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Merge branch 'develop' into develop_m2_8_1_2
[jalview.git] / src /
2013-06-09 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-09 Jim ProcterJAL-674 avoid runtime dependency on annotate3d webservi... tree | commitdiff
2013-06-09 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-09 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into develop tree | commitdiff
2013-06-09 Jim Procterfix for JAL-1298 tree | commitdiff
2013-06-09 Jim ProcterJAL-715 - TODO tree | commitdiff
2013-06-07 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-07 Jim ProcterMerge branch '2_8_1_patch_multiharmony' into develop tree | commitdiff
2013-06-07 Jim ProcterJAL-1309 fix broken partition computation for adding... tree | commitdiff
2013-06-07 Jim ProcterJAL-945 uniquify prior to submission tree | commitdiff
2013-06-07 Jim Procterformatting tree | commitdiff
2013-06-07 Jim ProcterJAL-715 allow headless construction for testing tree | commitdiff
2013-06-07 Jim ProcterJAL-724 JAL-715 refactor and create new test for RSBS... tree | commitdiff
2013-06-07 Jim Procterfix for JAL-1246 tree | commitdiff
2013-06-07 Jim ProcterJAL-1307 patch to squash number format exceptions when... tree | commitdiff
2013-06-07 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-06-07 Jim ProcterMerge branch 'JAL-1161_optimisingAnnotationPanel' into... tree | commitdiff
2013-05-31 Jim ProcterMerge branch 'develop' into develop_m2_8_1_2 tree | commitdiff
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE tree | commitdiff
2013-05-31 Jim ProcterJAL-1259 patch to avoid NPE tree | commitdiff
2013-05-24 Jim ProcterMerge branch 'menard' into develop_m2_8_1_2 tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 reinstate fastPaint flag manipulation to make... tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 TODO: revised graphGroup model so grouped... tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 - don't touch the graphics object until after... tree | commitdiff
2013-05-24 Jim ProcterJAL-1291 conditional output of rendering debugging... tree | commitdiff
2013-05-24 Jim Procterpatch for JAL-1300 fixes JAL-1294: read and write COMBI... tree | commitdiff
2013-05-24 Jim ProcterJAL-1295 relaxed test for Annotation element equivalenc... tree | commitdiff
2013-05-24 Jim ProcterJAL-381 Desktop.addInternalFrame cannot be called in... tree | commitdiff
2013-05-24 Jim ProcterJAL-1299 fix: ensure a new graphGroup is created if... tree | commitdiff
2013-05-24 Jim Procterfix for JAL-1297: COMBINE output now follows specificat... tree | commitdiff
2013-05-24 Jim Procterjavadoc and formatting tree | commitdiff
2013-05-24 Jim ProcterJAL-1297 JAL-1295 JAL-1294 sensible toString for benefi... tree | commitdiff
2013-05-24 Jim ProcterJAL-1070 - [ not a real patch ] - include offending... tree | commitdiff
2013-05-24 Jim ProcterJAL-966 paintrefresher should be abstract [ Merge branc... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 conditional parameters for controlling clipping tree | commitdiff
2013-05-24 Jim ProcterJAL-1292 avoid exception by using bitset of arbitrary... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 changed signature to allow clipping bounds... tree | commitdiff
2013-05-24 Jim Procterformatting tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 only trigger an annotation repaint in unwrappe... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 enable fastPaint for nudges from scroll bars... tree | commitdiff
2013-05-24 Jim ProcterJAL-1161 stick to api tree | commitdiff
2013-05-24 Jim Proctertypo tree | commitdiff
2013-05-21 Jim ProcterJAL-1140 JAL-674 process with annotate3d and Jmol to... tree | commitdiff
2013-05-21 Jim ProcterJAL-674 ensure annotation is properly annotated tree | commitdiff
2013-05-21 Jim ProcterJAL-1231 add chain ID tree | commitdiff
2013-05-21 Jim ProcterJAL-1231 allow Jmol file handler to read from a stream tree | commitdiff
2013-05-13 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... tree | commitdiff
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into Release_2_8_B... tree | commitdiff
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into develop tree | commitdiff
2013-05-13 Jim ProcterJAL-1289 call oninit callback even if no alignment... tree | commitdiff
