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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
2016-10-04	gmungoc	JAL-2232 some fix / partial fix of failing tests	commit \| commitdiff \| tree
2016-10-04	gmungoc	JAL-2232 added test that failed before last fix, passes...	commit \| commitdiff \| tree
2016-10-04	gmungoc	JAL-2232 JAL-2154 update dbrefs to newly created dataset...	commit \| commitdiff \| tree
2016-10-03	gmungoc	JAL-2110 javadoc formatting only	commit \| commitdiff \| tree
2016-10-03	gmungoc	JAL-2110 JAL-1705 handle not found (400) better	commit \| commitdiff \| tree
2016-10-03	gmungoc	JAL-2110 additional tests for setDatasetSequence, javadoc...	commit \| commitdiff \| tree
2016-09-30	gmungoc	JAL-2236 code restored (and some compiler warnings...	commit \| commitdiff \| tree
2016-09-30	gmungoc	Merge branch 'develop' into features/JAL-1856dbRefFetcherMes...	commit \| commitdiff \| tree
2016-09-30	gmungoc	JAL-2234 FER1_ARATH renamed FER2_ARATH and vice versa	commit \| commitdiff \| tree
2016-09-30	gmungoc	JAL-2236 fixes for desktop and applet implementation...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-1856 better warning messages for sequence matching...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-2213 code warnings addressed (typed collections...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-2213 removed PDB from db sources list; also code...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-2213 made RESNUM constant private (not used elsewhere...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-2213 corrected wait for files to load in Jmol;...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-2237 apply default filter as sort in initial search	commit \| commitdiff \| tree
2016-09-29	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-2047 allow title to be shrunk; spelling fix	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-1544 typo	commit \| commitdiff \| tree
2016-09-29	gmungoc	JAL-1903 increase REST reply timeout from 5 to 15 seconds	commit \| commitdiff \| tree
2016-09-27	gmungoc	JAL-2233 less verbose logging for Jmol	commit \| commitdiff \| tree
2016-09-27	gmungoc	JAL-2231 save preferred scroll height _without_ progress...	commit \| commitdiff \| tree
2016-09-27	gmungoc	JAL-2230 JAL-2049 added sequence feature transfer to	commit \| commitdiff \| tree
2016-09-27	gmungoc	JAL-2230 use correct mapping to transfer features to...	commit \| commitdiff \| tree
2016-09-23	gmungoc	JAL-2214 Javadoc	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-1421 use declared type of ResidueProperties.propHash	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-1421 typed ResidueProperties.propHash; JAL-2176...	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 null currentAlignFrame on close all windows...	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 finalize call super.finalize()	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 finalise corrected to finalize	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 explicitly null AnnotationPanel and AnnotationRende...	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 finalize() refactored so not called programmatically	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 new dispose() method to null references	commit \| commitdiff \| tree
2016-09-22	gmungoc	JAL-2216 finalize call super.finalize()	commit \| commitdiff \| tree
2016-09-20	gmungoc	JAL-1306 calculate Quality also when Conservation not...	commit \| commitdiff \| tree
2016-09-19	gmungoc	JAL-2118 reorder annotations after add/delete/hide...	commit \| commitdiff \| tree
2016-09-19	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-09-19	gmungoc	JAL-2172 test and code updates for readonly selection...	commit \| commitdiff \| tree
2016-09-19	gmungoc	JAL-1353 small tidy of test	commit \| commitdiff \| tree
2016-09-19	gmungoc	JAL-1270 use test properties file	commit \| commitdiff \| tree
2016-09-16	gmungoc	JAL-2157 JAL-1803 refactored Sequence.updatePDBIds...	commit \| commitdiff \| tree
2016-09-16	gmungoc	JAL-2183 don't open two free text panels; give input...	commit \| commitdiff \| tree
2016-09-16	gmungoc	JAL-2183 avoid duplicate closeDialog()	commit \| commitdiff \| tree
2016-09-16	gmungoc	JAL-2164 removed unused parameters from JmolParser...	commit \| commitdiff \| tree
