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JAL-3417 prototype sdppred calculation as groovy script
[jalview.git]
/
src
/
jalview
/
io
/
2018-01-16
kiramt
JAL-2759 Moved alignment annotation code out of HiddenC...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Rename hideInsertionsFor to hideList, after...
tree
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commitdiff
2018-01-15
kiramt
JAL-2759 Refactor of hideInsertionsFor after review
tree
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commitdiff
2018-01-10
gmungoc
JAL-1793 update spike branch to latest
tree
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commitdiff
2017-12-08
gmungoc
JAL-2843 read/write feature filters from/to Jalview...
tree
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commitdiff
2017-12-05
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-12-04
gmungoc
JAL-2808 JAL-2850 update spike build to latest
tree
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commitdiff
2017-12-04
gmungoc
Merge branch 'spikes/mungo' into features/JAL-1793VCF
tree
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commitdiff
2017-12-04
gmungoc
JAL-2850 JAL-1766 option to load contig sequence refere...
tree
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commitdiff
2017-12-04
gmungoc
JAL-2845 locate reverse strand insertion as complement...
tree
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commitdiff
2017-12-04
gmungoc
JAL-2835 small refactor to only extract transcript...
tree
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commitdiff
2017-12-01
gmungoc
JAL-2835 spike updated to latest (use specific SO term...
tree
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commitdiff
2017-12-01
gmungoc
JAL-2835 refactored to extract specific consequence...
tree
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commitdiff
2017-12-01
gmungoc
JAL-2835 additional sub-terms of sequence_variant added
tree
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commitdiff
2017-11-30
gmungoc
JAL-2850 improved use of htsjdk api to read contig...
tree
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commitdiff
2017-11-30
Jim Procter
JAL-2849 fix
tree
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commitdiff
2017-11-27
gmungoc
JAL-2850 VCFLoader refactored to load VCF to contig...
tree
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commitdiff
2017-11-23
gmungoc
JAL-2808 update spike to latest (filter range, Present...
tree
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commitdiff
2017-11-23
gmungoc
JAL-2808 removed field filters; sort CSQ data by key
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 spike updated with latest
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 take all CSQ fields; catch invalid field match...
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 support filter/colour by nested attribute...
tree
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commitdiff
2017-11-15
gmungoc
JAL-2835 add filters for VCF/VEP 'fields of interest'
tree
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commitdiff
2017-11-13
gmungoc
JAL-2738 stubs for filtering VEP and VCF fields of...
tree
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commitdiff
2017-11-13
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-11-13
Jim Procter
Merge branch 'imp/JAL-2810_ftsIDtab' into develop
tree
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commitdiff
2017-11-13
gmungoc
JAL-2176 removed unused Sequence.index
tree
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commitdiff
2017-11-07
gmungoc
JAL-2069 update spike branch with latest
tree
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commitdiff
2017-11-06
gmungoc
JAL-2820 include attribute value used for feature colou...
tree
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commitdiff
2017-10-27
Jim Procter
JAL-2804 kludge method to test if last key event handle...
tree
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commitdiff
2017-10-27
gmungoc
JAL-1793 spike branch updated to latest
tree
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commitdiff
2017-10-27
gmungoc
Merge branch 'develop' into features/JAL-1793VCF
tree
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commitdiff
2017-10-27
gmungoc
JAL-2792 capture feature metadata and render in Feature...
tree
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commitdiff
2017-10-26
Jim Procter
Merge branch 'feature/JAL-2488finalize' into develop
tree
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commitdiff
2017-10-26
gmungoc
JAL-2792 html table for Feature Details report
tree
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commitdiff
2017-10-25
gmungoc
JAL-2743 fall back to parsing description if chromosome...
tree
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commitdiff
2017-10-24
gmungoc
JAL-2743 slightly fancier species/assembly matching...
tree
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commitdiff
2017-10-24
gmungoc
JAL-2738 update spike branch with latest
tree
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commitdiff
2017-10-24
gmungoc
Merge branch 'develop' into features/JAL-1793VCF; lambd...
tree
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commitdiff
2017-10-20
gmungoc
Push 1793 latest to spike branch
tree
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commitdiff
2017-10-20
gmungoc
JAL-2755 update caller for method rename!
