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JAL-2154 test for CDS->protein map
[jalview.git] / src / jalview / ext /
2016-08-01 tcofoegbuJAL-2164 bugfix to convert insCodes of '\000' to '... tree | commitdiff
2016-07-22 tcofoegbuJAL-2148 Bugfix in structureImportSettings string-to... tree | commitdiff
2016-07-21 tcofoegbuResolve merge conflict for StructureImportSettings tree | commitdiff
2016-07-21 tcofoegbuJAL-2148 fix to heuristically determine chain terminati... tree | commitdiff
2016-07-21 Jim ProcterMerge branch 'apifix/JAL-1926_JAL-2106' into develop tree | commitdiff
2016-07-20 Jim ProcterJAL-1926 JAL-2106 fix name for flag controlling additio... tree | commitdiff
2016-07-19 tcofoegbuMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-07-19 tcofoegbuJAL-1919 set default structure file format to mmCIF... tree | commitdiff
2016-07-18 gmungocJAL-2105 check content of Ensembl REST ping response tree | commitdiff
2016-07-13 Jim ProcterMerge branch 'develop' into features/JAL-2110_crossRefD... tree | commitdiff
2016-07-13 tcofoegbuJAL-2135 minor house-keeping tree | commitdiff
2016-07-12 tcofoegbuJAL-2135 NPE bugfix when parsing a structure file with... tree | commitdiff
2016-07-09 gmungocMerge branch 'develop' into features/JAL-2110_crossRefD... features/JAL-2110_crossRefDuplications tree | commitdiff
2016-07-08 tcofoegbuJAL-1919 Fixed failing tests, enabled HETATM processing... tree | commitdiff
2016-07-06 gmungocJAL-2110 ensuring mapped dbrefs between protein and cds tree | commitdiff
2016-07-01 tcofoegbuJAL-2135 bugfix for error preventing processing of... tree | commitdiff
2016-06-30 tcofoegbuJAL-1919 updated PDBSequenceFetcherTest and JMol parser... tree | commitdiff
2016-06-23 gmungocJAL-2130 now simply viewer.dispose() to close down... tree | commitdiff
2016-06-21 Jim ProcterMerge branch 'features/JAL-1956_featureStyles' into... tree | commitdiff
2016-06-20 gmungocJAL-2130 call viewer.dispose() on closing Jmol tree | commitdiff
2016-06-10 Jim ProcterJAL-1941 added test URL and notes about PyRNA restclient tree | commitdiff
2016-05-31 gmungocJAL-2123 use "rlabel" command to highlight with label... tree | commitdiff
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi... tree | commitdiff
2016-05-10 gmungocMerge branch 'develop' into features/JAL-1956_featureStyles tree | commitdiff
2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated... tree | commitdiff
2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g.... tree | commitdiff
2016-04-11 gmungocJAL-1705 code/comment tidy only tree | commitdiff
2016-04-11 gmungocJAL-2051 fetch Ensembl Gene accessions one at a time tree | commitdiff
2016-04-06 tcofoegbumerge tree | commitdiff
2016-04-06 tcofoegbuJAL-2047 JAL-1919 fixed empty tooltip text when a cell... tree | commitdiff
2016-04-04 Jim ProcterJAL-2010 refactoring todo tree | commitdiff
2016-04-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms) tree | commitdiff
2016-03-24 tcofoegbuJAL-1919 Added ability to generate temprature factor... tree | commitdiff
2016-03-23 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-23 gmungocJAL-1705 add DBRefEntry for 'self' to retrieved transcr... tree | commitdiff
2016-03-22 tcofoegburesolve conflict with Mungo's merge tree | commitdiff
2016-03-22 tcofoegbuJAL-1919 code improvement to make PDB sequence fetcher... tree | commitdiff
2016-03-22 gmungocJAL-1191 isolated SequenceOntology (BioJava wrapper... tree | commitdiff
2016-03-21 tcofoegbudevelop merge tree | commitdiff
2016-03-16 gmungocJAL-1705 xref ENST to correct (ENSP) accession id tree | commitdiff
2016-03-15 gmungocJAL-2016 FeatureSettingsI now FeatureSettingsModelI tree | commitdiff
2016-03-15 gmungocJAL-1705 code tidy/comment only tree | commitdiff
2016-03-15 gmungocJAL-1705 compute reverse complement of variants on... tree | commitdiff
2016-03-15 tcofoegbuJAL-1919 refined structure view annotation settings... tree | commitdiff
2016-03-11 gmungocJAL-1705 check Retry-After response header tree | commitdiff
2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot tree | commitdiff
