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2016-06-27	gmungoc	JAL-2133 refactored duplicated code to AlignmentViewport	commit \| commitdiff \| tree
2016-06-27	gmungoc	JAL-1369 additional asserts in testStoreAndRecoverReferenceS...	commit \| commitdiff \| tree
2016-06-27	gmungoc	JAL-1270 unit tests for HiddenSequences	commit \| commitdiff \| tree
2016-06-23	gmungoc	JAL-2130 now simply viewer.dispose() to close down...	commit \| commitdiff \| tree
2016-06-22	gmungoc	JAL-2015 fixed bug in copy constructor and added tests	commit \| commitdiff \| tree
2016-06-22	gmungoc	JAL-1982 defensive checks for null annotations array	commit \| commitdiff \| tree
2016-06-22	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-06-22	gmungoc	JAL-1982 defensive test for null array of annotations	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2074 suppress prompt to save closed Groovy script...	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-1270 remove test artefact file after test	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-1270 added runAlways=true to setUp method	commit \| commitdiff \| tree
2016-06-21	gmungoc	JAL-2074 reuse Groovy window when reopening; rebind...	commit \| commitdiff \| tree
2016-06-20	gmungoc	JAL-2130 call viewer.dispose() on closing Jmol	commit \| commitdiff \| tree
2016-06-20	gmungoc	JAL-1667 updated PDB example query to a valid id (without...	commit \| commitdiff \| tree
2016-06-17	gmungoc	JAL-1557 selection from annotation (and group annotation...	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-1993 close sequence fetcher when opening database...	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-2124 JAL-1990 additional translations	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-2112 optimisation of EMBL CDS parsing	commit \| commitdiff \| tree
2016-06-16	gmungoc	JAL-1993 hide sequence fetcher dialogue until database...	commit \| commitdiff \| tree
2016-06-15	gmungoc	JAL-2025 unit tests added	commit \| commitdiff \| tree
2016-06-15	gmungoc	JAL-2101 unit test updated to match config file	commit \| commitdiff \| tree
2016-06-14	gmungoc	JAL-2114 more helpful reporting of parse failures	commit \| commitdiff \| tree
2016-06-14	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-06-09	gmungoc	JAL-2114 corrected Javadoc	commit \| commitdiff \| tree
2016-06-02	gmungoc	JAL-2124 additional Spanish text strings	commit \| commitdiff \| tree
2016-06-02	gmungoc	JAL-1424 corrected typos in message text keys	commit \| commitdiff \| tree
2016-06-02	gmungoc	JAL-1424 removed duplicate entry and unneeded full...	commit \| commitdiff \| tree
2016-06-01	gmungoc	JAL-1424 clearer messaging	commit \| commitdiff \| tree
2016-06-01	gmungoc	JAL-1424 utility to check resource bundle labels used...	commit \| commitdiff \| tree
2016-05-31	gmungoc	JAL-2023 adjustments to mappings added for split frame...	commit \| commitdiff \| tree
2016-05-31	gmungoc	JAL-2110 refactor + tests to allow a dbref version...	commit \| commitdiff \| tree
2016-05-31	gmungoc	JAL-1011 JAL-1989 don't mirror column-only selections...	commit \| commitdiff \| tree
2016-05-31	gmungoc	JAL-2123 use "rlabel" command to highlight with label...	commit \| commitdiff \| tree
2016-05-30	gmungoc	JAL-1670 JAL-2018 updated unit test for added example...	commit \| commitdiff \| tree
2016-05-30	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-05-30	gmungoc	JAL-1989 equals method strengthened to fully match...	commit \| commitdiff \| tree
2016-05-30	gmungoc	JAL-2119 help links checker added to /utils	commit \| commitdiff \| tree
2016-05-30	gmungoc	JAL-2119 updated Valdar group link	commit \| commitdiff \| tree
2016-05-29	gmungoc	JAL-2119 fixes for broken links in help files	commit \| commitdiff \| tree
2016-05-27	gmungoc	JAL-1989 tightened up use of flag for 'column selection...	commit \| commitdiff \| tree
2016-05-27	gmungoc	JAL-1989 added hashCode and equals, renamed field to...	commit \| commitdiff \| tree
2016-05-27	gmungoc	JAL-1911 use existing object when setting 'Prompt each...	commit \| commitdiff \| tree
2016-05-27	gmungoc	JAL-1942 small tidy (formatting, explict imports, typed...	commit \| commitdiff \| tree
2016-05-27	gmungoc	JAL-1911 correct typo in field name	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-391 add reverse / complement to command history...	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-2035 relocated a comment	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-1670 add non-positional feature with link to demonstrate...	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-1993 open sequence fetcher tree on 'fetch sequences'	commit \| commitdiff \| tree
