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jalview.git
2017-10-10
kiramt
JAL-2690attemptedmerge seems to work
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2017-10-10
Jim Procter
JAL-2392 wrap public progress bar methods as InvokeLate...
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2017-10-10
Jim Procter
JAL-2392 formatting
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2017-10-10
Jim Procter
Merge branch 'codereviews/JAL-1990_IProgressIndicator_j...
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2017-10-10
Jim Procter
JAL-2523 release notes
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2017-10-10
Jim Procter
Merge branch 'features/JAL-2523httpRetries' into develop
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2017-10-10
kiramt
JAL-2690attemptedmerge partial merge
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2017-10-10
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-10-09
gmungoc
JAL-2480 use interface type for sequenceFeatureStore
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2017-10-09
gmungoc
JAL-2523 basic sleep and retry (3 times) on 429 respons...
features/JAL-2523httpRetries
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2017-10-09
gmungoc
JAL-2523 convenience method to get model organisms
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2017-10-09
Jim Procter
Merge branch 'patch/JAL-2446_mergeconflictmissed' into...
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2017-10-09
Jim Procter
JAL-2446 remove duplicate code from pulled up method.
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2017-10-09
gmungoc
JAL-2738 ensure variant feature is in forward sense
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2017-10-09
gmungoc
JAL-2738 assertion for derived protein variant added
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2017-10-09
gmungoc
JAL-2738 remove commented code, unit test coverage
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2017-10-06
Jim Procter
Merge branch 'patch/JAL-2116_java9_antjnlpfix' into...
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2017-10-06
Jim Procter
JAL-2116 fix jnlp file post-processing so java 9 module...
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2017-10-06
gmungoc
JAL-2753 add new jar to lib folder!
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2017-10-06
gmungoc
JAL-2753 update to htsjdk 2.12.0 (requires Java 8)
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2017-10-06
gmungoc
JAL-2754 update to Java 1.8
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2017-10-06
gmungoc
JAL-2738 unit test for mapping failure case
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2017-10-05
Jim Procter
JAL-2757 reset textbox after a non HTTP 200 response
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2017-10-05
gmungoc
JAL-2738 warn (in console) when non chromosomal coordin...
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2017-10-05
gmungoc
JAL-2738 helper method for convolving mappings
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2017-10-05
gmungoc
JAL-2755 transfer chromosomal reference from transcript...
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2017-10-05
gmungoc
JAL-2738 method to compound / traverse / convolve two...
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2017-10-05
gmungoc
JAL-2744 add score to feature details report, descripti...
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2017-10-04
gmungoc
JAL-2738 fix bug of premature exit from adding attributes
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2017-10-04
gmungoc
JAL-2523 start of refactoring...
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2017-10-04
gmungoc
JAL-2738 match consequence "Allele" to VCF allele;...
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2017-10-04
gmungoc
JAL-2744 handle null features list
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2017-10-03
Jim Procter
Merge branch 'releases/Release_2_10_2b1_Branch' into...
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2017-10-03
gmungoc
JAL-2738 update test for threaded VCFLoader
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2017-10-03
gmungoc
JAL-2738 code formatting
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2017-10-02
gmungoc
JAL-2738 code tidy up, null checks &c
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2017-10-02
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-10-02
gmungoc
JAL-2525 lookup transcript features by Ontology
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2017-10-02
gmungoc
JAL-2738 filter VEP consequence data to that for curren...
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2017-10-01
Jim Procter
Merge branch 'documentation/JAL-2751patch2102b2' into...
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2017-10-01
Jim Procter
JAL-2751 what's new for 2.10.2b2 patch
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2017-10-01
Jim Procter
JAL-2751 patch release notes
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2017-09-30
Jim Procter
JAL-2751 bump version and new releases entry
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2017-09-29
Jim Procter
Merge branch 'feature/JAL-2745ebiHttps' into develop
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2017-09-29
Jim Procter
JAL-2748 JAL-2745 remove uniprot from EBI fetch client...
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2017-09-29
Jim Procter
JAL-2745 patch tests for https
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2017-09-29
Jim Procter
JAL-2748 formatting
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2017-09-29
Jim Procter
JAL-2745 JAL-2748 direct download of XML from uniprot.org
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2017-09-29
Jim Procter
JAL-2748 JAL-2745 remove uniprot from EBI fetch client...
