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2016-12-08	gmungoc	Merge branch 'bug/JAL-2358phantomChimera' into spikes...	commit \| commitdiff \| tree
2016-12-08	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-12-08	gmungoc	JAL-2358 ensure mappings removed on close Chimera;...	commit \| commitdiff \| tree
2016-12-08	gmungoc	JAL-2359 add Window menu entry only after all danger...	commit \| commitdiff \| tree
2016-12-07	gmungoc	JAL-2356 use cached Sifts file if not expired	commit \| commitdiff \| tree
2016-12-07	gmungoc	JAL-2354 handle error response when fetching features	commit \| commitdiff \| tree
2016-12-07	gmungoc	JAL-2344 handle null format, simplify JalviewFileChooser...	commit \| commitdiff \| tree
2016-12-05	gmungoc	JAL-1753 JAL-1596 JAL-1933 ensure AWT updates are on...	commit \| commitdiff \| tree
2016-12-05	gmungoc	Merge branch 'features/JAL-1933_occupancy' into features...	commit \| commitdiff \| tree
2016-12-02	gmungoc	Merge branch 'features/JAL-1933_occupancy' into features...	commit \| commitdiff \| tree
2016-12-02	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-12-02	gmungoc	JAL-1933 gap value as description; minor formatting	commit \| commitdiff \| tree
2016-11-30	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-30	gmungoc	JAL-2344 use ".cif" for saved mmCIF file (and refactor...	commit \| commitdiff \| tree
2016-11-30	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-29	gmungoc	JAL-2329 tests to confirm behaviour of Java extended...	commit \| commitdiff \| tree
2016-11-29	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-29	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-11-29	gmungoc	JAL-2344 corrected conversion of Type enum to FileFormat	commit \| commitdiff \| tree
2016-11-29	gmungoc	JAL-2344 FileFormat.isStructureFile replaces	commit \| commitdiff \| tree
2016-11-28	gmungoc	Merge branch 'develop' into trialMerge	commit \| commitdiff \| tree
2016-11-28	gmungoc	JAL-2344 added FileFormatI.isStructureFile()	commit \| commitdiff \| tree
2016-11-28	gmungoc	JAL-2345 cache generated ImageIcon per file path	commit \| commitdiff \| tree
2016-11-25	gmungoc	JAL-2344 dynamically determine recognised extensions...	commit \| commitdiff \| tree
2016-11-25	gmungoc	Merge branch 'develop' into trialMerge	commit \| commitdiff \| tree
2016-11-25	gmungoc	JAL-2344 override to ignore (obsolete?) JalviewFileView	commit \| commitdiff \| tree
2016-11-25	gmungoc	JAL-2344 use .equals() to compare FileFormatI objects	commit \| commitdiff \| tree
2016-11-25	gmungoc	JAL-2344 correct roundtrip test to exclude Jalview...	commit \| commitdiff \| tree
2016-11-24	gmungoc	Distinguish text-only output formats and others (.jar...	commit \| commitdiff \| tree
2016-11-24	gmungoc	Further tweaks to get tests passing	commit \| commitdiff \| tree
2016-11-24	gmungoc	FileFormatI further tweaks, clean compile	commit \| commitdiff \| tree
2016-11-23	gmungoc	JAL-1738 Spanish versions added	commit \| commitdiff \| tree
2016-11-23	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-22	gmungoc	JAL-2337 fix: only adjust once for scroll offset	commit \| commitdiff \| tree
2016-11-22	gmungoc	JAL-1919 JAL-2177 handle empty pdbentries list correctly	commit \| commitdiff \| tree
2016-11-22	gmungoc	JAL-2277 refactored AlignmentPanel.printUnwrapped to...	commit \| commitdiff \| tree
2016-11-21	gmungoc	JAL-2333 test beefed up with gaps	commit \| commitdiff \| tree
2016-11-21	gmungoc	JAL-2333 corrected select columns with 'contact' feature	commit \| commitdiff \| tree
2016-11-21	gmungoc	Merge branch 'develop' into bug/JAL-2323disulfideOverview	commit \| commitdiff \| tree
2016-11-18	gmungoc	JAL-98 with the two types missing from last commit...	commit \| commitdiff \| tree
2016-11-17	gmungoc	JAL-2323 revert to thread-safe iteration over array...	commit \| commitdiff \| tree
2016-11-17	gmungoc	JAL-98 ProfilesI container for profiles for columns	commit \| commitdiff \| tree
2016-11-17	gmungoc	JAL-98 javadoc, third party acknowledgements (and very...	commit \| commitdiff \| tree
2016-11-17	gmungoc	JAL-2327 disulfide bond abstracted to SequenceFeature...	commit \| commitdiff \| tree
2016-11-17	gmungoc	JAL-2327 add isContactFeature	commit \| commitdiff \| tree
2016-11-16	gmungoc	JAL-2296 unit test for reading Chimera attributes to...	commit \| commitdiff \| tree
2016-11-16	gmungoc	JAL-2323 render disulfide bond correctly on overview...	commit \| commitdiff \| tree
2016-11-16	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-16	gmungoc	JAL-2324 fix and tests for comparison of Float.NaN...	commit \| commitdiff \| tree
2016-11-16	gmungoc	JAL-2319 corrected reporting of SIFTS mapping	commit \| commitdiff \| tree
2016-11-16	gmungoc	Merge branch 'develop' into features/JAL-2295setChimeraAttri...	commit \| commitdiff \| tree
2016-11-16	gmungoc	JAL-2296 don't copy attribute with value False	commit \| commitdiff \| tree
2016-11-16	gmungoc	JAL-2295 don't exclude RESNUM from transfer to Chimera	commit \| commitdiff \| tree
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
2016-11-10	gmungoc	JAL-2320 thread to close Chimera viewer panel if Chimera...	commit \| commitdiff \| tree
2016-11-10	gmungoc	JAL-2320 added getViewer() method to return Chimera...	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
2016-11-04	gmungoc	JAL-966 JAL-1854 removed redundant methods / modifiers...	commit \| commitdiff \| tree
2016-11-04	gmungoc	JAL-2302 unit tests added for Finder	commit \| commitdiff \| tree
2016-11-03	gmungoc	JAL-2310 don't double-count sequence matches; code...	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
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