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Merge branch 'WIP_fix_JAL-1423' into Release_2_8_Branch
2014-01-14 Jim ProcterMerge branch 'WIP_fix_JAL-1423' into Release_2_8_Branch
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2014-01-14 Jim ProcterJAL-1400 specify minimum 1.6 JRE
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2014-01-13 Jim ProcterMerge branch 'JAL-1422_srs' into Release_2_8_Branch
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2014-01-13 Jim ProcterJAL-1422 update any existing configuration to replace...
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2014-01-13 Jim ProcterJAL-1422 change default link to EMBL-EBI Search
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2014-01-13 Jim ProcterJAL-1422 remove SRS and expasy links and replace with...
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2014-01-07 Jim ProcterMerge branch 'fix_JAL-1423' into Release_2_8_Branch
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2014-01-07 Jim ProcterJAL-1423 - console error reporting and graceful handling...
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2013-11-26 Jim ProcterMerge branch 'JAL-1400_signapplet' into Release_2_8_Branch
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2013-11-26 Jim ProcterJAL-1400 update manifest in the JmolApplet jar
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2013-11-26 Jim ProcterMerge branch 'JAL-1400_signapplet' into Release_2_8_Branch
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2013-11-26 Jim ProcterJAL-1400 disable 'Permissions' in manifest to see if...
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2013-11-26 Jim ProcterMerge branch 'JAL-1400_signapplet' into Release_2_8_Branch
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2013-11-26 Jim Proctersandbox permissions
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2013-11-26 Jim Procternew required parameter for deploying the applet
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2013-11-26 Jim ProcterMerge branch 'JAL-1400_signapplet' into Release_2_8_Branch
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2013-11-26 Jim ProcterJAL-1400 add codebase and caller allowable codebase
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2013-11-25 Jim ProcterMerge branch 'JAL-1139_proguard' into Release_2_8_Branch
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2013-11-25 Jim ProcterJAL-1139 specified SHA1WithRSA for sig algorithm and...
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2013-11-25 Jim Procteradivce from http://ant.apache.org/manual/Tasks/signjar...
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2013-11-25 Jim ProcterMerge branch 'JAL-1139_proguard' into Release_2_8_Branch
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2013-11-25 Jim ProcterJAL-1139 need to explicitly specify SHA1 for java 6...
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2013-11-25 Jim ProcterMerge branch 'JAL-1139_proguard' into Release_2_8_Branch
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2013-11-25 Jim ProcterJAL-1139 supress dependency warnings from proguard
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2013-11-25 Jim ProcterMerge branch 'JAL-1139_proguard' into Release_2_8_Branch
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2013-11-25 Jim ProcterJAL-1139 latest version of proguard needed for Java...
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2013-11-07 Jim ProcterMerge branch 'JAL-1286' into Release_2_8_Branch
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2013-11-07 Jim ProcterJAL-1286 additional tests to ensure that non-GZ files...
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2013-11-07 Jim ProcterJAL-1286 check if local file ends with .gz and opens...
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2013-11-07 Jim ProcterJAL-1286 test input of gzip stream from local file
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2013-11-05 Jim ProcterJAL-1400 found a fix for the sandbox exception - need...
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2013-11-05 Jim Procterexperiment with reinstating the sandbox permissions
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2013-11-05 Jim ProcterJAL-1400 try putting explicit domain for jalviewLite...
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2013-11-05 Jim ProcterJAL-1400 Always create indices for jar before signing
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2013-11-05 Jim ProcterJAL-1400 sign everything !
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2013-11-05 Jim ProcterJAL-1400 explicit security settings for applet
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2013-11-05 Jim ProcterJAL-1400 explicit security permissions for Desktop
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2013-10-11 Jim ProcterMerge branch 'JAL-1164_disorderforselection' into Release_2_...
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2013-10-11 Jim ProcterJAL-1164 regression on JAL-1292 use bitset to mark...
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2013-10-11 Jim ProcterJAL-1164 scope bySequence analysis methods to start...
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2013-10-11 Jim ProcterJAL-1114 javadoc
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2013-10-11 Jim ProcterJAL-1114 promote start/end attributes to gettable fields...
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2013-10-11 Jim ProcterJAL-1114 API javadoc
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2013-10-11 Jim ProcterJAL-1164 only predict on currently selected sequences...
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2013-10-11 Jim ProcterJAL-1385 expose core view model methods in interface
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2013-07-12 Jim ProcterMerge branch 'JAL-1347' into Release_2_8_Branch
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2013-07-12 Jim ProcterJAL-1347 RNA Structure consensus follows the alignment...
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2013-07-12 Jim ProcterJAL-1347 flow control for display of profile data is...
