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Merge branch 'develop' into develop_m2_8_1_2
2013-05-24
Jim Procter
JAL-1295 relaxed test for Annotation element equivalence...
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2013-05-24
Jim Procter
JAL-381 Desktop.addInternalFrame cannot be called in...
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2013-05-24
Jim Procter
JAL-1299 fix: ensure a new graphGroup is created if...
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2013-05-24
Jim Procter
JAL-1295 JAL-1296 clearer assertion failed message
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2013-05-24
Jim Procter
JAL-1295 JAL-1297 enhance test to check graph visiblity...
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2013-05-24
Jim Procter
fix for JAL-1297: COMBINE output now follows specification...
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2013-05-24
Jim Procter
JAL-1296 JAL-1291 JAL-1297 JAL-1295 JAL-1294
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2013-05-24
Jim Procter
JAL-1291 JAL-1297 JAL-1295 JAL-1294 allow alignment...
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2013-05-24
Jim Procter
javadoc and formatting
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2013-05-24
Jim Procter
JAL-1297 JAL-1295 JAL-1294 sensible toString for benefit...
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2013-05-24
Jim Procter
JAL-1297 JAL-1295 JAL-1294 improve test logic for comparing...
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2013-05-24
Jim Procter
JAL-1296 reinstated tab characters so example annotation...
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2013-05-24
Jim Procter
JAL-1070 - [ not a real patch ] - include offending...
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2013-05-24
Jim Procter
JAL-966 paintrefresher should be abstract [ Merge branch...
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2013-05-24
Jim Procter
JAL-1161 conditional parameters for controlling clipping
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2013-05-24
Jim Procter
JAL-1292 avoid exception by using bitset of arbitrary...
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2013-05-24
Jim Procter
JAL-1161 changed signature to allow clipping bounds...
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2013-05-24
Jim Procter
formatting
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2013-05-24
Jim Procter
JAL-1161 only trigger an annotation repaint in unwrapped...
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2013-05-24
Jim Procter
JAL-1161 enable fastPaint for nudges from scroll bars...
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2013-05-24
Jim Procter
JAL-1161 stick to api
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2013-05-24
Jim Procter
typo
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2013-05-21
Jim Procter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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2013-05-21
Jim Procter
JAL-1140 JAL-674 process with annotate3d and Jmol to...
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2013-05-21
Jim Procter
JAL-674 ensure annotation is properly annotated
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2013-05-21
Jim Procter
JAL-1231 add chain ID
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2013-05-21
Jim Procter
JAL-1231 allow Jmol file handler to read from a stream
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2013-05-21
Jim Procter
Merge branch 'JAL-1199-Stk_writing' into rnaml_test
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2013-05-21
Jim Procter
split test for general Stockholm IO consistency (JAL...
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2013-05-21
Jim Procter
JAL-1199 JAL-1272 remove main() method from test class
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2013-05-21
Jim Procter
formatting
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2013-05-21
Jim Procter
JAL-1199 JAL-1272 refactored Natasha's test to a generic...
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2013-05-13
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStream...
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2013-05-13
Jim Procter
Merge branch 'JAL-1289_initCallBack' into Release_2_8_Branch
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2013-05-13
Jim Procter
Merge branch 'JAL-1289_initCallBack' into develop
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2013-05-13
Jim Procter
JAL-1289 call oninit callback even if no alignment...
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2013-04-12
Jim Procter
Merge branch 'JAL-1286_gzip' into Release_2_8_Branch
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2013-04-12
Jim Procter
JAL-1286 URL stream reader tries to use a GZIPInputStream...
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2013-02-15
Jim Procter
JAL-1140 JAL-1215 JAL-1272 test import of RNAML and...
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2013-02-15
Jim Procter
split test for general Stockholm IO consistency (JAL...
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2013-02-15
Jim Procter
JAL-1199 JAL-1272 remove main() method from test class
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2013-02-15
Jim Procter
formatting
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2013-02-15
Jim Procter
JAL-1199 JAL-1272 refactored Natasha's test to a generic...
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2013-02-14
Jim Procter
Merge branch 'JAL-1199-Stk_writing' into rnaml_test
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2013-02-14
Jim Procter
JAL-1140 reinstate the simpler version of parsing code...
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2013-02-14
Jim Procter
patch for bizarre ConcurrentModificationException that...
