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Merge branch 'develop' into features/JAL-653_JAL-1766_htslib_refseqsupport
[jalview.git] / src /
2016-02-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard... tree | commitdiff
2016-01-30 gmungocJAL-1705 refactored cross-reference fetching (CCDS... tree | commitdiff
2016-01-29 tcofoegbuJAL-1979 refactor out duplicated similar block of code... tree | commitdiff
2016-01-29 gmungocJAL-1705 fetch Uniprot and PDB xrefs for Ensembl protei... tree | commitdiff
2016-01-29 gmungocJAL-1705 copy feature settings when opening a split... tree | commitdiff
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... tree | commitdiff
2016-01-28 gmungocJAL-1705 tests added, minor bugfix and refactoring tree | commitdiff
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge tree | commitdiff
2016-01-28 gmungocJAL-1705 merge contiguous ranges when constructing... tree | commitdiff
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid... tree | commitdiff
2016-01-27 tcofoegbuJAL-1479 fixed off-by-one error in SIFTS mapping output... tree | commitdiff
2016-01-27 gmungocJAL-1705 use GET for single queries; set gene name... tree | commitdiff
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence... tree | commitdiff
2016-01-26 tcofoegbuJAL-1999 JAL-1479 implemented configurable fail-safe... tree | commitdiff
2016-01-25 tcofoegbuJAL-1998 bugfix for division by zero error for PDB... tree | commitdiff
2016-01-25 gmungocJAL-1705 EnsemblGene added, and related refactoring tree | commitdiff
2016-01-25 gmungocJAL-1997 database browser support tooltip if available tree | commitdiff
2016-01-23 gmungocJAL-1355 get dialog title from message bundle tree | commitdiff
2016-01-23 gmungocJAL-1705 copy 'show sequence features' setting in ... tree | commitdiff
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea... tree | commitdiff
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... tree | commitdiff
2016-01-21 tcofoegbuJAL-1479 JAL-1979 bugfix to check entire annotation... tree | commitdiff
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence... tree | commitdiff
2016-01-21 gmungocJAL-1705 reworked Ensembl clients now fetching and... tree | commitdiff
2016-01-21 gmungocJAL-653 refactor / tidy tree | commitdiff
2016-01-21 gmungocJAL-653 JAL-1705 set strand for GFF sequence feature tree | commitdiff
2016-01-21 gmungocJAL-653 comments/javadoc tidy only tree | commitdiff
2016-01-21 gmungocJAL-1796 parse ensembl genomic coordinates to set start... tree | commitdiff
2016-01-21 gmungocJAL-1705 AlignmentUtils method renamed tree | commitdiff
2016-01-21 gmungocJAL-1705 ENSEMBL added, unused constants removed tree | commitdiff
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon... tree | commitdiff
2016-01-21 gmungocJAL-1705 redundant comment removed tree | commitdiff
2016-01-21 gmungocJAL-1705 suppress jvsuffix (for sequence id matching... tree | commitdiff
2016-01-21 gmungocJAL-1705 unused import removed tree | commitdiff
2016-01-21 gmungocJAL-1705 include dummy sequences in returned alignment tree | commitdiff
2016-01-21 tcofoegbuJAL-1479 JAL-1979 updated the modified-aminoacid triple... tree | commitdiff
2016-01-21 gmungocJAL-1705 added isSequenceVariant(), commonly used SO... tree | commitdiff
2016-01-21 gmungocJAL-1705 isFromForwardStrand added; toString (for debug... tree | commitdiff
2016-01-21 gmungocJAL-1705 canonicalise ENSEMBL name; code tidy tree | commitdiff
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy tree | commitdiff
2016-01-21 gmungocJAL-1705 toString() added (for debugging) tree | commitdiff
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added tree | commitdiff
2016-01-12 gmungocJAL-1191 cache isA (great-)grandparents as well for... tree | commitdiff
2016-01-11 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-01-11 gmungocJAL-1989 additional ways to 'mirror' show/hide columns... tree | commitdiff
2016-01-11 tcofoegbuJAL-1990 added a progress indicator for Structure Choos... tree | commitdiff
2016-01-11 tcofoegbumerge tree | commitdiff
2016-01-11 tcofoegbuJAL-1991 bug fix for some flat-file printers to check... tree | commitdiff
2016-01-11 gmungocJAL-1989 map hidden column ranges tree | commitdiff
