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jalview.git
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbuJAL-1479 JAL-1979 bugfix to check entire annotation... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 transfer features to the dataset sequence... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 reworked Ensembl clients now fetching and... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-653 refactor / tidy commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-653 JAL-1705 set strand for GFF sequence feature commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 removed (only) usage of otherwise unused constant commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-653 comments/javadoc tidy only commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1796 parse ensembl genomic coordinates to set start... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 AlignmentUtils method renamed commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 ENSEMBL added, unused constants removed commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 features transferred to CDS sequence; makeExon... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 redundant comment removed commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 suppress jvsuffix (for sequence id matching... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 unused import removed commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 include dummy sequences in returned alignment commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbuJAL-1479 JAL-1979 updated the modified-aminoacid triple... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 tidy and todo comment, no functional change commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 tests for amended toString commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 added isSequenceVariant(), commonly used SO... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 isFromForwardStrand added; toString (for debug... commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 canonicalise ENSEMBL name; code tidy commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 get xrefs only for dna/peptide; code tidy commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 toString() added (for debugging) commit | commitdiff | tree | snapshot
2016-01-21 gmungocJAL-1705 isEmpty() and (debug) toString() methods added commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbuJAL-1986 JAL-1996 separated out appletDeploment page... commit | commitdiff | tree | snapshot
2016-01-21 Jim ProcterJAL-1995 remove jalviewApplet.jar from tree and added... commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-01-21 tcofoegbuJAL-1994 bugfix in build.xml to prevent proguard from... bug/JAL-1994_Jalviewlite-json-parser-in-browsers commit | commitdiff | tree | snapshot
2016-01-12 gmungocJAL-1191 cache isA (great-)grandparents as well for... commit | commitdiff | tree | snapshot
2016-01-11 gmungocMerge branch 'develop' of https://source.jalview.org... commit | commitdiff | tree | snapshot
2016-01-11 gmungocJAL-1989 additional ways to 'mirror' show/hide columns... commit | commitdiff | tree | snapshot
2016-01-11 tcofoegbuJAL-1990 added a progress indicator for Structure Choos... commit | commitdiff | tree | snapshot
2016-01-11 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-01-11 tcofoegbuJAL-1991 bug fix for some flat-file printers to check... commit | commitdiff | tree | snapshot
2016-01-11 gmungocJAL-1989 map hidden column ranges commit | commitdiff | tree | snapshot
2016-01-11 gmungocJAL-1989 more unit tests and encapsulation for ColumnSe... commit | commitdiff | tree | snapshot
2016-01-11 gmungocJAL-1544 "more than" not "more that" commit | commitdiff | tree | snapshot
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods... commit | commitdiff | tree | snapshot
2016-01-07 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-01-07 tcofoegbuJAL-1479 implemented timestamp based caching of SIFTS... commit | commitdiff | tree | snapshot
2016-01-05 gmungocJAL-653 updating 'align as' tests to match latest tweak... commit | commitdiff | tree | snapshot
2016-01-05 gmungocMerge remote-tracking branch 'origin/features/JAL-1705_... commit | commitdiff | tree | snapshot
2016-01-05 gmungocJAL-653 typed map for feature colours in method signature commit | commitdiff | tree | snapshot
2016-01-05 gmungocJAL-1191 check for obsolete term when descriptions... commit | commitdiff | tree | snapshot
2015-12-23 gmungocJAL-1191 unzipped OBO file removed commit | commitdiff | tree | snapshot
2015-12-23 gmungocJAL-1191 zipped SO OBO file added to /resources, more... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 more test cases commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 and provide the SO OBO file in /resources :-) commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 SequenceOntology wrapping/caching SO.OBO via... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1191 stub class for a SequenceOntology wrapper commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1551 don't autoformat /* comments */ commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-1421 parameterised map constructor used commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 encapsulate Strand, Attributes, Status of Seque... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 realise virtual mappings and align when adding... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-391 new Calculate options to Reverse, Reverse Compl... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 AlignedCodonFrame collections changed from... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 set showSequenceFeatures=true on loading a... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 GFF new/refactored helper classes commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 AlignedCodonFrame internal refactor, merge... commit | commitdiff | tree | snapshot
2015-12-22 gmungocJAL-653 hold AlignedCodonFrame collections as list... commit | commitdiff | tree | snapshot
2015-12-09 Jim ProcterJAL-1982 hotfix to prevent NPE with applet launch on... commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 code tidy / tests for 'realise gff mappings' commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 handle reverse strand mapping in SearchResults... commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 mappings always reside on the dataset alignment... commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-653 handle reverse strand mappings also commit | commitdiff | tree | snapshot
2015-12-03 gmungocJAL-1827 code and comment tidy up commit | commitdiff | tree | snapshot
2015-12-02 gmungocJAL-1827 refactored to handle missing residues better commit | commitdiff | tree | snapshot
2015-12-02 gmungocJAL-1827 added overloaded method for convenience commit | commitdiff | tree | snapshot
2015-12-02 gmungocJAL-1827 reverted text on generic sequence fetcher... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1421 generics loop syntax; 'bug?' comment added commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 test for 'resolving GFF mappings to sequences... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 small comment change only commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-652 refactored to remove one method commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 (experimental) 'realise' dummy sequences in... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1980 check for null alignment; JAL-1551 @Override... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 (experimental) methods to resolve dummy to... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1270 constructor test added commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 getStrand javadoc/refactor/test commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1421 use generics JAL-1551 @Override annotations... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-1270 constructor tests added, compiler warnings... commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-652 further refactoring / tests commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-652 correct case for test file name commit | commitdiff | tree | snapshot
2015-11-30 gmungocJAL-653 MapList constructor merges any contiguous ranges commit | commitdiff | tree | snapshot
2015-11-25 tcofoegbuJAL-1479 refactored DBRef fetching code to StructureCho... commit | commitdiff | tree | snapshot
2015-11-25 tcofoegbuJAL-1479 applet build debug commit | commitdiff | tree | snapshot
2015-11-25 tcofoegbuJAL-1479 bugfix after decoupling SIFTS preference settings commit | commitdiff | tree | snapshot
2015-11-23 tcofoegbuJAL-1479 commented out DBRef fetching code from SIFTS... commit | commitdiff | tree | snapshot
2015-11-23 gmungocJAL-653 Gff tests moved back in to FeaturesFileTest commit | commitdiff | tree | snapshot
2015-11-22 gmungocJAL-653 test for 'groups file' and mixed Jalview/GFF commit | commitdiff | tree | snapshot
2015-11-21 gmungocJAL-1968 remove feature links commit | commitdiff | tree | snapshot
2015-11-21 gmungocJAL-653 JAL-1968 FeaturesFile now handles Jalview or... commit | commitdiff | tree | snapshot
2015-11-17 tcofoegbuJAL-1479 Refactored Sifts configuration preference... commit | commitdiff | tree | snapshot
2015-11-17 gmungocJAL-1961 update link to GFF2 spec commit | commitdiff | tree | snapshot
2015-11-16 tcofoegbuJAL-1967 JAL-1479 refactored sequence<->structure mappi... commit | commitdiff | tree | snapshot
2015-11-13 tcofoegbuJAL-1479 added transfer of residue annotation for SIFTS... commit | commitdiff | tree | snapshot
2015-11-11 tcofoegbuJAL-1479 JAL-1957 Added code to enable simultaneous... commit | commitdiff | tree | snapshot
2015-11-11 tcofoegbumerge of SIFTs Branch commit | commitdiff | tree | snapshot
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