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Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD
[jalview.git]
/
src
/
jalview
/
datamodel
/
2022-11-21
Jim Procter
Merge commit 'alpha/update_2_12_for_2_11_2_series_merge...
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
2021-09-21
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
2021-06-09
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
2020-12-14
Jim Procter
Merge branch 'Jalview-JS/develop' into merge_js_develop
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
2020-06-30
gmungoc
JAL-3446 unused imports removed
tree
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commitdiff
2020-06-06
BobHanson
JAL-3446 adds Jmol viewer embedding.
tree
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commitdiff
2020-06-04
gmungoc
JAL-3446 post-merge unit test fixes, formatting
tree
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commitdiff
2020-06-03
BobHanson
JAL-3664 support for user.home, user.dir, user
tree
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commitdiff
2020-06-03
BobHanson
JAL-3446 from JAL-3253 ApplicationSingletonProvider...
tree
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commitdiff
2020-06-03
BobHanson
JAL-3446 from JAL-3253 ApplicationSingletonProvider
tree
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commitdiff
2020-06-03
BobHanson
JAL-3446 from JAL-3253 ApplicationSingletonProvider...
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
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
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
2020-04-23
Jim Procter
Merge branch 'develop' into alpha/JAL-3362_Jalview_212_...
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
Jim Procter
JAL-3070 allow SequenceI.findPositions(0,column+1)...
tree
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commitdiff
2019-09-26
gmungoc
JAL-2481 remove code duplication left by merge
tree
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commitdiff
2019-09-26
Jim Procter
JAL-3070 JAL-3066 AlignmentI.findOrAddAnnotation(Alignm...
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
2019-08-13
Jim Procter
Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into...
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
2019-07-10
Jim Procter
Merge branch 'merge/JAL-3285_mchmmer_with_211_develop...
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
2019-07-03
tva
JAL-2629 evalues and bit scores now conserved after...
tree
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commitdiff
2019-07-03
tva
JAL-2629 can now filter by sequence e-value or bit...
tree
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commitdiff
2019-07-02
tva
JAL-2629 add simple jackhmmer functionality
tree
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commitdiff
2019-06-28
tva
JAL-2629 add HMM Match Score colour scheme
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
tva
JAL-3297 pad gaps in alignment to ensure hmmalign runs
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
tva
JAL-3291 issue fixed, passing tests added
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
2019-06-05
tva
JAL-3285 add unmerged code to AlignmentAnnotation
tree
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commitdiff
2019-06-05
tva
JAL-3285 add unmerged code to SequenceGroup
tree
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commitdiff
2019-06-04
Jim Procter
Merge branch 'develop' into developtomchmmer
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
2019-03-04
gmungoc
Merge remote-tracking branch 'origin/bug/JAL-3082select...
tree
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commitdiff
2019-03-04
gmungoc
Merge branch 'bug/JAL-3099alignmentVisibleWidth' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'bug/JAL-3164complementOverview' into...
tree
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commitdiff
2019-03-01
gmungoc
Merge branch 'feature/intervalStoreJ' into merge/JAL...
tree
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commitdiff
2019-03-01
gmungoc
JAL-3140 reduced coupling to intervalstore.jar
feature/intervalStoreJ
tree
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commitdiff
2019-02-28
gmungoc
JAL-3140 confine intervalstore imports to jalview.datam...
tree
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commitdiff
2019-02-24
gmungoc
JAL-3198 SequenceGroup 'bulk constructor' without dupli...
tree
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commitdiff
2019-02-21
gmungoc
JAL-3187 handle no mapping / complement features withou...
tree
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commitdiff
2019-02-20
gmungoc
JAL-3187 read peptide variant from CSQ:HGVSp if present...
tree
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commitdiff
2019-02-19
gmungoc
JAL-3187 hacks to get peptide variant in to Jmol hover...
tree
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commitdiff
2019-02-04
hansonr
refactoring for DBMODList
tree
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commitdiff
2019-01-29
hansonr
iterators
tree
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commitdiff
2019-01-26
hansonr
Platform.timecheck calls removed or commented out.
tree
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commitdiff
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