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jalview.git
2016-03-11 gmungocJAL-1705 javadoc added only commit | commitdiff | tree | snapshot
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot commit | commitdiff | tree | snapshot
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset commit | commitdiff | tree | snapshot
2016-03-04 gmungocJAL-1705 EnsemblGenomes a top level db source commit | commitdiff | tree | snapshot
2016-03-04 gmungocJAL-1705 parse 'description' from GFF as sequence descr... commit | commitdiff | tree | snapshot
2016-03-03 gmungocJAL-1705 unit test for aligning with incomplete start... commit | commitdiff | tree | snapshot
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support... commit | commitdiff | tree | snapshot
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when... commit | commitdiff | tree | snapshot
2016-03-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2016-03-01 gmungocJAL-1705 align CDS to transcripts commit | commitdiff | tree | snapshot
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts commit | commitdiff | tree | snapshot
2016-02-26 tcofoegbuJAL-2009 reverted 'RES NUM' feature back to 'RESNUM' commit | commitdiff | tree | snapshot
2016-02-26 tcofoegbuJAL-1994 updated implementation for broken tests commit | commitdiff | tree | snapshot
2016-02-26 tcofoegbuJAL-1994 fix for broken tests commit | commitdiff | tree | snapshot
2016-02-25 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2016-02-23 tcofoegbuJAL-1720 renamed Structure Chooser filters according... commit | commitdiff | tree | snapshot
2016-02-22 tcofoegbuJAL-1720 JAL-2002 improvement for 'uniprot coverage... commit | commitdiff | tree | snapshot
2016-02-22 tcofoegbuJAL-1944 bugfix for error when exporting hidden sequenc... commit | commitdiff | tree | snapshot
2016-02-22 gmungocJAL-1705 first pass at applying preset feature colourin... commit | commitdiff | tree | snapshot
2016-02-20 gmungocMerge branch 'mungo_develop' into features/JAL-653_JAL... commit | commitdiff | tree | snapshot
2016-02-20 gmungocMerge branch 'JAL-1956_featureStyles' into features... commit | commitdiff | tree | snapshot
2016-02-20 gmungocJAL-2016 first draft of pre-set feature colour scheme commit | commitdiff | tree | snapshot
2016-02-20 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 handle case of sequence with no dataset sequence commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 regular expression updates, tests, other refac... commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 updated for change to CrossRef signature commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 refactor show products, set initial split... commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 more lenient test for 'sequence retrieved' commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 return Ensembl genes for model species for... commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 JAL-1191 more terms added to hard-coded version commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1706 reverted setting start position as too confusi... commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 lenient DBRef matcher added (accession id... commit | commitdiff | tree | snapshot
2016-02-19 gmungocJAL-1705 helper method for mapping excluding stop codon commit | commitdiff | tree | snapshot
2016-02-19 tcofoegbuJAL-2009 Codes to enable storing inserted residues... commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-1270 remove trailing space + test commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl... commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-1191 additions to SOLite, tweak to test commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-1705 take feature ID for description if nothing... commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-282 wrap very long id in tooltip commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-1705 JAL-1686 stronger SequenceFeature.equals(... commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-2010 simple prototype of 'Highlight Selection'... commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-2008 updates for String[] to List<String> change commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-2008 avoid unnecessary repaints; signatures changed... commit | commitdiff | tree | snapshot
2016-02-12 gmungocJAL-265 updated help text commit | commitdiff | tree | snapshot
2016-02-12 gmungocMerge branch 'develop' into commit | commitdiff | tree | snapshot
2016-02-09 tcofoegbuJAL-1976 catch and handle OOM Error commit | commitdiff | tree | snapshot
2016-02-09 tcofoegbuJAL-1976 Added progress indicators for HTML_SVG and... commit | commitdiff | tree | snapshot
2016-02-09 tcofoegbuJAL-1975 updated image export pipeline to produce more... commit | commitdiff | tree | snapshot
2016-02-09 tcofoegbuJAL-1957 deleted stale comment commit | commitdiff | tree | snapshot
2016-02-09 tcofoegbumerge commit | commitdiff | tree | snapshot
2016-02-09 tcofoegbuJAL-1957 enabled multi-chain mapping and highlight... commit | commitdiff | tree | snapshot
2016-02-05 gmungocJAL-2006 scale even very small score ranges to a usable... commit | commitdiff | tree | snapshot
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
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