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JAL-1027 fix errors in alternative codon table
[jalview.git]
/
src
/
2013-06-17
Jim Procter
JAL-1027 fix errors in alternative codon table
tree
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commitdiff
2013-06-17
Jim Procter
JAL-1027 use alternative codon table in ResidueProperti...
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commitdiff
2013-06-17
Jim Procter
JAL-1035 option to allow 'STOP' codon to translate...
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commitdiff
2013-06-17
Jim Procter
JAL-1312 patch for regression noticed after patch to...
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commitdiff
2013-06-17
Jim Procter
JAL-1312 rewrite of code for first reported exception...
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commitdiff
2013-06-17
Jim Procter
JAL-1312 more helpful error message when translation...
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commitdiff
2013-06-17
Jim Procter
JAL-529 - IUBMB nucleotide ambiguity codes and programm...
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commitdiff
2013-06-17
Jim Procter
JAL-1318 - route warnings to stderr (need to find a...
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commitdiff
2013-06-17
Jim Procter
JAL-1318 avoid failure if SequenceI objects don't have...
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commitdiff
2013-06-17
Jim Procter
JAL-966 avoid using java.util.Vector
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commitdiff
2013-06-14
Jim Procter
JAL-1316 compact '' to '
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commitdiff
2013-06-14
Jim Procter
JAL-1316 recognise and extract quoted region as nodename
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commitdiff
2013-06-13
Jim Procter
JAL-1314 allow 'nogui' and 'headless' as synonyms for...
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commitdiff
2013-06-13
Jim Procter
fix for JAL-1315
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commitdiff
2013-06-09
Jim Procter
fix for JAL-1298
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commitdiff
2013-06-09
Jim Procter
JAL-715 - TODO
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commitdiff
2013-06-07
Jim Procter
JAL-1309 fix broken partition computation for adding...
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commitdiff
2013-06-07
Jim Procter
JAL-945 uniquify prior to submission
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commitdiff
2013-06-07
Jim Procter
formatting
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commitdiff
2013-06-07
Jim Procter
JAL-715 allow headless construction for testing
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commitdiff
2013-06-07
Jim Procter
JAL-724 JAL-715 refactor and create new test for RSBS...
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commitdiff
2013-06-07
Jim Procter
fix for JAL-1246
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commitdiff
2013-06-07
Jim Procter
JAL-1307 patch to squash number format exceptions when...
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commitdiff
2013-05-31
Jim Procter
JAL-1259 patch to avoid NPE
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commitdiff
2013-05-24
Jim Procter
JAL-1291 reinstate fastPaint flag manipulation to make...
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commitdiff
2013-05-24
Jim Procter
JAL-1291 TODO: revised graphGroup model so grouped...
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commitdiff
2013-05-24
Jim Procter
JAL-1291 - don't touch the graphics object until after...
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commitdiff
2013-05-24
Jim Procter
JAL-1291 conditional output of rendering debugging...
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commitdiff
2013-05-24
Jim Procter
patch for JAL-1300 fixes JAL-1294: read and write COMBI...
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commitdiff
2013-05-24
Jim Procter
JAL-1295 relaxed test for Annotation element equivalenc...
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commitdiff
2013-05-24
Jim Procter
JAL-381 Desktop.addInternalFrame cannot be called in...
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commitdiff
2013-05-24
Jim Procter
JAL-1299 fix: ensure a new graphGroup is created if...
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commitdiff
2013-05-24
Jim Procter
fix for JAL-1297: COMBINE output now follows specificat...
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commitdiff
2013-05-24
Jim Procter
javadoc and formatting
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commitdiff
2013-05-24
Jim Procter
JAL-1297 JAL-1295 JAL-1294 sensible toString for benefi...
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commitdiff
2013-05-24
Jim Procter
JAL-1070 - [ not a real patch ] - include offending...
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commitdiff
2013-05-24
Jim Procter
JAL-966 paintrefresher should be abstract [ Merge branc...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 conditional parameters for controlling clipping
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commitdiff
2013-05-24
Jim Procter
JAL-1292 avoid exception by using bitset of arbitrary...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 changed signature to allow clipping bounds...
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commitdiff
2013-05-24
Jim Procter
formatting
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commitdiff
2013-05-24
Jim Procter
JAL-1161 only trigger an annotation repaint in unwrappe...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 enable fastPaint for nudges from scroll bars...
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commitdiff
2013-05-24
Jim Procter
JAL-1161 stick to api
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commitdiff
2013-05-24
Jim Procter
typo
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commitdiff
2013-05-13
Jim Procter
Merge branch 'JAL-1289_initCallBack' into Release_2_8_B...
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commitdiff
2013-05-13
Jim Procter
JAL-1289 call oninit callback even if no alignment...
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commitdiff
2013-04-12
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStre...
