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2013-11-07	Jim Procter	Merge branch 'JAL-1286' into develop	commit \| commitdiff \| tree
2013-11-07	Jim Procter	JAL-1286 additional tests to ensure that non-GZ files...	commit \| commitdiff \| tree
2013-11-07	Jim Procter	JAL-1286 check if local file ends with .gz and opens...	commit \| commitdiff \| tree
2013-11-07	Jim Procter	JAL-1286 test input of gzip stream from local file	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 found a fix for the sandbox exception - need...	commit \| commitdiff \| tree
2013-11-05	Jim Procter	experiment with reinstating the sandbox permissions	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 try putting explicit domain for jalviewLite...	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 Always create indices for jar before signing	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 sign everything !	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 explicit security settings for applet	commit \| commitdiff \| tree
2013-11-05	Jim Procter	JAL-1400 explicit security permissions for Desktop	commit \| commitdiff \| tree
2013-10-17	Jim Procter	Merge branch 'JAL-1397' into develop	commit \| commitdiff \| tree
2013-10-17	Jim Procter	fix for JAL-1398 - original colourscheme is enabled...	commit \| commitdiff \| tree
2013-10-17	Jim Procter	JAL-1233 TODO concerning the way we propagate annotation...	commit \| commitdiff \| tree
2013-10-17	Jim Procter	JAL-1397 make sure annotation colourscheme is up to...	commit \| commitdiff \| tree
2013-10-17	Jim Procter	JAL-1397 store colour by sequence and originalColour...	commit \| commitdiff \| tree
2013-10-17	Jim Procter	JAL-1397 make sure ColourschemeI instances are up to...	commit \| commitdiff \| tree
2013-10-17	Jim Procter	JAL-1397 propagate any consensus/conservation colourscheme...	commit \| commitdiff \| tree
2013-10-17	Jim Procter	JAL-1397 getters for originalColours flag	commit \| commitdiff \| tree
2013-10-16	Jim Procter	Merge branch 'JAL-1395' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-10-16	Jim Procter	Merge branch 'JAL-1395' into develop	commit \| commitdiff \| tree
2013-10-16	Jim Procter	JAL-1395 do not calculate non-gap consensus when no...	commit \| commitdiff \| tree
2013-10-15	Jim Procter	workaround for JAL-1395	commit \| commitdiff \| tree
2013-10-15	Jim Procter	Merge branch 'dev_from_2_8_1' into develop	commit \| commitdiff \| tree
2013-10-15	Jim Procter	JAL-1159 Merging 2.8.1 patches and Anne Menards work...	commit \| commitdiff \| tree
2013-10-14	Jim Procter	Merge branch 'develop' into dev_from_2_8_1	commit \| commitdiff \| tree
2013-10-11	Jim Procter	Merge branch 'JAL-1292_regression' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 regression on JAL-1292 use bitset to mark...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	Merge branch 'JAL-1164_disorderforselection' into Release_2_...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 regression on JAL-1292 use bitset to mark...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	Merge branch 'JAL-1164_disorderforselection' into Release_2_...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 scope bySequence analysis methods to start...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1114 javadoc	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1114 promote start/end attributes to gettable fields...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1114 API javadoc	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1164 only predict on currently selected sequences...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1385 expose core view model methods in interface	commit \| commitdiff \| tree
2013-10-11	Jim Procter	Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1354 watch for exceptions when initialising (Security...	commit \| commitdiff \| tree
2013-10-11	Jim Procter	JAL-1354 ensure resource bundles are copied into JalviewAppl...	commit \| commitdiff \| tree
2013-10-08	Jim Procter	reindexed Jmol jar with 'jar -i' to fix JAL-1389	commit \| commitdiff \| tree
2013-10-08	Jim Procter	Merge branch 'Release_2_8_1_Branch_i18n' into Release_2_8_1_...	commit \| commitdiff \| tree
2013-10-08	Jim Procter	localisation for JAL-1384 and JAL-1388	commit \| commitdiff \| tree
2013-10-08	Jim Procter	Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branc...	commit \| commitdiff \| tree
2013-10-08	Jim Procter	Merge branch 'JAL-643_JAL-1384' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-10-08	Jim Procter	JAL-1384 JAL-1388 revised popup menu documentation...	commit \| commitdiff \| tree
2013-10-08	Jim Procter	JAL-1384 Create Group in selection popup menu	commit \| commitdiff \| tree
2013-10-08	Jim Procter	fix for JAL-1387	commit \| commitdiff \| tree
2013-10-08	Jim Procter	JAL-1384 documentation and consistent ordering for...	commit \| commitdiff \| tree
2013-10-08	Jim Procter	JAL-1384 group/ungroup sequences with command/ctrl...	commit \| commitdiff \| tree
