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JAL-1563 smarter support for advanced querying of Uniprot FTS
[jalview.git] / src / jalview / ext /
2016-05-13 gmungocJAL-2105 capture Ensembl data version, check REST versi... 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
2015-08-03 Jim ProcterJAL-1821 JAL-1759 updated Jmol has different model... tree | commitdiff
2015-08-03 Jim ProcterJAL-1821 avoid race condition when multiple structures... tree | commitdiff
2015-07-08 gmungocJAL-1759 merge from develop tree | commitdiff
2015-07-03 gmungocJAL-892 1 second delay for correct initial rendering... tree | commitdiff
2015-06-30 gmungocJAL=1759 fix Jmol state command bug; remove debug output tree | commitdiff
2015-06-30 gmungocJAL-1759 unused JmolPopup removed, code tidy for generics tree | commitdiff
2015-06-30 gmungocJAL-1759 JMol now Jmol ! tree | commitdiff
2015-06-29 gmungocJAL-1759 correct conversion of Jmol Chain.chainId ... tree | commitdiff
2015-06-28 Jim ProcterJAl-1705 ENSEMBL cDNA type cannot be queried with pepti... tree | commitdiff
2015-06-28 Jim ProcterJAL-1705 javadoc tree | commitdiff
2015-06-28 Jim ProcterJAL-1705 concrete classes for different ENSEMBL sequenc... tree | commitdiff
2015-06-28 Jim ProcterJAL-1705 renamed SeqFetcherTest to EnsemblSeqProxyTest tree | commitdiff
2015-06-26 Jim ProcterJAL-1705 basic client & tests for rest.ensembl.org... tree | commitdiff
2015-06-26 gmungocJAL-1759 updates for Jmol 14.2.14_25.06.11 tree | commitdiff
2015-06-18 gmungocJAL-892 JAL-1779 save/restore Varna viewer to/from... tree | commitdiff
2015-06-08 Jim ProcterJAL-1766 test and buggy implementation of fasta index... tree | commitdiff
2015-06-05 gmungocJAL-1622 fix bug computing superposition + associated... tree | commitdiff
2015-06-04 gmungocJAL-1750 View Mapping scoped to that viewer's mappings... tree | commitdiff
2015-06-04 gmungocJAL-1743 new Chimera menu option to 'fit to window' tree | commitdiff
2015-06-04 gmungocJAL-1757 match only first altloc CA in PDB structure... tree | commitdiff
2015-05-22 tcofoegbuMerge branch 'features/JAL-1745_PDB-redownload' into... tree | commitdiff
2015-05-22 tcofoegbuJAL-1745, JAL-1717 improvement to ensure cached PDB... tree | commitdiff
2015-05-20 gmungocJAL-1741 nucleotide-aware colour schemes applied to... tree | commitdiff
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