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jalview.git
2016-02-04 gmungocJAL-1544 spelling fix commit | commitdiff | tree | snapshot
2016-02-04 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2016-02-04 gmungocJAL-2005 added (stable) sort methods parameterised by commit | commitdiff | tree | snapshot
2016-02-04 gmungocJAL-599 bug fixed so array of visible types is populated commit | commitdiff | tree | snapshot
2016-02-04 gmungocJAL-1705 temporary variable to aid inspection in debugger commit | commitdiff | tree | snapshot
2016-02-04 gmungocJAL-1705 additional tests, validation regexp tweaks... commit | commitdiff | tree | snapshot
2016-02-04 gmungocJAL-2003 export features on alignment, not alignment... commit | commitdiff | tree | snapshot
2016-02-01 gmungocJAL-1705 further unit tests commit | commitdiff | tree | snapshot
2016-02-01 gmungocJAL-1705 set Uniprot xref as 'source dbref' (for SIFTS... commit | commitdiff | tree | snapshot
2016-02-01 gmungocJAL-1191 more terms added to SequenceOntologyLite commit | commitdiff | tree | snapshot
2016-02-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2016-02-01 gmungocJAL-1705 tests added commit | commitdiff | tree | snapshot
2016-02-01 gmungocJAL-1705 JAL-1191 SequenceOntologyLite added as hard... commit | commitdiff | tree | snapshot
2016-01-30 gmungocJAL-1705 refactored cross-reference fetching (CCDS... commit | commitdiff | tree | snapshot
2016-01-29 tcofoegbuJAL-1979 refactor out duplicated similar block of code... commit | commitdiff | tree | snapshot
2016-01-29 gmungocJAL-1705 fetch Uniprot and PDB xrefs for Ensembl protei... commit | commitdiff | tree | snapshot
2016-01-29 gmungocJAL-1705 copy feature settings when opening a split... commit | commitdiff | tree | snapshot
2016-01-28 gmungocJAL-1705 more correct title (CDS not cDNA) on split... commit | commitdiff | tree | snapshot
2016-01-28 gmungocJAL-1705 refine feature copying to including 5' and... commit | commitdiff | tree | snapshot
2016-01-28 gmungocJAL-1705 tests added, minor bugfix and refactoring commit | commitdiff | tree | snapshot
2016-01-28 gmungocMerge branch 'develop' into JAL-1705_trialMerge commit | commitdiff | tree | snapshot
2016-01-28 gmungocJAL-1551 wrap enum declarations commit | commitdiff | tree | snapshot
2016-01-28 gmungocJAL-1705 merge contiguous ranges when constructing... commit | commitdiff | tree | snapshot
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid... commit | commitdiff | tree | snapshot
2016-01-27 tcofoegbuJAL-1479 fixed off-by-one error in SIFTS mapping output... commit | commitdiff | tree | snapshot
2016-01-27 gmungocJAL-1705 use GET for single queries; set gene name... commit | commitdiff | tree | snapshot
2016-01-26 gmungocJAL-1705 derive transcript sequences from gene sequence... commit | commitdiff | tree | snapshot
2016-01-26 tcofoegbuJAL-1999 JAL-1479 implemented configurable fail-safe... commit | commitdiff | tree | snapshot
2016-01-25 tcofoegbuJAL-1998 bugfix for division by zero error for PDB... commit | commitdiff | tree | snapshot
2016-01-25 gmungocJAL-1705 EnsemblGene added, and related refactoring commit | commitdiff | tree | snapshot
2016-01-25 gmungocJAL-1997 database browser support tooltip if available commit | commitdiff | tree | snapshot
2016-01-23 gmungocJAL-1355 get dialog title from message bundle commit | commitdiff | tree | snapshot
2016-01-23 gmungocJAL-1705 copy 'show sequence features' setting in ... commit | commitdiff | tree | snapshot
2016-01-23 gmungocJAL-1705 todo comment re writing DBRefEntry/SequenceFea... commit | commitdiff | tree | snapshot
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
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