2016-03-11 tcofoegbuJAL-1818 reimplemented sequence and annotation processi... tree | commitdiff
2016-03-04 gmungocJAL-1705 EnsemblGenomes a top level db source tree | commitdiff
2016-03-04 gmungocJAL-1705 parse 'description' from GFF as sequence descr... tree | commitdiff
2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support... tree | commitdiff
2016-03-03 tcofoegbuJAL-1919 PDBfile and JmolParser refactor tree | commitdiff
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts tree | commitdiff
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API.... tree | commitdiff
2016-02-22 gmungocJAL-1705 first pass at applying preset feature colourin... tree | commitdiff
2016-02-19 gmungocJAL-1705 regular expression updates, tests, other refac... tree | commitdiff
2016-02-19 gmungocJAL-1705 return Ensembl genes for model species for... tree | commitdiff
2016-02-12 gmungocJAL-1705 various refactoring towards Uniprot-to-Ensembl... tree | commitdiff
2016-02-12 gmungocJAL-2010 simple prototype of 'Highlight Selection'... tree | commitdiff
2016-02-12 gmungocMerge branch 'develop' into tree | commitdiff
2016-02-09 tcofoegbumerge develop tree | commitdiff
2016-02-09 tcofoegbuJAL-1957 deleted stale comment tree | commitdiff
2016-02-09 tcofoegbuJAL-1957 enabled multi-chain mapping and highlight... tree | commitdiff
2016-02-04 gmungocJAL-1705 additional tests, validation regexp tweaks... tree | commitdiff
2016-02-04 gmungocJAL-2003 export features on alignment, not alignment... tree | commitdiff
2016-02-01 gmungocJAL-1705 further unit tests tree | commitdiff
2016-02-01 gmungocJAL-1705 set Uniprot xref as 'source dbref' (for SIFTS... 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 gmungocJAL-1705 fetch Uniprot and PDB xrefs for Ensembl protei... 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
2016-01-27 gmungocJAL-1705 add exon name to features and render on peptid... 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
2016-01-25 gmungocJAL-1705 EnsemblGene added, and related refactoring tree | commitdiff
2016-01-23 gmungocJAL-1705 compute peptide variants from dna; add "conseq... tree | commitdiff
2016-01-21 gmungocJAL-1705 reworked Ensembl clients now fetching and... tree | commitdiff
2016-01-21 tcofoegbuJAL-1919 basic support for importing and viewing mmCIF... tree | commitdiff
2016-01-08 gmungocJAL-1705 DbSourceProxy properties converted to methods... tree | commitdiff
2016-01-05 gmungocMerge remote-tracking branch 'origin/features/JAL-1705_... 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
2015-11-11 tcofoegbuJAL-1479 JAL-1957 Added code to enable simultaneous... tree | commitdiff
2015-11-11 tcofoegbuJAL-1957 JAL-1479 Further optimisation of SIFTs Client... features/JAL-1479_SIFTS-mapping tree | commitdiff
2015-11-10 Jim ProcterMerge branch 'features/JAL-1705_ensembl' of source... features/JAL-1705_ensembl tree | commitdiff
2015-11-09 gmungocJAL-1705 type enum can encapsulate the corresponding... tree | commitdiff
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2015-10-15 Jim ProcterMerge branch 'develop' into features/JAL-1705_ensembl tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 licencing for new files in src tree | commitdiff
2015-09-10 Jim ProcterJAL-1645 source formatting and organise imports tree | commitdiff
2015-09-03 gmungocJAL-1859 removed unneeded dependency on package not... tree | commitdiff
2015-09-03 gmungocJAL-1828 lookup table to convert MSE to MET when parsin... tree | commitdiff
2015-08-28 gmungocJAL-1836 temporary workaround for negative resNumIns... tree | commitdiff
2015-08-26 gmungocJAL-1596 check for null pointer (thread running after... tree | commitdiff
2015-08-26 gmungocJAL-1759 corrected syntax for 'atom picked' callback... tree | commitdiff
2015-08-19 gmungocJAL-1742 suppress 'add chain' option for Jmol, pull... tree | commitdiff
2015-08-05 Jim ProcterJAL-1821 patch for completeness - first model number... tree | commitdiff
2015-08-03 Jim ProcterJAL-1821 JAL-1759 reinstate rotation speed configuratio... tree | commitdiff
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