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2014-01-13	Jim Procter	Merge branch 'JAL-1422_srs_r281' into develop	commit \| commitdiff \| tree
2014-01-13	Jim Procter	Merge branch 'JAL-1422_srs' into JAL-1422_srs_r281	commit \| commitdiff \| tree
2014-01-13	Jim Procter	JAL-1422 update any existing configuration to replace...	commit \| commitdiff \| tree
2014-01-13	Jim Procter	JAL-1422 change default link to EMBL-EBI Search	commit \| commitdiff \| tree
2014-01-13	Jim Procter	JAL-1422 remove SRS and expasy links and replace with...	commit \| commitdiff \| tree
2014-01-07	Jim Procter	Merge branch 'fix_JAL-1423' into develop	commit \| commitdiff \| tree
2014-01-07	Jim Procter	Merge branch 'fix_JAL-1423' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2014-01-07	Jim Procter	JAL-1423 - console error reporting and graceful handling...	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'trialMergeDev' into develop	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'testMerge' into trialMergeDev	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'JAL-1400_signapplet' into testMerge	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-26	Jim Procter	JAL-1400 update manifest in the JmolApplet jar	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-26	Jim Procter	JAL-1400 disable 'Permissions' in manifest to see if...	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-26	Jim Procter	sandbox permissions	commit \| commitdiff \| tree
2013-11-26	Jim Procter	new required parameter for deploying the applet	commit \| commitdiff \| tree
2013-11-26	Jim Procter	Merge branch 'JAL-1400_signapplet' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-26	Jim Procter	JAL-1400 add codebase and caller allowable codebase	commit \| commitdiff \| tree
2013-11-25	Jim Procter	JAL-1139 add SHA1WithRSA for applet signjar	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into develop	commit \| commitdiff \| tree
2013-11-25	Jim Procter	JAL-1139 add SHA1WithRSA for applet signjar	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	JAL-1139 specified SHA1WithRSA for sig algorithm and...	commit \| commitdiff \| tree
2013-11-25	Jim Procter	adivce from http://ant.apache.org/manual/Tasks/signjar...	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	JAL-1139 need to explicitly specify SHA1 for java 6...	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into develop	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	JAL-1139 supress dependency warnings from proguard	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into develop	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_1_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	Merge branch 'JAL-1139_proguard' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-25	Jim Procter	JAL-1139 latest version of proguard needed for Java...	commit \| commitdiff \| tree
2013-11-07	Jim Procter	Merge branch 'JAL-1286' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-11-07	Jim Procter	Merge branch 'JAL-1286' into develop	commit \| commitdiff \| tree
2013-11-07	Jim Procter	Merge branch 'JAL-1286' into Release_2_8_1_Branch	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	Merge branch 'JAL-1397' into Release_2_8_1_Branch	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
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