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2016-11-14	gmungoc	JAL-2296 new code and refactoring for 'copy Chimera...	commit \| commitdiff \| tree
2016-11-14	gmungoc	JAL-2295 don't copy 'Chimera' features back to Chimera	commit \| commitdiff \| tree
2016-11-14	gmungoc	JAL-2296 parse Chimera atomspec to AtomSpec	commit \| commitdiff \| tree
2016-11-14	gmungoc	JAL-2296 report whether SequenceFeature actually added...	commit \| commitdiff \| tree
2016-11-14	gmungoc	JAL-2295 JAL-2296 skeleton 'attributes to features...	commit \| commitdiff \| tree
2016-11-11	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 tests now 'network-free' with local PDB and...	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 JAL-2269 JAL-2319 mockable SIFTS file, fix...	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 improved integrity of 'isFinishedInit' flag	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-1270 corrected command-line args	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 set finishedInit to false before checking...	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 test that verifies transfer of features to...	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 sorted properties for readability	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 (optionally) return Chimera command reply	commit \| commitdiff \| tree
2016-11-11	gmungoc	JAL-2295 correct test for Float.isNaN(score) !	commit \| commitdiff \| tree
2016-11-10	gmungoc	JAL-2295 additional tests, stronger sanitisation of...	commit \| commitdiff \| tree
2016-11-09	gmungoc	JAL-2295 set attributes commands include feature value...	commit \| commitdiff \| tree
2016-11-09	gmungoc	JAL-2295 single constant for "RESNUM" feature name	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2295 JAL-1596 method to pass a command script file...	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2301 corrected search example to match AA properties...	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2301 made T hydrophobic as per the cited conservation...	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-1961 added link to GFF3 format as well as GFF2	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2295 feature and colour commands refactored to...	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2295 method added to return a compact mapped range...	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2295 extracted AtomSpecModel for reuse in Chimera...	commit \| commitdiff \| tree
2016-11-08	gmungoc	JAL-2295 make RangeComparator a top level class for...	commit \| commitdiff \| tree
2016-11-07	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-1270 renamed helper method so it is not run as...	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2272 another test case	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-1805 groups=Functional added where missing	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2272 unit tests added for Platform.isControlDown	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2318 updated help text	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2282 show url links that need checked; remove ...	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2295 handle no progress bar message properly	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2295 small tidy of javadoc only	commit \| commitdiff \| tree
2016-11-07	gmungoc	JAL-2295 (unoptimised) write Jalview features as Chimera...	commit \| commitdiff \| tree
2016-11-04	gmungoc	JAL-2272 right mouse button on Mac is not Cmd equivalent!	commit \| commitdiff \| tree
2016-11-03	gmungoc	JAL-2281 test added to show searchRefs is now not case...	commit \| commitdiff \| tree
2016-11-03	gmungoc	JAL-2295 step 1 new menu item to transfer Jalview attributes...	commit \| commitdiff \| tree
2016-11-02	gmungoc	JAL-2301 table formatted, and corrected to match the...	commit \| commitdiff \| tree
2016-11-02	gmungoc	JAL-98 JAL-1854 encapsulate 'magic number' threshold...	commit \| commitdiff \| tree
2016-11-02	gmungoc	JAL-98 ProfileI interface for Profile	commit \| commitdiff \| tree
2016-11-02	gmungoc	JAL-98 test updated for percentage rounded	commit \| commitdiff \| tree
2016-11-02	gmungoc	JAL-98 Profile and ResidueCount moved from analysis...	commit \| commitdiff \| tree
2016-11-02	gmungoc	JAL-98 wording "negatively conserved" now "absence...	commit \| commitdiff \| tree
2016-11-01	gmungoc	Conservation now using ResidueCount; tests added	commit \| commitdiff \| tree
2016-11-01	gmungoc	JAL-98 use Integer constants; tests added for propHash...	commit \| commitdiff \| tree
2016-11-01	gmungoc	JAL-98 typo in javadoc	commit \| commitdiff \| tree
2016-11-01	gmungoc	JAL-98 simplified repeat() method	commit \| commitdiff \| tree
2016-11-01	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-10-31	gmungoc	JAL-98 round when formatting dec places	commit \| commitdiff \| tree