2016-05-26	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-1797 non-case-sensitive counting of residues /...	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-2008 drag to reorder features not available in...	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-2079 update examples to new pfam.xfam.org domain	commit \| commitdiff \| tree
2016-05-26	gmungoc	JAL-2113 additions to embl_mapping.xml / data models...	commit \| commitdiff \| tree
2016-05-23	gmungoc	JAL-2113 remove spaces in sequence from unmarshalling...	commit \| commitdiff \| tree
2016-05-23	gmungoc	JAL-2114 save 'raw' ENA location as a sequence feature...	commit \| commitdiff \| tree
2016-05-23	gmungoc	JAL-2113 tidy variable naming / javadoc	commit \| commitdiff \| tree
2016-05-23	gmungoc	JAL-2113 EBIFetchClient refactor / unit tests / remove...	commit \| commitdiff \| tree
2016-05-23	gmungoc	Merge branch 'develop' into features/JAL-2113_emblXml1.2	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2114 explicit invalid test cases added	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2113 corrected test to use valid location syntax	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2113 removed classes deleted from mapping	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2113 embl_mapping.xml and code updated for EMBL...	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2114 accept "<123..178" or "123..>178" format	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2115 updated web link for MAFFT (and one typo)	commit \| commitdiff \| tree
2016-05-20	gmungoc	JAL-2049 unit test updated for HGVS syntax, feature...	commit \| commitdiff \| tree
2016-05-19	gmungoc	JAL-2114 added single-locus case and more error tests	commit \| commitdiff \| tree
2016-05-19	gmungoc	JAL-2114 parser + tests for GenBank location descriptors	commit \| commitdiff \| tree
2016-05-18	gmungoc	JAL-2049 set sequence feature group to "Jalview" for...	commit \| commitdiff \| tree
2016-05-18	gmungoc	JAL-2049 use HGVS notation for variant on protein residue	commit \| commitdiff \| tree
2016-05-13	gmungoc	JAL-2105 capture Ensembl data version, check REST version...	commit \| commitdiff \| tree
2016-05-12	gmungoc	JAL-2104 format tooltips to wrap correctly	commit \| commitdiff \| tree
2016-05-10	gmungoc	Merge branch 'develop' into features/JAL-1956_featureStyles	commit \| commitdiff \| tree
2016-05-09	gmungoc	JAL-2098 identify feature file with "<" in feature...	commit \| commitdiff \| tree
2016-05-09	gmungoc	JAL-2018 export graduated feature colours correctly	commit \| commitdiff \| tree
2016-05-05	gmungoc	JAL-2068 better documentation in example script	commit \| commitdiff \| tree
2016-05-04	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-05-04	gmungoc	JAL-2074 reinstated xerces-impl.jar	commit \| commitdiff \| tree
2016-05-04	gmungoc	JAL-2092 hide columns with/without feature	commit \| commitdiff \| tree
2016-05-04	gmungoc	JAL-2074 corrected classpathentry for Groovy 2.4.6	commit \| commitdiff \| tree
2016-05-04	gmungoc	Merge branch 'groovy/JAL-2074_upgradeto2.4.4' into...	commit \| commitdiff \| tree
2016-05-04	gmungoc	JAL-2090 removed test for Java > 1.1 to enable transparency	commit \| commitdiff \| tree
2016-05-03	gmungoc	JAL-2050 hide introns also when fetching Ensembl xrefs...	commit \| commitdiff \| tree
2016-05-02	gmungoc	JAL-1812 bind Groovy to Jalview rather than Desktop...	commit \| commitdiff \| tree
2016-04-29	gmungoc	JAL-2051 better checking of retrieved / duplicated...	commit \| commitdiff \| tree
2016-04-29	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-04-29	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-04-28	gmungoc	JAL-2083 removed use of reflection for Groovy	commit \| commitdiff \| tree
2016-04-26	gmungoc	JAL-1981 catch any exception when setting QuaQua look...	commit \| commitdiff \| tree
2016-04-26	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-04-26	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-04-26	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-04-25	gmungoc	JAL-2078 fixed broken link to groovy page	commit \| commitdiff \| tree
2016-04-25	gmungoc	JAL-1812 JAL-2068 only allow one Groovy console open...	commit \| commitdiff \| tree
2016-04-22	gmungoc	JAL-1812 JAL-2068 add Run Groovy Script to AlignFrame...	commit \| commitdiff \| tree
2016-04-22	gmungoc	JAL-2068 code and test for case of minValue == maxValue	commit \| commitdiff \| tree
2016-04-22	gmungoc	JAL-2068 framework and example scripts for pluggable...	commit \| commitdiff \| tree
2016-04-22	gmungoc	JAL-2068 Javadoc added	commit \| commitdiff \| tree
2016-04-22	gmungoc	JAL-2068 redundant implements clauses removed	commit \| commitdiff \| tree
2016-04-22	gmungoc	JAL-2068 convenience helper method for graduated score...	commit \| commitdiff \| tree
2016-04-21	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
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