jalview.git
2017-10-19 gmungocJAL-2755 put chromosomal dbref first in report
2017-10-19 gmungocJAL-2755 add lookup of cds/cdna gene loci
2017-10-19 gmungocJAL-2755 add species lookup
2017-10-19 gmungocJAL-2755 add missing Javadoc
2017-10-19 gmungocJAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
2017-10-11 gmungocJAL-2738 javadoc correction
2017-10-10 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-09 gmungocJAL-2480 use interface type for sequenceFeatureStore
2017-10-09 Jim ProcterMerge branch 'patch/JAL-2446_mergeconflictmissed' into...
2017-10-09 Jim ProcterJAL-2446 remove duplicate code from pulled up method.
2017-10-09 gmungocJAL-2738 ensure variant feature is in forward sense
2017-10-09 gmungocJAL-2738 assertion for derived protein variant added
2017-10-09 gmungocJAL-2738 remove commented code, unit test coverage
2017-10-06 Jim ProcterMerge branch 'patch/JAL-2116_java9_antjnlpfix' into...
2017-10-06 Jim ProcterJAL-2116 fix jnlp file post-processing so java 9 module...
2017-10-06 gmungocJAL-2753 add new jar to lib folder!
2017-10-06 gmungocJAL-2753 update to htsjdk 2.12.0 (requires Java 8)
2017-10-06 gmungocJAL-2754 update to Java 1.8
2017-10-06 gmungocJAL-2738 unit test for mapping failure case
2017-10-05 gmungocJAL-2738 warn (in console) when non chromosomal coordin...
2017-10-05 gmungocJAL-2738 helper method for convolving mappings
2017-10-05 gmungocJAL-2755 transfer chromosomal reference from transcript...
2017-10-05 gmungocJAL-2738 method to compound / traverse / convolve two...
2017-10-05 gmungocJAL-2744 add score to feature details report, descripti...
2017-10-04 gmungocJAL-2738 fix bug of premature exit from adding attributes
2017-10-04 gmungocJAL-2738 match consequence "Allele" to VCF allele;...
2017-10-04 gmungocJAL-2744 handle null features list
2017-10-03 Jim ProcterMerge branch 'releases/Release_2_10_2b1_Branch' into...
2017-10-03 gmungocJAL-2738 update test for threaded VCFLoader
2017-10-03 gmungocJAL-2738 code formatting
2017-10-02 gmungocJAL-2738 code tidy up, null checks &c
2017-10-02 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-10-02 gmungocJAL-2525 lookup transcript features by Ontology
2017-10-02 gmungocJAL-2738 filter VEP consequence data to that for curren...
2017-10-01 Jim ProcterMerge branch 'documentation/JAL-2751patch2102b2' into...
2017-10-01 Jim ProcterJAL-2751 what's new for 2.10.2b2 patch
2017-10-01 Jim ProcterJAL-2751 patch release notes
2017-09-30 Jim ProcterJAL-2751 bump version and new releases entry
2017-09-29 Jim ProcterMerge branch 'feature/JAL-2745ebiHttps' into develop
2017-09-29 Jim ProcterJAL-2748 JAL-2745 remove uniprot from EBI fetch client...
2017-09-29 Jim ProcterJAL-2745 patch tests for https
2017-09-29 Jim ProcterJAL-2748 formatting
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org
2017-09-29 Jim ProcterJAL-2748 JAL-2745 remove uniprot from EBI fetch client...
2017-09-29 Jim ProcterJAL-2745 patch tests for https
2017-09-29 Jim ProcterJAL-2748 formatting
2017-09-29 Jim ProcterJAL-2745 JAL-2748 direct download of XML from uniprot.org
2017-09-29 gmungocJAL-2738 one sequence feature per (SNP) VCF allele
2017-09-29 gmungocJAL-2744 indent CSQ lines to catch the eye
2017-09-29 Jim ProcterMerge branch 'feature/JAL-2745ebiHttps' into develop
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS"
2017-09-29 Jim ProcterRevert "JAL-2745 update SIFTS FTP URL to HTTPS"
2017-09-29 Jim ProcterMerge branch 'feature/JAL-2745ebiHttps' into develop
2017-09-29 Jim ProcterJAL-2745 update default EBI-eye search URL to HTTPS
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS
2017-09-29 Jim ProcterJAL-2745 update default EBI-eye search URL to HTTPS feature/JAL-2745ebiHttps
2017-09-29 Jim ProcterJAL-2745 update SIFTS FTP URL to HTTPS
2017-09-29 Jim ProcterMerge branch 'feature/JAL-2745ebiHttps' into develop
2017-09-29 Jim ProcterJAL-2745 stderr rather than stdout for unexpected HTTP...
