| 2017-10-27 |
gmungoc | JAL-2792 include source in copy constructor; null pointer...
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commit | commitdiff | tree |
| 2017-10-27 |
gmungoc | JAL-2754 update to specify Java 1.8(+)
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commit | commitdiff | tree |
| 2017-10-27 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF
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commit | commitdiff | tree |
| 2017-10-27 |
gmungoc | JAL-2792 capture feature metadata and render in Feature...
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commit | commitdiff | tree |
| 2017-10-26 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF
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commit | commitdiff | tree |
| 2017-10-26 |
gmungoc | JAL-2792 html table for Feature Details report
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commit | commitdiff | tree |
| 2017-10-25 |
gmungoc | JAL-2743 fall back to parsing description if chromosome...
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-2495 highlight all mapped sequences from structure...
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-2743 slightly fancier species/assembly matching...
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-2738 tidy Javadoc, remove debug logging
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-2743 look up species and gene loci for Ensembl...
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-1739 Javadoc updated for Lambda expression parser...
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF; lambda...
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-2788 corrected merge error in propertyChange
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commit | commitdiff | tree |
| 2017-10-24 |
gmungoc | JAL-2787 set start/end seq explicitly for test
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commit | commitdiff | tree |
| 2017-10-23 |
gmungoc | JAL-2776 repaint everything on toggle group colour
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commit | commitdiff | tree |
| 2017-10-23 |
gmungoc | JAL-1854 keep fallthrough but with comment to suppress...
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commit | commitdiff | tree |
| 2017-10-23 |
gmungoc | JAL-1854 remove fallthrough of switch case (Checkstyle...
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commit | commitdiff | tree |
| 2017-10-23 |
gmungoc | JAL-2737 JAL-1854 corrected package suppressions, updated...
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commit | commitdiff | tree |
| 2017-10-20 |
gmungoc | JAL-2253 pull up constant, additional unit test
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commit | commitdiff | tree |
| 2017-10-20 |
gmungoc | JAL-2755 update caller for method rename!
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commit | commitdiff | tree |
| 2017-10-20 |
gmungoc | JAL-2609 fully erase scale above, tidy code change
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2609 adjustments for test findings
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2755 find gene loci for fetched xrefs where possible
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2755 put chromosomal dbref first in report
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2755 add lookup of cds/cdna gene loci
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2755 add species lookup
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2755 add missing Javadoc
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commit | commitdiff | tree |
| 2017-10-19 |
gmungoc | JAL-2755 rename EnsemblInfo as EnsemblData, add 'true...
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | JAL-2609 tests updated for revised label width
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | JAL-2772 check array bounds for sequence access
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | JAL-2609 tidy label width code, some checkstyle warnings
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | Merge branch 'bug/JAL-2742' into develop
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | JAL-2742 set HiddenColumns null for no hidden coluns...
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | Merge branch 'bug/JAL-2757_uniprotftsbadquery' into...
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | JAL-2757 fix PDB also; suppress stack trace and compiler...
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commit | commitdiff | tree |
| 2017-10-11 |
gmungoc | JAL-2738 javadoc correction
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commit | commitdiff | tree |
| 2017-10-10 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF
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commit | commitdiff | tree |
| 2017-10-09 |
gmungoc | JAL-2480 use interface type for sequenceFeatureStore
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commit | commitdiff | tree |
| 2017-10-09 |
gmungoc | JAL-2523 basic sleep and retry (3 times) on 429 response...
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commit | commitdiff | tree |
| 2017-10-09 |
gmungoc | JAL-2523 convenience method to get model organisms
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commit | commitdiff | tree |
| 2017-10-09 |
gmungoc | JAL-2738 ensure variant feature is in forward sense
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commit | commitdiff | tree |
| 2017-10-09 |
gmungoc | JAL-2738 assertion for derived protein variant added
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commit | commitdiff | tree |
| 2017-10-09 |
gmungoc | JAL-2738 remove commented code, unit test coverage
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commit | commitdiff | tree |
| 2017-10-06 |
gmungoc | JAL-2753 add new jar to lib folder!
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commit | commitdiff | tree |
| 2017-10-06 |
gmungoc | JAL-2753 update to htsjdk 2.12.0 (requires Java 8)
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commit | commitdiff | tree |
| 2017-10-06 |
gmungoc | JAL-2754 update to Java 1.8
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commit | commitdiff | tree |
| 2017-10-06 |
gmungoc | JAL-2738 unit test for mapping failure case
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commit | commitdiff | tree |
| 2017-10-05 |
gmungoc | JAL-2738 warn (in console) when non chromosomal coordinates...
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commit | commitdiff | tree |
| 2017-10-05 |
gmungoc | JAL-2738 helper method for convolving mappings
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commit | commitdiff | tree |
| 2017-10-05 |
gmungoc | JAL-2755 transfer chromosomal reference from transcript...
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commit | commitdiff | tree |
| 2017-10-05 |
gmungoc | JAL-2738 method to compound / traverse / convolve two...
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commit | commitdiff | tree |
| 2017-10-05 |
gmungoc | JAL-2744 add score to feature details report, description...
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commit | commitdiff | tree |
| 2017-10-04 |
gmungoc | JAL-2738 fix bug of premature exit from adding attributes
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commit | commitdiff | tree |
| 2017-10-04 |
gmungoc | JAL-2523 start of refactoring...
