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JAL-192 fix bounds when no hidden regions, and when sequence contained in hidden...
[jalview.git] / src /
2016-04-01 tcofoegbuJAL-2048 Update to structureviz2 package from cytoscape tree | commitdiff
2016-04-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and... tree | commitdiff
2016-04-01 gmungocJAL-1705 tweak to MapList.toString for debugging tree | commitdiff
2016-04-01 gmungocJAL-1705 generalised getLength() to handle [start1... tree | commitdiff
2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so... tree | commitdiff
2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL... tree | commitdiff
2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms) tree | commitdiff
2016-04-01 tcofoegbuJAL-2045 JAL-2047 improvement for sorting PDB quality... tree | commitdiff
2016-03-31 tcofoegbuJAL-2035 improvement to add binding to multiple model tree | commitdiff
2016-03-30 tcofoegbuJAL-1668 further clean-up of popup menu and NPE check... tree | commitdiff
2016-03-30 tcofoegbuJAL-2038 bug fix for NPE while setting progress message... tree | commitdiff
2016-03-28 tcofoegbumerge tree | commitdiff
2016-03-28 tcofoegbuJAL-1668 removed redundant UI elements in PopupMenu... tree | commitdiff
2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks tree | commitdiff
2016-03-28 gmungocJAL-2016 push getFeatureColourScheme(source) into Seque... tree | commitdiff
2016-03-28 gmungocJAL-2036 update AlignFrame menus when dbreffetcher... tree | commitdiff
2016-03-25 tcofoegbuJAL-2035 improvement to bind Jalview to Chimera model... tree | commitdiff
2016-03-24 tcofoegbuJAL-1919 Settings to disable duplicate generation of... tree | commitdiff
2016-03-24 tcofoegbuJAL-1479 Commented out debug sysout's for SiftsClient tree | commitdiff
2016-03-24 tcofoegbuJAL-1919 Added ability to generate temprature factor... tree | commitdiff
2016-03-24 tcofoegbumerge tree | commitdiff
2016-03-24 tcofoegbufixed applet build tree | commitdiff
2016-03-24 gmungocJAL-1705 removed experimental 'highlight selection... tree | commitdiff
2016-03-24 gmungocJAL-2032 structure follow mouseover in a copy of a... tree | commitdiff
2016-03-24 tcofoegbuJAL-1919 set DEFUALT_STRUCTURE_FORMAT to PDB tree | commitdiff
2016-03-23 tcofoegbumerge tree | commitdiff
2016-03-23 tcofoegbuJAL-2009 added programmatic custom feature setting... 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
2016-03-23 gmungocJAL-1997 default empty tooltip required for correct... 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 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu... tree | commitdiff
2016-03-22 gmungocJAL-1705 add xref seqs to 'parent' dataset only if... tree | commitdiff
2016-03-22 gmungocJAL-1191 isolated SequenceOntology (BioJava wrapper... tree | commitdiff
2016-03-22 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-21 tcofoegbuJAL-1919 refactor moved StructureViewerSettings tree | commitdiff
2016-03-21 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsu... tree | commitdiff
2016-03-21 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs... tree | commitdiff
2016-03-21 tcofoegbudevelop merge features/JAL-1919_mmCIF-Support tree | commitdiff
2016-03-21 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-03-21 gmungocJAL-1855 dbfetch from /ena_sequence/, /ena_coding/ tree | commitdiff
2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings tree | commitdiff
2016-03-21 tcofoegbuJAL-2028 added improvement for preconfigured ordering... tree | commitdiff
2016-03-21 tcofoegbudevelop merge tree | commitdiff
2016-03-21 tcofoegbumungo merge tree | commitdiff
2016-03-21 tcofoegbudevelop merge tree | commitdiff
2016-03-21 tcofoegbuJAL-1667 Changed PDBSearchPanel's search result layout... tree | commitdiff
2016-03-16 gmungocMerge branch 'develop' of https://source.jalview.org... tree | commitdiff
2016-03-16 gmungocJAL-1705 xref ENST to correct (ENSP) accession id tree | commitdiff
2016-03-16 tcofoegbuJAL-2028 improvment to the displayed column customisation tree | commitdiff
2016-03-15 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... mungo_develop tree | commitdiff
2016-03-15 gmungocJAL-2016 corrected Javadoc, added test for anonymous... 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 tcofoegbuJAL-1478 Fixed ArrayIndexOutOfBoundsException while... tree | commitdiff
2016-03-11 tcofoegbumerge tree | commitdiff
2016-03-11 tcofoegbuJAL-2026 Bug fix for best quality filter tree | commitdiff
2016-03-11 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-03-11 gmungocJAL-1270 unit test for SequenceIdMatcher.SeqIdName tree | commitdiff
2016-03-11 gmungocJAL-1705 check Retry-After response header tree | commitdiff
2016-03-11 gmungocJAL-1705 javadoc added only 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
2016-03-10 tcofoegbudevelop merge tree | commitdiff
2016-03-10 tcofoegbuJAL-2025 added code to stanitise query for structure... tree | commitdiff
2016-03-10 tcofoegbuJAL-2024 code to enforce case insensitivity for manual... tree | commitdiff
2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset 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 tcofoegbuJAL-1919 fixed bug causing PDBfile test failure tree | commitdiff
2016-03-03 tcofoegbuJAL-1919 updated unicode mapping symbol tree | commitdiff
2016-03-03 tcofoegbuJAL-1919 updated unicode symbol for mapping 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
2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when... tree | commitdiff
2016-03-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-03-01 gmungocJAL-1705 align CDS to transcripts tree | commitdiff
2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts tree | commitdiff
2016-02-26 tcofoegbudevelop merge tree | commitdiff
2016-02-26 tcofoegbuJAL-2009 reverted 'RES NUM' feature back to 'RESNUM' tree | commitdiff
2016-02-26 tcofoegbuJAL-1994 updated implementation for broken tests tree | commitdiff
2016-02-26 tcofoegbuJAL-1994 fix for broken tests tree | commitdiff
2016-02-25 tcofoegbuJAL-1919 initial support for mmCIF using JMol API.... tree | commitdiff
2016-02-25 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-02-23 tcofoegbudevelop merge tree | commitdiff
2016-02-23 tcofoegbuJAL-1720 renamed Structure Chooser filters according... tree | commitdiff
2016-02-22 tcofoegbuJAL-1720 JAL-2002 improvement for 'uniprot coverage... tree | commitdiff
2016-02-22 tcofoegbuJAL-1944 bugfix for error when exporting hidden sequenc... tree | commitdiff
2016-02-22 gmungocJAL-1705 first pass at applying preset feature colourin... tree | commitdiff
2016-02-20 gmungocMerge branch 'mungo_develop' into features/JAL-653_JAL... tree | commitdiff
2016-02-20 gmungocMerge branch 'JAL-1956_featureStyles' into features... tree | commitdiff
2016-02-20 gmungocJAL-2016 first draft of pre-set feature colour scheme tree | commitdiff
2016-02-20 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_h... tree | commitdiff
2016-02-19 gmungocJAL-1705 handle case of sequence with no dataset sequence tree | commitdiff
2016-02-19 gmungocJAL-1705 regular expression updates, tests, other refac... tree | commitdiff
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