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2013-02-13
Jim Procter
Merge branch 'jims_annotate3d_update' into menard_finalsep2012
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2013-02-13
jprocter
fix merge conflicts for finess on JAL-1140 (introduced...
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2013-02-13
jprocter
JAL-1216 switch to official release of VARNA 3.9
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2013-02-13
jprocter
JAL-1213 JAL-674 robust test with an existing structure...
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2013-02-13
jprocter
JAL-1214 todo
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2013-02-13
jprocter
JAL-1213 JAL-674 - import a PDB file using Jmol data...
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2013-02-13
jprocter
JAL-674 commented out annotate3d calling code for Jmol...
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2013-02-13
jprocter
JAL-1028 JAL-674 hooks to call external processing...
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2013-02-11
jprocter
patch for 'This parser does not support specification...
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2013-02-11
jprocter
json simple library
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2013-02-11
jprocter
upgrade to latest paradise services model using JSon...
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2013-02-06
jprocter
Merge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing
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2013-02-06
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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2013-02-06
jprocter
JAL-1265 basic support for parsing database accessions...
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2013-02-06
jprocter
JAL-1199 added test for Rfam Stockholm file example
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2013-02-06
jprocter
JAL-1199 refactored stockholm test code from main class...
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2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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2013-02-05
jprocter
formatting
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2013-02-05
jprocter
Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch
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2013-01-20
jprocter
Merge branch 'Dbfetch_hotfix-JAL-1238' into develop
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2013-01-20
jprocter
Merge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8_Branch
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2013-01-18
jprocter
JAL-1238 test to see if the primary Uniprot source...
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2013-01-18
jprocter
JAL-1238 order to place primary sources before lower...
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2013-01-18
jprocter
JAL-1238 method to test if DAS source is a primary...
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2013-01-18
jprocter
JAL-1238 tier index indicating distance of a source...
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2013-01-18
jprocter
Merge branch 'JAL-1254-hotfix' into develop
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2013-01-18
jprocter
Merge branch 'JAL-1254-hotfix' into Release_2_8_Branch
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2013-01-18
jprocter
JAL-1255 don't show 'Right click to add annotations...
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2013-01-18
jprocter
JAL-1254 patch for NPE in annotation renderer when...
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2012-12-11
jprocter
JAL-1217 check and avoid NPE if no datastore object...
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2012-12-11
jprocter
JAL-1217 report exception for service when no datastore...
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2012-12-07
jprocter
revised renderer and annotation model to support different...
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2012-12-07
jprocter
convenience function to get the RNA model for an annotation...
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2012-12-07
jprocter
use new secstructure process algorithm
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2012-12-07
jprocter
Anne's refined RNAML parser. Seems to have some bugs...
...have some bugs still (merge with
jprocter
's bugfixed parser)
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2012-12-07
jprocter
Anne reinstated general stockholm parser code but extended...
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2012-12-07
jprocter
typing
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2012-12-07
jprocter
consensus secondary structure algorithm (possibly came...
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2012-12-07
jprocter
revised RNA stem/loop processing code that copes with...
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2012-12-07
jprocter
update authors for RNA processing routines
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2012-12-07
jprocter
menu for choosing between 'protein' and 'RNA' mode...
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2012-12-07
jprocter
formatting and error report cleanup
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2012-12-07
jprocter
gui hooks for contrafold and RNAfold services. commented...
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2012-12-07
jprocter
Exception signature change (will be overwritten by...
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2012-12-07
jprocter
formatting
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2012-12-07
jprocter
tidy import
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2012-12-07
jprocter
remove mentions of non-functional RNAInteraction colourscheme
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2012-12-07
jprocter
tidy debug messages
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2012-12-07
jprocter
proxy commit for Anne Menard <menard.annec@gmail.com...
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2012-12-04
jprocter
bogus source dir for jmol (only for jim - fix for yourself!)
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2012-12-04
jprocter
JAL-1140 - handled VARNA specific RNA exceptions within...
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2012-12-04
jprocter
JAL-1140 - handle VARNA specific RNA exceptions within...
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2012-12-04
jprocter
JAL-1140 - IO classes should only raise generic IOExceptions
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2012-12-04
jprocter
JAL-1216 switch to official release of VARNA 3.9
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