2013-10-07	Jim Procter	JAL-1385 refactor logic to AlignmentViewController	commit \| commitdiff \| tree
2013-10-07	Jim Procter	JAL-1385 JAL-535 refactor sequence colour settings...	commit \| commitdiff \| tree
2013-10-07	Jim Procter	JAL-1385 expose core view model methods in interface	commit \| commitdiff \| tree
2013-10-07	Jim Procter	JAL-1385 Alignment view controller logic implementation...	commit \| commitdiff \| tree
2013-10-05	Jim Procter	Merge branch 'JAL-1378_jb2.1cli' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-10-05	Jim Procter	JAL-1379 graceful degradation to legacy service when...	commit \| commitdiff \| tree
2013-10-05	Jim Procter	JAL-1379 JAL-1378 exclusion list property to ignore...	commit \| commitdiff \| tree
2013-10-05	Jim Procter	JAL-1378 hack to place 'Predictors' into Secondary...	commit \| commitdiff \| tree
2013-10-05	Jim Procter	JAL-1364 use gapMap to map RNAalifold annotation onto...	commit \| commitdiff \| tree
2013-10-05	Jim Procter	JAL-1379 JAL-1358 only enable/disable menu entries...	commit \| commitdiff \| tree
2013-10-04	Jim Procter	JAL-1383 - disable startup of the Envision2 workflow...	commit \| commitdiff \| tree
2013-10-04	Jim Procter	JAL-940 JAL-1378 EOL comment on JWS v1 services	commit \| commitdiff \| tree
2013-10-04	Jim Procter	update JABA client dependency in InstallAnywhere build	commit \| commitdiff \| tree
2013-10-04	Jim Procter	Merge branch 'RNAalifold' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-10-04	Jim Procter	fix for JAL-1380 and efficiency todo for JAL-1381	commit \| commitdiff \| tree
2013-10-04	Jim Procter	JAL-1378 JWS-71 update to from-source build of JABA...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1365 test that RNAAliFold service settings are...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	formatting	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1365 unified GUI building for AACon and RNAAliFold...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1365 use AlignAnalysisUIText class to provide metadata...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1365 refactored core methods from RNAAliFold and...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1365 new metadata class to describe instantaneous...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1270 nominal jalview version string for projects...	commit \| commitdiff \| tree
2013-09-25	Jim Procter	JAL-1270 Desktop.instance is null during headless jalview...	commit \| commitdiff \| tree
2013-09-20	Jim Procter	formatting	commit \| commitdiff \| tree
2013-09-18	Jim Procter	JAL-1355 - fix compilation errors: typos and missing...	commit \| commitdiff \| tree
2013-09-13	Jim Procter	tweak - v is lowercase in Jalview	commit \| commitdiff \| tree
2013-09-03	Jim Procter	Merge branch 'JAL-1373_precision' into RNAalifold	commit \| commitdiff \| tree
2013-09-03	Jim Procter	Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-09-03	Jim Procter	JAL-1373 tweak precision calculation so alignments...	commit \| commitdiff \| tree
2013-09-03	Jim Procter	JAL-920 compute a consensus for single sequence	commit \| commitdiff \| tree
2013-09-02	Jim Procter	Merge branch 'JAL-1373_precision' into develop	commit \| commitdiff \| tree
2013-09-02	Jim Procter	Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1373 JAL-520 wrap tooltips for columns in annotation...	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1373 generate percentages with appropriate precision	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1373 pass size of sequence set to consensus rendering...	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1358 monday morning commits :(	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1358 jabaws not jaba	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1358 update jabaws client for installanywhere	commit \| commitdiff \| tree
2013-09-02	Jim Procter	JAL-1358 remove old v2 jaba min-client	commit \| commitdiff \| tree
2013-08-27	Jim Procter	Merge branch 'JAL-1359_patch' into develop	commit \| commitdiff \| tree
2013-08-27	Jim Procter	Merge branch 'JAL-1359_patch' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-08-27	Jim Procter	JAL-1359 simpler logic for deciding if all threads...	commit \| commitdiff \| tree
2013-08-27	Jim Procter	Merge branch 'JAL-1332_regression' into develop	commit \| commitdiff \| tree
2013-08-27	Jim Procter	Merge branch 'JAL-1332_regression' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-08-27	Jim Procter	JAL-1332 regression from 7ce72ca7fadf35a249427ecb836b22abb04...	commit \| commitdiff \| tree
2013-08-27	Jim Procter	JAL-1332 - defer SSM provision to root provider for...	commit \| commitdiff \| tree
2013-08-20	Jim Procter	Merge branch 'JAL-1353-bugdemo' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-08-20	Jim Procter	JAL-1353 test demonstrating the freeze with minimal...	commit \| commitdiff \| tree
2013-08-14	Jim Procter	JAL-1354 i18n bundle for Spanish	commit \| commitdiff \| tree
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