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2017-09-29
Jim Procter
JAL-2745 patch tests for https
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2017-09-29
Jim Procter
JAL-2748 formatting
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2017-09-29
Jim Procter
JAL-2745 JAL-2748 direct download of XML from uniprot.org
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2017-09-29
gmungoc
JAL-2738 one sequence feature per (SNP) VCF allele
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2017-09-29
gmungoc
JAL-2744 indent CSQ lines to catch the eye
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2017-09-29
Jim Procter
Merge branch 'feature/JAL-2745ebiHttps' into develop
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2017-09-29
Jim Procter
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
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2017-09-29
Jim Procter
Revert "JAL-2745 update SIFTS FTP URL to HTTPS"
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2017-09-29
Jim Procter
Merge branch 'feature/JAL-2745ebiHttps' into develop
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2017-09-29
Jim Procter
JAL-2745 update default EBI-eye search URL to HTTPS
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2017-09-29
Jim Procter
JAL-2745 update SIFTS FTP URL to HTTPS
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2017-09-29
Jim Procter
JAL-2745 update default EBI-eye search URL to HTTPS
feature/JAL-2745ebiHttps
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2017-09-29
Jim Procter
JAL-2745 update SIFTS FTP URL to HTTPS
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2017-09-29
Jim Procter
Merge branch 'feature/JAL-2745ebiHttps' into develop
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2017-09-29
Jim Procter
JAL-2745 stderr rather than stdout for unexpected HTTP...
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2017-09-29
Jim Procter
JAL-2745 stderr rather than stdout for unexpected HTTP...
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2017-09-29
gmungoc
JAL-2745 update www.ebi.ac.uk to https
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2017-09-28
gmungoc
JAL-2745 update www.ebi.ac.uk to https
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2017-09-28
gmungoc
JAL-2738 separate thread to load VCF; update FeatureSet...
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2017-09-28
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-09-28
gmungoc
JAL-2036 set menus after fully loading AlignFrame
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2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
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2017-09-28
gmungoc
JAL-2744 simple Feature Details report from Popup menu
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2017-09-28
gmungoc
JAL-2744 refactor PopupMenu constructor to enable addin...
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2017-09-26
kiramt
JAL-2742 uncomment test
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2017-09-26
kiramt
JAL-2742 fixed
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2017-09-26
kiramt
JAL-2742 CigarArray constructor unit test
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2017-09-26
gmungoc
JAL-2738 transfer VCF variant features to CDS sequences
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2017-09-26
gmungoc
JAL-2738 JAL-2154 add DBRef from transcript to synthesi...
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2017-09-26
gmungoc
JAL-2738 unit test for reverse strand gene
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2017-09-26
gmungoc
JAL-2738 promote setGeneLoci to SequenceI!
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2017-09-25
gmungoc
JAL-2738 use complement base for a VCF variant on rever...
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2017-09-25
gmungoc
JAL-2738 getGeneLoci promoted to SequenceI
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2017-09-25
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
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2017-09-25
gmungoc
JAL-2525 return no features if none matches ontology...
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2017-09-25
gmungoc
JAL-2738 query unindexed file, unit test for VCFLoader
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2017-09-25
gmungoc
JAL-2738 one constant in codebase for "alleles" attribu...
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2017-09-25
gmungoc
JAL-2738 extract SNP variants from SNP or MIXED variant...
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2017-09-22
gmungoc
JAL-2738 extract utility method to MappingUtils
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2017-09-22
gmungoc
JAL-2738 correct handling of reverse strand genes
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2017-09-22
kiramt
JAL-2739 Fix ported to 2.10.3
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2017-09-22
gmungoc
JAL-2738 lookup GRCh38/37 gene mapping
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2017-09-21
gmungoc
JAL-2738 compute VCF on peptide, extract AF (allele...
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2017-09-21
gmungoc
JAL-2738 add chromosome coordinate mappings to transcripts
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2017-09-21
gmungoc
JAL-2738 PoC of Load VCF file on to gene sequence
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2017-09-21
gmungoc
JAL-2738 GeneLoci holds mapping of sequence to chromosome
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2017-09-20
kiramt
JAL-2662 Adjustments to hidden columns benchmark
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2017-09-19
gmungoc
JAL-1793 wrapper for plain or indexed VCF + simple...
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2017-09-19
kiramt
JAL-2662 Updated README
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2017-09-19
kiramt
JAL-2737 Checkstyle error fixes
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2017-09-19
kiramt
JAL-2622 Tidied up gitignore, added to README
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