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2013-07-11 Jim ProcterMerge branch 'JAL-1347' into Release_2_8_Branch
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2013-07-11 Jim ProcterJAL-1347 identify and set rendering settings for consensus...
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2013-07-11 Jim ProcterJAL-1347 refactor logic for setting display flags for...
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2013-07-11 Jim ProcterJAL-1347 make it efficient to call getConsensus to...
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2013-07-08 Jim ProcterMerge branch 'Release_2_8_1_Branch' into Release_2_8_Branch
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2013-07-08 Jim Proctermake sure 'example alignment' can be found in documentation
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2013-07-07 Jim ProcterMerge branch 'structures/JAL-1016' into Release_2_8_Branch
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2013-07-07 Jim ProcterJAL-1345 - set nSeconds arg for http://chemapps.stolaf...
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2013-07-07 Jim ProcterJAL-1016 Instruct user to report situations where the...
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2013-07-07 Jim ProcterJAL-1332 make SSM context discovery safer (particularly...
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2013-07-07 Jim ProcterJAL-583 refactor todo about separating code to construct...
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2013-07-07 Jim Procterfix for JAL-1016 - wait around until we have a complete...
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2013-07-07 Jim ProcterJAL-1016 - do our assertions immediatly
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2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch
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2013-06-23 Jim ProcterJAL-1230 update alignment state for annotation edits...
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2013-06-23 Jim ProcterJAL-1230 proxy method for synchronising internal AlignmentI...
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2013-06-23 Jim ProcterJAL-1230 simplify initialisation of consensus, conservation...
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2013-06-23 Jim ProcterMerge branch 'bug/JAL-1230' into Release_2_8_Branch
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2013-06-23 Jim ProcterMerge commit '72c628b' into Release_2_8_Branch
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2013-06-22 Jim ProcterMerge branch 'feature/JAL-1330' into Release_2_8_Branch
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2013-06-22 Jim ProcterJAL-1330 pick primary seqeunce data source for authority...
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2013-06-21 Jim ProcterJAL-1230 comment unused code to avoid NPE
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2013-06-21 Jim ProcterJAL-1327 TODO
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2013-06-21 Jim ProcterJAL-1326 JAL-1327 update all graphline thresholds with...
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2013-06-21 Jim ProcterJAL-1241 - generate colour for all annotation values...
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2013-06-21 Jim ProcterMerge branch 'JAL-1294_iupredexportimport' into Release_2_8_...
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2013-06-21 Jim ProcterJAL-1325 formatting
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2013-06-21 Jim ProcterJAL-1325 JAL-1294 resolve SEQUENCE_REF and GROUP_REF...
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2013-06-21 Jim ProcterJAL-1294 JAL-1325 store graphline for individual annotation...
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2013-06-21 Jim ProcterJAL-1294 JAL-1325 bugfix equals
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2013-06-21 Jim ProcterJAL-1294 JAL-1325 test annotation threshold line equivalence
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2013-06-21 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
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2013-06-21 Jim ProcterJAL-1127 set option widgets to service defaults only...
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2013-06-19 Jim ProcterJAL-1240 avoid NPE when source has no proxy available
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2013-06-19 Jim ProcterMerge branch 'JAL-1321_jws2_tooltips' into Release_2_8_Branch
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2013-06-18 Jim ProcterJAL-1320 ascending alphabetical order
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2013-06-18 Jim ProcterJAL-1320 preserve option/parameter order with LinkedHashMap
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2013-06-18 Jim ProcterJAL-1320 sort options and parameters according to their...
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2013-06-18 Jim Proctertypo
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2013-06-18 Jim ProcterJAL-1321 don't show a tooltip for empty strings
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2013-06-17 Jim ProcterMerge branch 'JAL-1319_jronn_npe' into Release_2_8_Branch
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2013-06-17 Jim ProcterJAL-1319 (blacklist fix) check for presence of a score...
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2013-06-17 Jim ProcterMerge branch 'JAL-1312_ambiguity_na' into Release_2_8_Branch
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2013-06-17 Jim ProcterJAL-1027 fix errors in alternative codon table
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2013-06-17 Jim ProcterJAL-1027 check that ResidueProperties.codonHash2 is...
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2013-06-17 Jim ProcterJAL-1027 use alternative codon table in ResidueProperties...
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2013-06-17 Jim ProcterJAL-1035 option to allow 'STOP' codon to translate...
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2013-06-17 Jim ProcterJAL-1312 patch for regression noticed after patch to...
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2013-06-17 Jim ProcterJAL-1312 rewrite of code for first reported exception...
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2013-06-17 Jim ProcterJAL-1312 formatting and more comprehensive test
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2013-06-17 Jim ProcterJAL-1312 remove unnecessary methods
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2013-06-17 Jim ProcterJAL-1312 more helpful error message when translation...
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