
Merge branch 'develop' into trialMerge
tree
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commitdiff
2019-03-11
gmungoc
Merge branch 'feature/JAL-3127_seqidChainshading' into...
tree
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commitdiff
2019-03-05
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-2839findWi...
tree
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3072scrollThread' into merge...
tree
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commitdiff
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