2017-09-29 Jim ProcterJAL-2745 stderr rather than stdout for unexpected HTTP...
2017-09-29 gmungocJAL-2745 update www.ebi.ac.uk to https
2017-09-28 gmungocJAL-2745 update www.ebi.ac.uk to https
2017-09-28 gmungocJAL-2738 separate thread to load VCF; update FeatureSet...
2017-09-28 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-09-28 gmungocJAL-2036 set menus after fully loading AlignFrame
2017-09-28 gmungocJAL-1796 GeneLociI as distinguished DBRefEntry
2017-09-28 gmungocJAL-2744 simple Feature Details report from Popup menu
2017-09-28 gmungocJAL-2744 refactor PopupMenu constructor to enable addin...
2017-09-26 gmungocJAL-2738 transfer VCF variant features to CDS sequences
2017-09-26 gmungocJAL-2738 JAL-2154 add DBRef from transcript to synthesi...
2017-09-26 gmungocJAL-2738 unit test for reverse strand gene
2017-09-26 gmungocJAL-2738 promote setGeneLoci to SequenceI!
2017-09-25 gmungocJAL-2738 use complement base for a VCF variant on rever...
2017-09-25 gmungocJAL-2738 getGeneLoci promoted to SequenceI
2017-09-25 gmungocMerge branch 'develop' into features/JAL-1793VCF
2017-09-25 gmungocJAL-2525 return no features if none matches ontology...
2017-09-25 gmungocJAL-2738 query unindexed file, unit test for VCFLoader
2017-09-25 gmungocJAL-2738 one constant in codebase for "alleles" attribu...
2017-09-25 gmungocJAL-2738 extract SNP variants from SNP or MIXED variant...
2017-09-22 gmungocJAL-2738 extract utility method to MappingUtils
2017-09-22 gmungocJAL-2738 correct handling of reverse strand genes
2017-09-22 gmungocJAL-2738 lookup GRCh38/37 gene mapping
2017-09-21 gmungocJAL-2738 compute VCF on peptide, extract AF (allele...
2017-09-21 gmungocJAL-2738 add chromosome coordinate mappings to transcripts
2017-09-21 gmungocJAL-2738 PoC of Load VCF file on to gene sequence
2017-09-21 gmungocJAL-2738 GeneLoci holds mapping of sequence to chromosome
2017-09-20 kiramtJAL-2662 Adjustments to hidden columns benchmark
2017-09-19 gmungocJAL-1793 wrapper for plain or indexed VCF + simple...
2017-09-19 kiramtJAL-2662 Updated README
2017-09-19 kiramtJAL-2737 Checkstyle error fixes
2017-09-19 kiramtJAL-2622 Tidied up gitignore, added to README
2017-09-19 kiramtMerge branch 'develop' of https://source.jalview.org...
2017-09-19 kiramtMerge remote-tracking branch 'origin/task/JAL-2662...
2017-09-19 gmungocJAL-1793 simple tests of reading raw and indexed VCF...
2017-09-18 gmungocMerge remote-tracking branch 'origin/patch/JAL-2732...
2017-09-18 gmungocJAL-2728 fine tuned initial split of split frame view
2017-09-15 Jim ProcterMerge branch 'documentation/JAL-2698_release2103' into...
2017-09-15 Jim ProcterJAL-2698 new releases.html entry, whatsNew.html and...
2017-09-15 Jim ProcterMerge branch 'bug/JAL-2728splitFrameDivision' into...
2017-09-15 Jim ProcterJAL-1625 ensure we don’t regress on JAL-20 - we always... patch/JAL-2732
next