| 2016-03-21 |
gmungoc | JAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
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| 2016-03-16 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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| 2016-03-16 |
gmungoc | JAL-1705 xref ENST to correct (ENSP) accession id
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| 2016-03-15 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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| 2016-03-15 |
gmungoc | JAL-2016 corrected Javadoc, added test for anonymous...
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-2016 FeatureSettingsI now FeatureSettingsModelI
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-1705 code tidy/comment only
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commit | commitdiff | tree |
| 2016-03-15 |
gmungoc | JAL-1705 compute reverse complement of variants on...
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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| 2016-03-11 |
gmungoc | JAL-1270 unit test for SequenceIdMatcher.SeqIdName
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1705 check Retry-After response header
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1705 javadoc added only
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commit | commitdiff | tree |
| 2016-03-11 |
gmungoc | JAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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| 2016-03-07 |
gmungoc | JAL-2023 CDS sequences added to / share alignment dataset
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commit | commitdiff | tree |
| 2016-03-04 |
gmungoc | JAL-1705 EnsemblGenomes a top level db source
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commit | commitdiff | tree |
| 2016-03-04 |
gmungoc | JAL-1705 parse 'description' from GFF as sequence description
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commit | commitdiff | tree |
| 2016-03-03 |
gmungoc | JAL-1705 unit test for aligning with incomplete start...
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commit | commitdiff | tree |
| 2016-03-03 |
gmungoc | JAL-1705 include stop codons in derived CDS; support...
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commit | commitdiff | tree |
| 2016-03-02 |
gmungoc | JAL-1705 include any unmapped protein start 'X' when...
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commit | commitdiff | tree |
| 2016-03-01 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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| 2016-03-01 |
gmungoc | JAL-1705 align CDS to transcripts
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commit | commitdiff | tree |
| 2016-03-01 |
gmungoc | JAL-1705 align CDS and peptide products to transcripts
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commit | commitdiff | tree |
| 2016-02-25 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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| 2016-02-22 |
gmungoc | JAL-1705 first pass at applying preset feature colouring...
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | Merge branch 'mungo_develop' into features/JAL-653_JAL...
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| 2016-02-20 |
gmungoc | Merge branch 'JAL-1956_featureStyles' into features...
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | JAL-2016 first draft of pre-set feature colour scheme
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commit | commitdiff | tree |
| 2016-02-20 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 handle case of sequence with no dataset sequence
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 regular expression updates, tests, other refactoring
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 updated for change to CrossRef signature
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| 2016-02-19 |
gmungoc | JAL-1705 refactor show products, set initial split...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 more lenient test for 'sequence retrieved'
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 return Ensembl genes for model species for...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 JAL-1191 more terms added to hard-coded version
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1706 reverted setting start position as too confusing...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 lenient DBRef matcher added (accession id...
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commit | commitdiff | tree |
| 2016-02-19 |
gmungoc | JAL-1705 helper method for mapping excluding stop codon
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1270 remove trailing space + test
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1705 various refactoring towards Uniprot-to-Ensembl...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1191 additions to SOLite, tweak to test
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-1705 take feature ID for description if nothing...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-282 wrap very long id in tooltip
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| 2016-02-12 |
gmungoc | JAL-1705 JAL-1686 stronger SequenceFeature.equals(...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-2010 simple prototype of 'Highlight Selection'...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-2008 updates for String[] to List<String> change
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-2008 avoid unnecessary repaints; signatures changed...
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | JAL-265 updated help text
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commit | commitdiff | tree |
| 2016-02-12 |
gmungoc | Merge branch 'develop' into
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commit | commitdiff | tree |
| 2016-02-05 |
gmungoc | JAL-2006 scale even very small score ranges to a usable...
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-1544 spelling fix
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-2005 added (stable) sort methods parameterised by
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-599 bug fixed so array of visible types is populated
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-1705 temporary variable to aid inspection in debugger
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-1705 additional tests, validation regexp tweaks...
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commit | commitdiff | tree |
| 2016-02-04 |
gmungoc | JAL-2003 export features on alignment, not alignment...
