jalview.git
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge
2016-01-28 gmungocJAL-1551 wrap enum declarations
2016-01-28 gmungocJAL-1705 merge contiguous ranges when constructing...
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid...
2016-01-27 gmungocJAL-1705 use GET for single queries; set gene name...
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence...
2016-01-25 gmungocJAL-1705 EnsemblGene added, and related refactoring
2016-01-25 gmungocJAL-1997 database browser support tooltip if available
2016-01-23 gmungocJAL-1355 get dialog title from message bundle
2016-01-23 gmungocJAL-1705 copy 'show sequence features' setting in ...
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea...
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq...
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence...
2016-01-21 gmungocJAL-1705 reworked Ensembl clients now fetching and...
2016-01-21 gmungocJAL-653 refactor / tidy
2016-01-21 gmungocJAL-653 JAL-1705 set strand for GFF sequence feature
2016-01-21 gmungocJAL-1705 removed (only) usage of otherwise unused constant
2016-01-21 gmungocJAL-653 comments/javadoc tidy only
2016-01-21 gmungocJAL-1796 parse ensembl genomic coordinates to set start...
2016-01-21 gmungocJAL-1705 AlignmentUtils method renamed
2016-01-21 gmungocJAL-1705 ENSEMBL added, unused constants removed
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon...
2016-01-21 gmungocJAL-1705 redundant comment removed
2016-01-21 gmungocJAL-1705 suppress jvsuffix (for sequence id matching...
2016-01-21 gmungocJAL-1705 unused import removed
2016-01-21 gmungocJAL-1705 include dummy sequences in returned alignment
2016-01-21 gmungocJAL-1705 tidy and todo comment, no functional change
2016-01-21 gmungocJAL-1705 tests for amended toString
2016-01-21 gmungocJAL-1705 added isSequenceVariant(), commonly used SO...
2016-01-21 gmungocJAL-1705 isFromForwardStrand added; toString (for debug...
2016-01-21 gmungocJAL-1705 canonicalise ENSEMBL name; code tidy
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy
2016-01-21 gmungocJAL-1705 toString() added (for debugging)
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added
2016-01-12 gmungocJAL-1191 cache isA (great-)grandparents as well for...
2016-01-11 gmungocMerge branch 'develop' of https://source.jalview.org...
2016-01-11 gmungocJAL-1989 additional ways to 'mirror' show/hide columns...
2016-01-11 tcofoegbuJAL-1990 added a progress indicator for Structure Choos...
2016-01-11 tcofoegbumerge
2016-01-11 tcofoegbuJAL-1991 bug fix for some flat-file printers to check...
2016-01-11 gmungocJAL-1989 map hidden column ranges
2016-01-11 gmungocJAL-1989 more unit tests and encapsulation for ColumnSe...
2016-01-11 gmungocJAL-1544 "more than" not "more that"
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods...
2016-01-07 tcofoegbumerge
2016-01-07 tcofoegbuJAL-1479 implemented timestamp based caching of SIFTS...
2016-01-05 gmungocJAL-653 updating 'align as' tests to match latest tweak...
2016-01-05 gmungocMerge remote-tracking branch 'origin/features/JAL-1705_...
2016-01-05 gmungocJAL-653 typed map for feature colours in method signature
2016-01-05 gmungocJAL-1191 check for obsolete term when descriptions...
2015-12-23 gmungocJAL-1191 unzipped OBO file removed
2015-12-23 gmungocJAL-1191 zipped SO OBO file added to /resources, more...
2015-12-22 gmungocJAL-1191 more test cases
2015-12-22 gmungocJAL-1191 and provide the SO OBO file in /resources :-)
2015-12-22 gmungocJAL-1191 SequenceOntology wrapping/caching SO.OBO via...
2015-12-22 gmungocJAL-1191 stub class for a SequenceOntology wrapper
2015-12-22 gmungocJAL-1551 don't autoformat /* comments */
2015-12-22 gmungocJAL-1421 parameterised map constructor used
2015-12-22 gmungocJAL-653 encapsulate Strand, Attributes, Status of Seque...
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding...
2015-12-22 gmungocJAL-391 new Calculate options to Reverse, Reverse Compl...
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from...
2015-12-22 gmungocJAL-653 set showSequenceFeatures=true on loading a...
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge...
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list...
2015-12-09 Jim ProcterJAL-1982 hotfix to prevent NPE with applet launch on...
2015-12-03 gmungocJAL-653 code tidy / tests for 'realise gff mappings'
2015-12-03 gmungocJAL-653 handle reverse strand mapping in SearchResults...
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment...
2015-12-03 gmungocJAL-653 handle reverse strand mappings also
2015-12-03 gmungocJAL-1827 code and comment tidy up
2015-12-02 gmungocJAL-1827 refactored to handle missing residues better
2015-12-02 gmungocJAL-1827 added overloaded method for convenience
2015-12-02 gmungocJAL-1827 reverted text on generic sequence fetcher...
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added
2015-11-30 gmungocJAL-653 test for 'resolving GFF mappings to sequences...
2015-11-30 gmungocJAL-653 small comment change only
2015-11-30 gmungocJAL-652 refactored to remove one method
2015-11-30 gmungocJAL-653 (experimental) 'realise' dummy sequences in...
2015-11-30 gmungocJAL-1980 check for null alignment; JAL-1551 @Override...
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to...
2015-11-30 gmungocJAL-1270 constructor test added
2015-11-30 gmungocJAL-653 getStrand javadoc/refactor/test
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations...
2015-11-30 gmungocJAL-1270 constructor tests added, compiler warnings...
2015-11-30 gmungocJAL-652 further refactoring / tests
2015-11-30 gmungocJAL-652 correct case for test file name
2015-11-30 gmungocJAL-653 MapList constructor merges any contiguous ranges
2015-11-25 tcofoegbuJAL-1479 refactored DBRef fetching code to StructureCho...
2015-11-25 tcofoegbuJAL-1479 applet build debug
2015-11-25 tcofoegbuJAL-1479 bugfix after decoupling SIFTS preference settings
2015-11-23 tcofoegbuJAL-1479 commented out DBRef fetching code from SIFTS...
2015-11-23 gmungocJAL-653 Gff tests moved back in to FeaturesFileTest
2015-11-22 gmungocJAL-653 test for 'groups file' and mixed Jalview/GFF
2015-11-21 gmungocJAL-1968 remove feature links
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or...
2015-11-17 tcofoegbuJAL-1479 Refactored Sifts configuration preference...
2015-11-17 gmungocJAL-1961 update link to GFF2 spec
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi...
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