2016-01-11 gmungocJAL-1989 more unit tests and encapsulation for ColumnSe... tree | commitdiff
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods... tree | commitdiff
2016-01-07 tcofoegbumerge tree | commitdiff
2016-01-07 tcofoegbuJAL-1479 implemented timestamp based caching of SIFTS... tree | commitdiff
2016-01-05 gmungocMerge remote-tracking branch 'origin/features/JAL-1705_... tree | commitdiff
2016-01-05 gmungocJAL-653 typed map for feature colours in method signature tree | commitdiff
2016-01-05 gmungocJAL-1191 check for obsolete term when descriptions... tree | commitdiff
2015-12-23 gmungocJAL-1191 zipped SO OBO file added to /resources, more... tree | commitdiff
2015-12-22 gmungocJAL-1191 and provide the SO OBO file in /resources :-) tree | commitdiff
2015-12-22 gmungocJAL-1191 SequenceOntology wrapping/caching SO.OBO via... tree | commitdiff
2015-12-22 gmungocJAL-1191 stub class for a SequenceOntology wrapper tree | commitdiff
2015-12-22 gmungocJAL-1421 parameterised map constructor used tree | commitdiff
2015-12-22 gmungocJAL-653 encapsulate Strand, Attributes, Status of Seque... tree | commitdiff
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding... tree | commitdiff
2015-12-22 gmungocJAL-391 new Calculate options to Reverse, Reverse Compl... tree | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... tree | commitdiff
2015-12-22 gmungocJAL-653 set showSequenceFeatures=true on loading a... tree | commitdiff
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes tree | commitdiff
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... tree | commitdiff
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list... tree | commitdiff
2015-12-09 Jim ProcterJAL-1982 hotfix to prevent NPE with applet launch on... tree | commitdiff
2015-12-03 gmungocJAL-653 code tidy / tests for 'realise gff mappings' tree | commitdiff
2015-12-03 gmungocJAL-653 handle reverse strand mapping in SearchResults... tree | commitdiff
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment... tree | commitdiff
2015-12-03 gmungocJAL-653 handle reverse strand mappings also tree | commitdiff
2015-12-03 gmungocJAL-1827 code and comment tidy up tree | commitdiff
2015-12-02 gmungocJAL-1827 refactored to handle missing residues better tree | commitdiff
2015-12-02 gmungocJAL-1827 added overloaded method for convenience tree | commitdiff
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added tree | commitdiff
2015-11-30 gmungocJAL-653 small comment change only tree | commitdiff
2015-11-30 gmungocJAL-652 refactored to remove one method tree | commitdiff
2015-11-30 gmungocJAL-653 (experimental) 'realise' dummy sequences in... tree | commitdiff
2015-11-30 gmungocJAL-1980 check for null alignment; JAL-1551 @Override... tree | commitdiff
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to... tree | commitdiff
2015-11-30 gmungocJAL-653 getStrand javadoc/refactor/test tree | commitdiff
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations... tree | commitdiff
2015-11-30 gmungocJAL-652 further refactoring / tests tree | commitdiff
2015-11-30 gmungocJAL-653 MapList constructor merges any contiguous ranges tree | commitdiff
2015-11-25 tcofoegbuJAL-1479 refactored DBRef fetching code to StructureCho... tree | commitdiff
2015-11-25 tcofoegbuJAL-1479 applet build debug tree | commitdiff
2015-11-25 tcofoegbuJAL-1479 bugfix after decoupling SIFTS preference settings tree | commitdiff
2015-11-23 tcofoegbuJAL-1479 commented out DBRef fetching code from SIFTS... tree | commitdiff
2015-11-21 gmungocJAL-1968 remove feature links tree | commitdiff
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or... tree | commitdiff
2015-11-17 tcofoegbuJAL-1479 Refactored Sifts configuration preference... tree | commitdiff
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi... tree | commitdiff
2015-11-13 tcofoegbuJAL-1479 added transfer of residue annotation for SIFTS... tree | commitdiff
2015-11-11 tcofoegbuJAL-1479 JAL-1957 Added code to enable simultaneous... tree | commitdiff
2015-11-11 tcofoegbumerge tree | commitdiff
2015-11-11 tcofoegbuJAL-1957 JAL-1479 Further optimisation of SIFTs Client... features/JAL-1479_SIFTS-mapping tree | commitdiff
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