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commit | commitdiff | tree |
| 2016-02-01 |
gmungoc | JAL-1705 further unit tests
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commit | commitdiff | tree |
| 2016-02-01 |
gmungoc | JAL-1705 set Uniprot xref as 'source dbref' (for SIFTS...
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commit | commitdiff | tree |
| 2016-02-01 |
gmungoc | JAL-1191 more terms added to SequenceOntologyLite
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commit | commitdiff | tree |
| 2016-02-01 |
gmungoc | Merge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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commit | commitdiff | tree |
| 2016-02-01 |
gmungoc | JAL-1705 tests added
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commit | commitdiff | tree |
| 2016-02-01 |
gmungoc | JAL-1705 JAL-1191 SequenceOntologyLite added as hard...
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commit | commitdiff | tree |
| 2016-01-30 |
gmungoc | JAL-1705 refactored cross-reference fetching (CCDS...
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commit | commitdiff | tree |
| 2016-01-29 |
gmungoc | JAL-1705 fetch Uniprot and PDB xrefs for Ensembl protein...
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commit | commitdiff | tree |
| 2016-01-29 |
gmungoc | JAL-1705 copy feature settings when opening a split...
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commit | commitdiff | tree |
| 2016-01-28 |
gmungoc | JAL-1705 more correct title (CDS not cDNA) on split...
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commit | commitdiff | tree |
| 2016-01-28 |
gmungoc | JAL-1705 refine feature copying to including 5' and...
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commit | commitdiff | tree |
| 2016-01-28 |
gmungoc | JAL-1705 tests added, minor bugfix and refactoring
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commit | commitdiff | tree |
| 2016-01-28 |
gmungoc | Merge branch 'develop' into JAL-1705_trialMerge
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commit | commitdiff | tree |
| 2016-01-28 |
gmungoc | JAL-1551 wrap enum declarations
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commit | commitdiff | tree |
| 2016-01-28 |
gmungoc | JAL-1705 merge contiguous ranges when constructing...
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commit | commitdiff | tree |
| 2016-01-27 |
gmungoc | JAL-1705 add exon name to features and render on peptide...
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commit | commitdiff | tree |
| 2016-01-27 |
gmungoc | JAL-1705 use GET for single queries; set gene name...
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commit | commitdiff | tree |
| 2016-01-26 |
gmungoc | JAL-1705 derive transcript sequences from gene sequence...
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commit | commitdiff | tree |
| 2016-01-25 |
gmungoc | JAL-1705 EnsemblGene added, and related refactoring
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commit | commitdiff | tree |
| 2016-01-25 |
gmungoc | JAL-1997 database browser support tooltip if available
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commit | commitdiff | tree |
| 2016-01-23 |
gmungoc | JAL-1355 get dialog title from message bundle
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commit | commitdiff | tree |
| 2016-01-23 |
gmungoc | JAL-1705 copy 'show sequence features' setting in ...
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commit | commitdiff | tree |
| 2016-01-23 |
gmungoc | JAL-1705 todo comment re writing DBRefEntry/SequenceFeature...
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commit | commitdiff | tree |
| 2016-01-23 |
gmungoc | JAL-1705 compute peptide variants from dna; add "consequence...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 transfer features to the dataset sequence...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 reworked Ensembl clients now fetching and...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-653 refactor / tidy
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-653 JAL-1705 set strand for GFF sequence feature
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 removed (only) usage of otherwise unused constant
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-653 comments/javadoc tidy only
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1796 parse ensembl genomic coordinates to set start...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 AlignmentUtils method renamed
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 ENSEMBL added, unused constants removed
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 features transferred to CDS sequence; makeExon...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 redundant comment removed
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 suppress jvsuffix (for sequence id matching...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 unused import removed
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 include dummy sequences in returned alignment
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 tidy and todo comment, no functional change
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 tests for amended toString
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 added isSequenceVariant(), commonly used SO...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 isFromForwardStrand added; toString (for debug...
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 canonicalise ENSEMBL name; code tidy
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