tree
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commitdiff
2017-10-19
gmungoc
JAL-2755 put chromosomal dbref first in report
tree
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commitdiff
2017-10-12
Jim Procter
JAL-2773 add new flag to paintAlignment(updateOverview...
features/JAL-2773_dontalwaysrecolourstructureonrepaintofoverview
tree
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commitdiff
2017-10-11
gmungoc
JAL-2738 javadoc correction
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
2017-10-05
gmungoc
JAL-2738 update spikes/mungo
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
2017-10-04
gmungoc
JAL-2738 fix bug of premature exit from adding attributes
tree
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commitdiff
2017-10-04
gmungoc
JAL-2738 match consequence "Allele" to VCF allele;...
tree
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commitdiff
2017-10-03
gmungoc
JAL-2738 copy to spikes/mungo
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
JAL-2738 filter VEP consequence data to that for curren...
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
2017-09-28
gmungoc
JAL-2738 separate thread to load VCF; update FeatureSet...
tree
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commitdiff
2017-09-28
gmungoc
JAL-1796 GeneLociI as distinguished DBRefEntry
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 unit test for reverse strand gene
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 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
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 PoC of Load VCF file on to gene sequence
tree
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commitdiff
2017-09-01
gmungoc
JAL-2488 remove finalize methods
tree
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commitdiff
2017-08-21
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
features/JAL-2446NCList
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 add GPL to main sources
tree
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commitdiff
2017-08-16
Jim Procter
JAL-2418 source formatting
tree
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commitdiff
2017-07-24
gmungoc
spike branch updated from latest features/JAL-2446
tree
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commitdiff
2017-06-27
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-14
gmungoc
JAL-2598 Sequence.getSequence return a copy of the...
tree
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commitdiff
2017-06-09
gmungoc
JAL-2446 merged to spike branch
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 Hidden columns regions can be output to string...
tree
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commitdiff
2017-06-07
kiramt
JAL-2591 simplifying hidden columns usage
tree
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commitdiff
2017-06-02
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-01
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-06-01
Jim Procter
Merge branch 'features/JAL-1648_cache_user_inputs'...
tree
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commitdiff
2017-05-31
tcofoegbu
Fixed failing tests
tree
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commitdiff
2017-05-30
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-29
Jim Procter
Merge branch 'features/JAL-2465_No-mapping_Jmol-structu...
tree
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commitdiff
2017-05-29
Jim Procter
JAL-2533 update javadoc
features/JAL-2465_No-mapping_Jmol-structures-loaded-via-url
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 Improvement to re-instate storing recently...
tree
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commitdiff
2017-05-26
tcofoegbu
JAL-2465 fix to prevent files loaded from the system...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2557 removal of Sequence.sequenceFeatures
tree
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commitdiff
2017-05-25
Jim Procter
Merge branch 'develop' into features/JAL-1648_cache_use...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2050 make SequenceFeature.score final, adjust const...
tree
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commitdiff
2017-05-25
gmungoc
JAL-2490 test coverage of empty and null feature group...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2490 find features for export as GFF, JAL-2548...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2490 tidy code and tests for feature export in...
tree
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commitdiff
2017-05-23
gmungoc
JAL-2490 improved lookup of features for Export Feature...
tree
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commitdiff
2017-05-22
gmungoc
JAL-2505 use setter not direct access to sf.description
tree
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commitdiff
2017-05-22
gmungoc
JAL-2543 identify as JSON before HTML
tree
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commitdiff
2017-05-22
gmungoc
JAL-2546 JAL-2490 efficient lookup of features, correct...
tree
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commitdiff
2017-05-19
gmungoc
JAL-2490 refactored test for 'hasFeatures'
tree
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commitdiff
2017-05-16
gmungoc
Merge branch 'develop' into features/JAL-2446NCList
tree
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commitdiff
2017-05-16
gmungoc
JAL-2505 refactor to set type and group in SequenceFeat...
tree
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commitdiff
2017-05-15
Jim Procter
Merge branch 'bug/JAL-2507_rnasecstrstockholm' into...
tree
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commitdiff
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