| 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 |
| 2015-12-02 |
gmungoc | JAL-1827 refactored to handle missing residues better
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commit | commitdiff | tree |
| 2015-12-02 |
gmungoc | JAL-1827 added overloaded method for convenience
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commit | commitdiff | tree |
| 2015-12-02 |
gmungoc | JAL-1827 reverted text on generic sequence fetcher...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-1421 generics loop syntax; 'bug?' comment added
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-653 test for 'resolving GFF mappings to sequences...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-653 small comment change only
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-652 refactored to remove one method
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-653 (experimental) 'realise' dummy sequences in...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-1980 check for null alignment; JAL-1551 @Override...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-653 (experimental) methods to resolve dummy to...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-1270 constructor test added
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-653 getStrand javadoc/refactor/test
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-1421 use generics JAL-1551 @Override annotations...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-1270 constructor tests added, compiler warnings...
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-652 further refactoring / tests
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-652 correct case for test file name
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commit | commitdiff | tree |
| 2015-11-30 |
gmungoc | JAL-653 MapList constructor merges any contiguous ranges
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commit | commitdiff | tree |
| 2015-11-23 |
gmungoc | JAL-653 Gff tests moved back in to FeaturesFileTest
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commit | commitdiff | tree |
| 2015-11-22 |
gmungoc | JAL-653 test for 'groups file' and mixed Jalview/GFF
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commit | commitdiff | tree |
| 2015-11-21 |
gmungoc | JAL-1968 remove feature links
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commit | commitdiff | tree |
| 2015-11-21 |
gmungoc | JAL-653 JAL-1968 FeaturesFile now handles Jalview or...
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commit | commitdiff | tree |
| 2015-11-17 |
gmungoc | JAL-1961 update link to GFF2 spec
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commit | commitdiff | tree |
| 2015-11-09 |
gmungoc | JAL-1705 type enum can encapsulate the corresponding...
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commit | commitdiff | tree |
| 2015-11-06 |
gmungoc | JAL-1946 unit tests (and comments) for PID() function
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commit | commitdiff | tree |
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