2016-09-16	gmungoc	JAL-1270 JAL-1919 ensure Temp Factor is OFF for test...	commit \| commitdiff \| tree
2016-09-13	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-09-13	gmungoc	JAL-1803 tests added for PDBEntry.Type	commit \| commitdiff \| tree
2016-09-13	gmungoc	JAL-2196 refactor PDBEntry.getProperty,setProperty...	commit \| commitdiff \| tree
2016-09-13	gmungoc	JAL-1803 extracted class ChainId to jalview.util.CaseInsensi...	commit \| commitdiff \| tree
2016-09-13	gmungoc	JAL-2119 use File.separator not "/"	commit \| commitdiff \| tree
2016-09-12	gmungoc	JAL-2119 case-sensitive href filename checking	commit \| commitdiff \| tree
2016-09-12	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-09-07	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-09-07	gmungoc	JAL-2164 fix failing test	commit \| commitdiff \| tree
2016-09-06	gmungoc	JAL-2106 DBRefEntry.isPrimary() renamed isPrimaryCandidate()	commit \| commitdiff \| tree
2016-09-06	gmungoc	JAL-2147 additional test coverage for findMappingsForSequenc...	commit \| commitdiff \| tree
2016-09-05	gmungoc	JAL-2154 made Java 7 compatible	commit \| commitdiff \| tree
2016-09-05	gmungoc	JAL-2106 increased coverage for testGetPrimaryDbRefs	commit \| commitdiff \| tree
2016-09-05	gmungoc	JAL-2106 corrections to DBRefEntry.isPrimary code and...	commit \| commitdiff \| tree
2016-09-02	gmungoc	JAL-1854 distinct messages for TODO/FIXME and DOCUMENT ME	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-2077 don't mess with the look and feel	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-2077 less drastic exit on close	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-2077 test harness for inspecting mouse events	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-2077 check isPopupTrigger in mouseReleased not...	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-1421 add generics to NJTree, refactor recursive...	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-1854 rule to disallow import of swing in appletgui	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-2077 do nothing in mousePressed if right button...	commit \| commitdiff \| tree
2016-09-01	gmungoc	JAL-2077 force defer right-click handling to mouseReleased...	commit \| commitdiff \| tree
2016-08-31	gmungoc	JAL-2077 test isPopupTrigger in mouseReleased or mouseClicke...	commit \| commitdiff \| tree
2016-08-31	gmungoc	JAL-2077 more javadoc	commit \| commitdiff \| tree
2016-08-31	gmungoc	Merge branch 'develop' of https://source.jalview.org...	commit \| commitdiff \| tree
2016-08-31	gmungoc	JAL-2077 check for isPopupTrigger() in mousePressed...	commit \| commitdiff \| tree
2016-08-31	gmungoc	JAL-1670 repositioned feature for backwards compatibility...	commit \| commitdiff \| tree
2016-08-30	gmungoc	JAL-2183 defensive check for openFrameCount < 0 (shouldn...	commit \| commitdiff \| tree
2016-08-30	gmungoc	JAL-2183 simplified database tree actionPerformed,...	commit \| commitdiff \| tree
2016-08-30	gmungoc	JAL-2183 revised change (= no change)	commit \| commitdiff \| tree
2016-08-30	gmungoc	JAL-2183 formatter added @Override (only)	commit \| commitdiff \| tree
2016-08-30	gmungoc	JAL-2183 removed redundant (overriden) add panel to...	commit \| commitdiff \| tree
2016-08-29	gmungoc	JAL-1854 tweaks to rules and README	commit \| commitdiff \| tree
2016-08-29	gmungoc	JAL-1854 checkstyle relocated to /utils, newlines to...	commit \| commitdiff \| tree
2016-08-29	gmungoc	Merge branch 'bug/JAL-1841rnaSecStr' into develop	commit \| commitdiff \| tree
2016-08-29	gmungoc	JAL-1448 updated unit test for last change	commit \| commitdiff \| tree
2016-08-29	gmungoc	JAL-1841 robustness fix	commit \| commitdiff \| tree
2016-08-29	gmungoc	Merge branch 'develop' into bug/JAL-1841rnaSecStr	commit \| commitdiff \| tree
2016-08-26	gmungoc	JAL-1854 two more rules, readme notes	commit \| commitdiff \| tree
2016-08-26	gmungoc	Merge branch 'develop' into bug/JAL-1841rnaSecStr	commit \| commitdiff \| tree
2016-08-26	gmungoc	JAL-1854 commented FallThrough rule	commit \| commitdiff \| tree
2016-08-26	gmungoc	JAL-1854 corrected nested package rule	commit \| commitdiff \| tree
2016-08-26	gmungoc	JAL-2049 set Ensembl variant source to ENSEMBL if ...	commit \| commitdiff \| tree
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