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commitdiff
2013-02-06
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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commitdiff
2013-02-06
jprocter
JAL-1265 basic support for parsing database accessions...
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commitdiff
2013-02-06
jprocter
JAL-1199 refactored stockholm test code from main class...
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commitdiff
2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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commitdiff
2013-02-05
jprocter
formatting
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commitdiff
2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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commitdiff
2013-01-18
jprocter
JAL-1238 order to place primary sources before lower...
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commitdiff
2013-01-18
jprocter
JAL-1238 method to test if DAS source is a primary...
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commitdiff
2013-01-18
jprocter
JAL-1238 tier index indicating distance of a source...
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commitdiff
2013-01-18
jprocter
JAL-1255 don't show 'Right click to add annotations...
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commitdiff
2013-01-18
jprocter
JAL-1254 patch for NPE in annotation renderer when...
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commitdiff
2012-12-17
Natasha
test for output a file in Stockholm format
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commitdiff
2012-12-12
Natasha
Output accession number for file in stockholm format
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commitdiff
2012-12-11
jprocter
JAL-1217 check and avoid NPE if no datastore object...
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commitdiff
2012-12-11
jprocter
JAL-1217 report exception for service when no datastore...
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commitdiff
2012-11-23
Natasha
stockholm file output code developed by Natasha Sherstneva
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commitdiff
2012-11-15
Paolo Di Tommaso
Fixed T-Coffee file scores parser to support extended...
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commitdiff
2012-11-09
jprocter
constructor takes settings from any existing feature...
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commitdiff
2012-11-08
jprocter
JAL-1193 ensure the 'loadedComplete' method gets called...
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commitdiff
2012-11-08
jprocter
remember to close input file!
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commitdiff
2012-11-08
jprocter
tidy imports
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commitdiff
2012-11-07
jprocter
JAL-957 manual update to applet authorlist - need to...
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commitdiff
2012-10-24
jprocter
JAL-1193 call setLoadingFromArchiveFinished(true) for...
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commitdiff
2012-10-24
jprocter
JAL-1193 patch prevents JalviewJmolBinding from handlin...
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commitdiff
2012-10-22
jprocter
Jalview 2.8 Source Header
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commitdiff
2012-10-04
jprocter
Merge branch 'develop' into Release_2_8_Branch
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commitdiff
2012-10-04
jprocter
JAL-636 switch to simple REST interface to dbfetch...
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commitdiff
2012-10-04
jprocter
avoid importing the mapping every time we parse a unipr...
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commitdiff
2012-10-04
jprocter
JAL-636 tweak main() based test to allow DAS sources...
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commitdiff
2012-10-04
jprocter
JAL-1188 - set the user agent to Jalview Desktop/$...
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commitdiff
2012-10-04
jprocter
JAL-1064 JAL-671 make sure all buttons are disabled...
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commitdiff
2012-10-03
jprocter
formatting
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commitdiff
2012-10-03
jprocter
formatting
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commitdiff
2012-10-03
jprocter
JAL-1026 - insert a sensible default for proxy so Jalvi...
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commitdiff
2012-10-03
jprocter
JAL-1183 JAL-343 - use dialog queue for JABA warning...
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commitdiff
2012-10-02
jprocter
JAL-1185 patch NPE - create new group for subtree on...
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commitdiff
2012-10-01
jprocter
JAL-1130 JAL-1137 messy hardcoding of author list to...
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commitdiff
2012-10-01
jprocter
JAL-1130 JAL-1139 hardcode preferred height to logo...
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commitdiff
2012-10-01
jprocter
JAL-1130 more robust loading code and different logos...
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commitdiff
2012-10-01
jprocter
JAL-1183 dialog thread is only started after the splash...
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commitdiff
2012-10-01
jprocter
JAL-1111 dialog flickers whilst example file starts...
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commitdiff
2012-10-01
jprocter
JAL-1184 apparent deadlock when launching jalview on...
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commitdiff
2012-10-01
jprocter
JAL-1183 showNews adds news discovery and display threa...
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commitdiff
2012-10-01
jprocter
JAL-1183 use dialog queue for usage statistics prompt
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commitdiff
2012-10-01
jprocter
JAL-1183 dialog queue
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commitdiff
2012-09-27
jprocter
JAL-1030 patch typo
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commitdiff
2012-09-27
jprocter
JAL-1179 - regression from JAL-1030 patch implicitly...
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commitdiff
2012-09-25
jprocter
JAL-1031 allow empty selections to pass through to...
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commitdiff
2012-09-25
jprocter
JAL-1179 note and patch for exceptions raised when...
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commitdiff
2012-09-25
jprocter
JAL-1031 JAL-1032 if selection is non-null but empty...
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commitdiff
2012-09-25
jprocter
JAL-1010 write validated value back to text field to...
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commitdiff
2012-09-25
jprocter
JAL-1173 - trap redraw buffer OOM errors. needs a test...
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commitdiff
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