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JAL-2850 MapList.isToForwardStrand added
[jalview.git]
/
src
/
2017-10-11
gmungoc
JAL-2609 tidy label width code, some checkstyle warnings
tree
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commitdiff
2017-10-11
gmungoc
Merge branch 'bug/JAL-2742' into develop
tree
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commitdiff
2017-10-11
gmungoc
Merge branch 'bug/JAL-2757_uniprotftsbadquery' into...
tree
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commitdiff
2017-10-11
gmungoc
JAL-2757 fix PDB also; suppress stack trace and compile...
bug/JAL-2757_uniprotftsbadquery
tree
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commitdiff
2017-10-11
gmungoc
JAL-2738 javadoc correction
tree
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commitdiff
2017-10-11
kiramt
JAL-2742 removed unused getViewAsCigars
tree
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commitdiff
2017-10-11
kiramt
JAL-2609attemptedmerge tidy
tree
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commitdiff
2017-10-10
kiramt
Merge remote-tracking branch 'origin/features/JAL-2609f...
tree
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commitdiff
2017-10-10
kiramt
JAL-2690attemptedmerge seems to work
tree
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commitdiff
2017-10-10
Jim Procter
JAL-2392 wrap public progress bar methods as InvokeLate...
tree
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commitdiff
2017-10-10
Jim Procter
JAL-2392 formatting
tree
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commitdiff
2017-10-10
Jim Procter
Merge branch 'codereviews/JAL-1990_IProgressIndicator_j...
tree
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commitdiff
2017-10-10
Jim Procter
Merge branch 'features/JAL-2523httpRetries' into develop
tree
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commitdiff
2017-10-10
kiramt
JAL-2690attemptedmerge partial merge
tree
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commitdiff
2017-10-10
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-09
gmungoc
JAL-2480 use interface type for sequenceFeatureStore
tree
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commitdiff
2017-10-09
gmungoc
JAL-2523 basic sleep and retry (3 times) on 429 respons...
features/JAL-2523httpRetries
tree
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commitdiff
2017-10-09
gmungoc
JAL-2523 convenience method to get model organisms
tree
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commitdiff
2017-10-09
Jim Procter
JAL-2446 remove duplicate code from pulled up method.
tree
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commitdiff
2017-10-09
gmungoc
JAL-2738 ensure variant feature is in forward sense
tree
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commitdiff
2017-10-09
gmungoc
JAL-2738 remove commented code, unit test coverage
tree
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commitdiff
2017-10-06
Jim Procter
JAL-2758 flag and tests for omitting uniprot accession...
features/JAL-2758_shorteruniprot
tree
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commitdiff
2017-10-05
Jim Procter
JAL-2757 reset textbox after a non HTTP 200 response
tree
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commitdiff
2017-10-05
gmungoc
JAL-2738 warn (in console) when non chromosomal coordin...
tree
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commitdiff
2017-10-05
gmungoc
JAL-2738 helper method for convolving mappings
tree
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commitdiff
2017-10-05
gmungoc
JAL-2755 transfer chromosomal reference from transcript...
tree
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commitdiff
2017-10-05
gmungoc
JAL-2738 method to compound / traverse / convolve two...
tree
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commitdiff
2017-10-05
gmungoc
JAL-2744 add score to feature details report, descripti...
tree
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commitdiff
2017-10-04
gmungoc
JAL-2738 fix bug of premature exit from adding attributes
tree
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commitdiff
2017-10-04
gmungoc
JAL-2523 start of refactoring...
tree
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commitdiff
2017-10-04
gmungoc
JAL-2738 match consequence "Allele" to VCF allele;...
tree
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commitdiff
2017-10-04
gmungoc
JAL-2744 handle null features list
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 code formatting
tree
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commitdiff
2017-10-02
gmungoc
JAL-2738 code tidy up, null checks &c
tree
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commitdiff
2017-10-02
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-02
gmungoc
JAL-2525 lookup transcript features by Ontology
tree
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commitdiff
2017-10-02
gmungoc
JAL-2738 filter VEP consequence data to that for curren...
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2748 formatting
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 JAL-2748 direct download of XML from uniprot.org
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2748 formatting
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 JAL-2748 direct download of XML from uniprot.org
tree
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commitdiff
2017-09-29
gmungoc
JAL-2738 one sequence feature per (SNP) VCF allele
tree
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commitdiff
2017-09-29
gmungoc
JAL-2744 indent CSQ lines to catch the eye
tree
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commitdiff
2017-09-29
Jim Procter
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
tree
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commitdiff
2017-09-29
Jim Procter
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 update default EBI-eye search URL to HTTPS
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 update SIFTS FTP URL to HTTPS
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 update default EBI-eye search URL to HTTPS
feature/JAL-2745ebiHttps
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 update SIFTS FTP URL to HTTPS
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 stderr rather than stdout for unexpected HTTP...