2016-10-27	gmungoc	JAL-2282 test assertions for 'other' dbsource	commit \| commitdiff \| tree
2016-10-27	gmungoc	JAL-98 refactor bleachColour() to ColorUtils	commit \| commitdiff \| tree
2016-10-27	gmungoc	JAL-2287 treat Escape like Cancel in dialog box	commit \| commitdiff \| tree
2016-10-26	gmungoc	JAL-2287 Cancel option on Close Chimera? dialog	commit \| commitdiff \| tree
2016-10-26	gmungoc	Merge branch 'bug/JAL-98consensusMemory' into develop	commit \| commitdiff \| tree
2016-10-26	gmungoc	JAL-2286 modal residue check + commenting	commit \| commitdiff \| tree
2016-10-26	gmungoc	JAL-98 null reference to globalColourScheme as it has...	commit \| commitdiff \| tree
2016-10-26	gmungoc	JAL-2286 javadoc, refactor, unit tests for threshold...	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-2286 use constant for fixed colours	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-98 javadoc corrected	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-98 javadoc added	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-98 minor fixes to / tests for annotation derivation	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-98 field comments updated	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-98 small efficiency fix + commenting	commit \| commitdiff \| tree
2016-10-25	gmungoc	JAL-98 javadoc / comments updated	commit \| commitdiff \| tree
2016-10-24	gmungoc	JAL-98 fixme comment removed - nothing to do	commit \| commitdiff \| tree
2016-10-24	gmungoc	JAL-98 ResidueCount 100% test coverage (and bug fixes!)	commit \| commitdiff \| tree
2016-10-24	gmungoc	JAL-2272 Cmd-drag to group edit sequences on Mac (Ctrl...	commit \| commitdiff \| tree
2016-10-24	gmungoc	JAL-2283 corrected preferences settings for test	commit \| commitdiff \| tree
2016-10-24	gmungoc	Merge branch 'develop' into bug/JAL-98consensusMemory	commit \| commitdiff \| tree
2016-10-24	gmungoc	JAL-2283 set 'by conservation' correctly when changing...	commit \| commitdiff \| tree
2016-10-14	gmungoc	Merge branch 'releases/Release_2_10_Branch' into task...	commit \| commitdiff \| tree
2016-10-13	gmungoc	JAL-2253 2 second timeout on ping URL, default 5 minutes...	commit \| commitdiff \| tree
2016-10-13	gmungoc	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-13	gmungoc	JAL-1479 revise warning message to suit all contexts	commit \| commitdiff \| tree
2016-10-13	gmungoc	JAL-2044 increase Jmol file load timeout from 5 to...	commit \| commitdiff \| tree
2016-10-13	gmungoc	JAL-2044 ensure AAStructureBindingModel.pdbEntry has...	commit \| commitdiff \| tree
2016-10-13	gmungoc	JAL-2044 include model name in progress bar message...	commit \| commitdiff \| tree
2016-10-11	gmungoc	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-11	gmungoc	JAL-2241 check for null jprovider when processing New...	commit \| commitdiff \| tree
2016-10-11	gmungoc	Merge branch 'releases/Release_2_10_Branch' into develop	commit \| commitdiff \| tree
2016-10-11	gmungoc	JAL-1479 small tidy of error message when Sifts mapping...	commit \| commitdiff \| tree
2016-10-11	gmungoc	JAL-2233 reverted changes to Jmol logging levels	commit \| commitdiff \| tree
2016-10-06	gmungoc	JAL-2254 map error text in root node of EMBL XML response	commit \| commitdiff \| tree
2016-10-06	gmungoc	Merge branch 'develop' into bug/JAL-98consensusMemory	commit \| commitdiff \| tree
2016-10-06	gmungoc	Merge branch 'develop' into task/JAL-2196pdbeProperties	commit \| commitdiff \| tree
2016-10-06	gmungoc	JAL-2252 now buffered read of 3 lines of a time in...	commit \| commitdiff \| tree
2016-10-06	gmungoc	JAL-2245 checks for null added (in case EMBL fetch...	commit \| commitdiff \| tree
2016-10-05	gmungoc	Merge branch 'develop' into task/JAL-2196pdbeProperties	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-1191 revert to using SequenceOntologyLite due to...	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-1191 configure full SO for desktop, SOLite for...	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-2245 defence against NullPointer if no EMBL data...	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-1191 use full SO in desktop application	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-2105 update Ensembl REST version to 4.7	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-1191 refined warning message	commit \| commitdiff \| tree
2016-10-05	gmungoc	JAL-1191 added mRNA isA transcript to SequenceOntologyLite...	commit \| commitdiff \| tree
2016-10-04	gmungoc	Merge branch 'bug/JAL-2245enaXmlChange' into develop	commit \| commitdiff \| tree
2016-10-04	gmungoc	Merge branch 'bug/JAL-2210_hack_for_Release_2_10' into...	commit \| commitdiff \| tree
2016-10-04	gmungoc	JAL-2245 Castor mapping and code changes for change...	commit \| commitdiff \| tree
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