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commit | commitdiff | tree |
| 2017-10-04 |
gmungoc | JAL-2738 match consequence "Allele" to VCF allele;...
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commit | commitdiff | tree |
| 2017-10-04 |
gmungoc | JAL-2744 handle null features list
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commit | commitdiff | tree |
| 2017-10-03 |
gmungoc | JAL-2738 update test for threaded VCFLoader
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commit | commitdiff | tree |
| 2017-10-03 |
gmungoc | JAL-2738 code formatting
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commit | commitdiff | tree |
| 2017-10-02 |
gmungoc | JAL-2738 code tidy up, null checks &c
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commit | commitdiff | tree |
| 2017-10-02 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF
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commit | commitdiff | tree |
| 2017-10-02 |
gmungoc | JAL-2525 lookup transcript features by Ontology
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commit | commitdiff | tree |
| 2017-10-02 |
gmungoc | JAL-2738 filter VEP consequence data to that for current...
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commit | commitdiff | tree |
| 2017-09-29 |
gmungoc | JAL-2738 one sequence feature per (SNP) VCF allele
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commit | commitdiff | tree |
| 2017-09-29 |
gmungoc | JAL-2744 indent CSQ lines to catch the eye
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commit | commitdiff | tree |
| 2017-09-29 |
gmungoc | JAL-2745 update www.ebi.ac.uk to https
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | JAL-2745 update www.ebi.ac.uk to https
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | JAL-2738 separate thread to load VCF; update FeatureSettings...
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | JAL-2036 set menus after fully loading AlignFrame
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | JAL-1796 GeneLociI as distinguished DBRefEntry
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | JAL-2744 simple Feature Details report from Popup menu
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commit | commitdiff | tree |
| 2017-09-28 |
gmungoc | JAL-2744 refactor PopupMenu constructor to enable adding...
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commit | commitdiff | tree |
| 2017-09-26 |
gmungoc | JAL-2738 transfer VCF variant features to CDS sequences
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commit | commitdiff | tree |
| 2017-09-26 |
gmungoc | JAL-2738 JAL-2154 add DBRef from transcript to synthesized...
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commit | commitdiff | tree |
| 2017-09-26 |
gmungoc | JAL-2738 unit test for reverse strand gene
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commit | commitdiff | tree |
| 2017-09-26 |
gmungoc | JAL-2738 promote setGeneLoci to SequenceI!
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | JAL-2738 use complement base for a VCF variant on reverse...
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | JAL-2738 getGeneLoci promoted to SequenceI
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | Merge branch 'develop' into features/JAL-1793VCF
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | JAL-2525 return no features if none matches ontology...
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | JAL-2738 query unindexed file, unit test for VCFLoader
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | JAL-2738 one constant in codebase for "alleles" attribute of
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commit | commitdiff | tree |
| 2017-09-25 |
gmungoc | JAL-2738 extract SNP variants from SNP or MIXED variant...
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commit | commitdiff | tree |
| 2017-09-22 |
gmungoc | JAL-2738 extract utility method to MappingUtils
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commit | commitdiff | tree |
| 2017-09-22 |
gmungoc | JAL-2738 correct handling of reverse strand genes
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commit | commitdiff | tree |
| 2017-09-22 |
gmungoc | JAL-2738 lookup GRCh38/37 gene mapping
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commit | commitdiff | tree |
| 2017-09-21 |
gmungoc | JAL-2738 compute VCF on peptide, extract AF (allele...
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commit | commitdiff | tree |
| 2017-09-21 |
gmungoc | JAL-2738 add chromosome coordinate mappings to transcripts
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commit | commitdiff | tree |
| 2017-09-21 |
gmungoc | JAL-2738 PoC of Load VCF file on to gene sequence
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commit | commitdiff | tree |
| 2017-09-21 |
gmungoc | JAL-2738 GeneLoci holds mapping of sequence to chromosome
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commit | commitdiff | tree |
| 2017-09-19 |
gmungoc | JAL-1793 wrapper for plain or indexed VCF + simple...
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commit | commitdiff | tree |
| 2017-09-19 |
gmungoc | JAL-1793 simple tests of reading raw and indexed VCF...
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commit | commitdiff | tree |
| 2017-09-18 |
gmungoc | Merge remote-tracking branch 'origin/patch/JAL-2732...
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commit | commitdiff | tree |
| 2017-09-18 |
gmungoc | JAL-2728 fine tuned initial split of split frame view
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commit | commitdiff | tree |
| 2017-09-15 |
gmungoc | JAL-2728 use right denominator for min/max ratio calculations
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commit | commitdiff | tree |
| 2017-09-15 |
gmungoc | JAL-2728 limit divider to ensure seqs visible (wip!)
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commit | commitdiff | tree |
| 2017-09-15 |
gmungoc | JAL-741 add tooltip to feature group checkbox
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commit | commitdiff | tree |
| 2017-09-14 |
gmungoc | JAL-2727 null more fields in AlignmentViewport.dispose...
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commit | commitdiff | tree |
| 2017-09-14 |
gmungoc | JAL-2727 add SelectionGroup, Tree and PCA to test
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commit | commitdiff | tree |
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