tree
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commitdiff
2017-09-29
Jim Procter
JAL-2745 stderr rather than stdout for unexpected HTTP...
tree
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commitdiff
2017-09-29
gmungoc
JAL-2745 update www.ebi.ac.uk to https
tree
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commitdiff
2017-09-28
gmungoc
JAL-2745 update www.ebi.ac.uk to https
tree
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commitdiff
2017-09-28
gmungoc
JAL-2738 separate thread to load VCF; update FeatureSet...
tree
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commitdiff
2017-09-28
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-09-28
gmungoc
JAL-2036 set menus after fully loading AlignFrame
tree
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commitdiff
2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
tree
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commitdiff
2017-09-28
gmungoc
JAL-2744 simple Feature Details report from Popup menu
tree
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commitdiff
2017-09-28
gmungoc
JAL-2744 refactor PopupMenu constructor to enable addin...
tree
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commitdiff
2017-09-26
kiramt
JAL-2742 fixed
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 transfer VCF variant features to CDS sequences
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 JAL-2154 add DBRef from transcript to synthesi...
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 unit test for reverse strand gene
tree
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commitdiff
2017-09-26
gmungoc
JAL-2738 promote setGeneLoci to SequenceI!
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 use complement base for a VCF variant on rever...
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 getGeneLoci promoted to SequenceI
tree
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commitdiff
2017-09-25
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-09-25
gmungoc
JAL-2525 return no features if none matches ontology...
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 query unindexed file, unit test for VCFLoader
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
tree
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commitdiff
2017-09-25
gmungoc
JAL-2738 extract SNP variants from SNP or MIXED variant...
tree
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commitdiff
2017-09-22
gmungoc
JAL-2738 extract utility method to MappingUtils
tree
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commitdiff
2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
tree
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commitdiff
2017-09-22
kiramt
JAL-2739 Fix ported to 2.10.3
tree
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commitdiff
2017-09-22
gmungoc
JAL-2738 lookup GRCh38/37 gene mapping
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 compute VCF on peptide, extract AF (allele...
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 add chromosome coordinate mappings to transcripts
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 PoC of Load VCF file on to gene sequence
tree
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commitdiff
2017-09-21
gmungoc
JAL-2738 GeneLoci holds mapping of sequence to chromosome
tree
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commitdiff
2017-09-19
gmungoc
JAL-1793 wrapper for plain or indexed VCF + simple...
tree
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commitdiff
2017-09-18
gmungoc
Merge remote-tracking branch 'origin/patch/JAL-2732...
tree
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commitdiff
2017-09-18
gmungoc
JAL-2728 fine tuned initial split of split frame view
tree
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commitdiff
2017-09-15
Jim Procter
JAL-1625 ensure we don’t regress on JAL-20 - we always...
patch/JAL-2732
tree
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commitdiff
2017-09-15
Jim Procter
JAL-1625 javadoc
tree
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commitdiff
2017-09-15
Jim Procter
JAL-2733 redraw after changing the memory status displa...
tree
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commitdiff
2017-09-15
Jim Procter
JAL-1625 JAL-1900 preserve the original DesktopManager...
tree
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commitdiff
2017-09-15
Jim Procter
JAL-1900 JAL-1625 back out OSX specific double buffer...
tree
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commitdiff
2017-09-15
Jim Procter
JAL-1551 standard code formatting
tree
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commitdiff
2017-09-15
Jim Procter
JAL-2732 force a redraw after resize/drag to clear...
tree
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commitdiff
2017-09-15
gmungoc
JAL-2728 use right denominator for min/max ratio calcul...
bug/JAL-2728splitFrameDivision
tree
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commitdiff
2017-09-15
gmungoc
JAL-2728 limit divider to ensure seqs visible (wip!)
tree
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commitdiff
2017-09-15
gmungoc
JAL-741 add tooltip to feature group checkbox
tree
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commitdiff
2017-09-14
gmungoc
JAL-2727 null more fields in AlignmentViewport.dispose...
tree
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commitdiff
2017-09-14
gmungoc
JAL-2727 method to check if PCAPanel thread is working
tree
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commitdiff
2017-09-13
gmungoc
JAL-2727 null additional references on close
tree
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commitdiff
2017-09-12
gmungoc
Merge branch 'bug/JAL-2721fastPaintNPE' into develop
tree
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commitdiff
2017-09-12
gmungoc
Revert "JAL-2727 null hconsensus, "
tree
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commitdiff
2017-09-12
gmungoc
JAL-2727 null hconsensus,
tree
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commitdiff
2017-09-12
gmungoc
JAL-2727 ensure ViewportRanges (and gapcounts) are...
tree
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commitdiff
2017-09-07
gmungoc
JAL-2511 invalidate scale panel holder on font change...
tree
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commitdiff
next