2013-04-12 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... tree | commitdiff
2013-02-14 Jim ProcterMerge branch 'JAL-1199-Stk_writing' into rnaml_test tree | commitdiff
2013-02-14 Jim ProcterJAL-1140 reinstate the simpler version of parsing code... tree | commitdiff
2013-02-14 Jim Procterpatch for bizarre ConcurrentModificationException that... tree | commitdiff
2013-02-13 Jim ProcterMerge branch 'jims_annotate3d_update' into menard_final... tree | commitdiff
2013-02-13 jprocterfix merge conflicts for finess on JAL-1140 (introduced... tree | commitdiff
2013-02-13 jprocterJAL-1216 switch to official release of VARNA 3.9 tree | commitdiff
2013-02-13 jprocterJAL-1214 todo tree | commitdiff
2013-02-13 jprocterJAL-1213 JAL-674 - import a PDB file using Jmol data... tree | commitdiff
2013-02-13 jprocterJAL-674 commented out annotate3d calling code for Jmol... tree | commitdiff
2013-02-13 jprocterJAL-1028 JAL-674 hooks to call external processing... tree | commitdiff
2013-02-11 jprocterpatch for 'This parser does not support specification... tree | commitdiff
2013-02-11 jprocterupgrade to latest paradise services model using JSon... tree | commitdiff
2013-02-06 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch tree | commitdiff
2013-02-06 jprocterJAL-1265 basic support for parsing database accessions... tree | commitdiff
2013-02-06 jprocterJAL-1199 refactored stockholm test code from main class... tree | commitdiff
2013-02-05 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch tree | commitdiff
2013-02-05 jprocterformatting tree | commitdiff
2013-02-05 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch tree | commitdiff
2013-01-20 jprocterMerge branch 'Dbfetch_hotfix-JAL-1238' into develop tree | commitdiff
2013-01-18 jprocterJAL-1238 order to place primary sources before lower... tree | commitdiff
2013-01-18 jprocterJAL-1238 method to test if DAS source is a primary... tree | commitdiff
2013-01-18 jprocterJAL-1238 tier index indicating distance of a source... tree | commitdiff
2013-01-18 jprocterMerge branch 'JAL-1254-hotfix' into develop tree | commitdiff
2013-01-18 jprocterJAL-1255 don't show 'Right click to add annotations... tree | commitdiff
2013-01-18 jprocterJAL-1254 patch for NPE in annotation renderer when... tree | commitdiff
2012-12-17 Natashatest for output a file in Stockholm format tree | commitdiff
2012-12-12 NatashaOutput accession number for file in stockholm format tree | commitdiff
2012-12-11 jprocterJAL-1217 check and avoid NPE if no datastore object... tree | commitdiff
2012-12-11 jprocterJAL-1217 report exception for service when no datastore... tree | commitdiff
2012-12-07 jprocterrevised renderer and annotation model to support differ... tree | commitdiff
2012-12-07 jprocterconvenience function to get the RNA model for an annota... tree | commitdiff
2012-12-07 jprocteruse new secstructure process algorithm tree | commitdiff
2012-12-07 jprocterAnne's refined RNAML parser. Seems to have some bugs... tree | commitdiff
2012-12-07 jprocterAnne reinstated general stockholm parser code but exten... tree | commitdiff
2012-12-07 jproctertyping tree | commitdiff
2012-12-07 jprocterconsensus secondary structure algorithm (possibly came... tree | commitdiff
2012-12-07 jprocterrevised RNA stem/loop processing code that copes with... tree | commitdiff
2012-12-07 jprocterupdate authors for RNA processing routines tree | commitdiff
2012-12-07 jproctermenu for choosing between 'protein' and 'RNA' mode... tree | commitdiff
2012-12-07 jprocterformatting and error report cleanup tree | commitdiff
2012-12-07 jproctergui hooks for contrafold and RNAfold services. commente... tree | commitdiff
2012-12-07 jprocterException signature change (will be overwritten by... tree | commitdiff
2012-12-07 jprocterformatting tree | commitdiff
2012-12-07 jproctertidy import tree | commitdiff
2012-12-07 jprocterremove mentions of non-functional RNAInteraction colour... tree | commitdiff
2012-12-07 jproctertidy debug messages tree | commitdiff
2012-12-07 jprocterproxy commit for Anne Menard <menard.annec@gmail.com... tree | commitdiff
2012-12-04 jprocterJAL-1140 - handled VARNA specific RNA exceptions within... tree | commitdiff
2012-12-04 jprocterJAL-1140 - handle VARNA specific RNA exceptions within... tree | commitdiff
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