| 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 |
| 2016-02-12 |
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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commit | commitdiff | tree |
| 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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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 get xrefs only for dna/peptide; code tidy
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 toString() added (for debugging)
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commit | commitdiff | tree |
| 2016-01-21 |
gmungoc | JAL-1705 isEmpty() and (debug) toString() methods added
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commit | commitdiff | tree |
| 2016-01-12 |
gmungoc | JAL-1191 cache isA (great-)grandparents as well for...
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commit | commitdiff | tree |
| 2016-01-11 |
gmungoc | Merge branch 'develop' of https://source.jalview.org...
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commit | commitdiff | tree |
| 2016-01-11 |
gmungoc | JAL-1989 additional ways to 'mirror' show/hide columns...
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commit | commitdiff | tree |
| 2016-01-11 |
gmungoc | JAL-1989 map hidden column ranges
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commit | commitdiff | tree |
| 2016-01-11 |
gmungoc | JAL-1989 more unit tests and encapsulation for ColumnSelection
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commit | commitdiff | tree |
| 2016-01-11 |
gmungoc | JAL-1544 "more than" not "more that"
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commit | commitdiff | tree |
| 2016-01-08 |
gmungoc | JAL-1705 DbSourceProxy properties converted to methods...
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commit | commitdiff | tree |
| 2016-01-05 |
gmungoc | JAL-653 updating 'align as' tests to match latest tweaks...
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commit | commitdiff | tree |
| 2016-01-05 |
gmungoc | Merge remote-tracking branch 'origin/features/JAL-1705_ensem...
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commit | commitdiff | tree |
| 2016-01-05 |
gmungoc | JAL-653 typed map for feature colours in method signature
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commit | commitdiff | tree |
| 2016-01-05 |
gmungoc | JAL-1191 check for obsolete term when descriptions...
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commit | commitdiff | tree |
| 2015-12-23 |
gmungoc | JAL-1191 unzipped OBO file removed
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commit | commitdiff | tree |
| 2015-12-23 |
gmungoc | JAL-1191 zipped SO OBO file added to /resources, more...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-1191 more test cases
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-1191 and provide the SO OBO file in /resources :-)
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-1191 SequenceOntology wrapping/caching SO.OBO via...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-1191 stub class for a SequenceOntology wrapper
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-1551 don't autoformat /* comments */
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-1421 parameterised map constructor used
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 encapsulate Strand, Attributes, Status of SequenceFe...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 realise virtual mappings and align when adding...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-391 new Calculate options to Reverse, Reverse Complement...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 AlignedCodonFrame collections changed from...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 set showSequenceFeatures=true on loading a...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 GFF new/refactored helper classes
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 AlignedCodonFrame internal refactor, merge...
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commit | commitdiff | tree |
| 2015-12-22 |
gmungoc | JAL-653 hold AlignedCodonFrame collections as list...
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commit | commitdiff | tree |
| 2015-12-03 |
gmungoc | JAL-653 code tidy / tests for 'realise gff mappings'
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commit | commitdiff | tree |
| 2015-12-03 |
gmungoc | JAL-653 handle reverse strand mapping in SearchResults...
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commit | commitdiff | tree |
| 2015-12-03 |
gmungoc | JAL-653 mappings always reside on the dataset alignment...
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commit | commitdiff | tree |
| 2015-12-03 |
gmungoc | JAL-653 handle reverse strand mappings also
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commit | commitdiff | tree |
| 2015-12-03 |
gmungoc | JAL-1827 code and comment tidy up
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commit | commitdiff | tree |
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