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jalview.git
2013-05-24 Jim ProcterMerge branch 'menard' into develop_m2_8_1_2 commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1140 JAL-674 process with annotate3d and Jmol to... commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-674 ensure annotation is properly annotated commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1231 add chain ID commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1231 allow Jmol file handler to read from a stream commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterMerge branch 'JAL-1199-Stk_writing' into rnaml_test commit | commitdiff | tree | snapshot
2013-05-21 Jim Proctersplit test for general Stockholm IO consistency (JAL... commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1199 JAL-1272 remove main() method from test class commit | commitdiff | tree | snapshot
2013-05-21 Jim Procterformatting commit | commitdiff | tree | snapshot
2013-05-21 Jim ProcterJAL-1199 JAL-1272 refactored Natasha's test to a generi... commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterJAL-1286 URL stream reader tries to use a GZIPInputStre... commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterMerge branch 'JAL-1289_initCallBack' into develop commit | commitdiff | tree | snapshot
2013-05-13 Jim ProcterJAL-1289 call oninit callback even if no alignment... commit | commitdiff | tree | snapshot
2013-02-15 Jim ProcterJAL-1140 JAL-1215 JAL-1272 test import of RNAML and... commit | commitdiff | tree | snapshot
2013-02-15 Jim Proctersplit test for general Stockholm IO consistency (JAL... commit | commitdiff | tree | snapshot
2013-02-15 Jim ProcterJAL-1199 JAL-1272 remove main() method from test class commit | commitdiff | tree | snapshot
2013-02-15 Jim Procterformatting commit | commitdiff | tree | snapshot
2013-02-15 Jim ProcterJAL-1199 JAL-1272 refactored Natasha's test to a generi... commit | commitdiff | tree | snapshot
2013-02-14 Jim ProcterMerge branch 'JAL-1199-Stk_writing' into rnaml_test commit | commitdiff | tree | snapshot
2013-02-14 Jim ProcterJAL-1140 reinstate the simpler version of parsing code... commit | commitdiff | tree | snapshot
2013-02-14 Jim Procterpatch for bizarre ConcurrentModificationException that... commit | commitdiff | tree | snapshot
2013-02-13 Jim ProcterMerge branch 'jims_annotate3d_update' into menard_final... commit | commitdiff | tree | snapshot
2013-02-13 jprocterfix merge conflicts for finess on JAL-1140 (introduced... commit | commitdiff | tree | snapshot
2013-02-13 jprocterJAL-1216 switch to official release of VARNA 3.9 commit | commitdiff | tree | snapshot
2013-02-13 jprocterJAL-1213 JAL-674 robust test with an existing structure... commit | commitdiff | tree | snapshot
2013-02-13 jprocterJAL-1214 todo commit | commitdiff | tree | snapshot
2013-02-13 jprocterJAL-1213 JAL-674 - import a PDB file using Jmol data... commit | commitdiff | tree | snapshot
2013-02-13 jprocterJAL-674 commented out annotate3d calling code for Jmol... commit | commitdiff | tree | snapshot
2013-02-13 jprocterJAL-1028 JAL-674 hooks to call external processing... commit | commitdiff | tree | snapshot
2013-02-11 jprocterpatch for 'This parser does not support specification... commit | commitdiff | tree | snapshot
2013-02-11 jprocterjson simple library commit | commitdiff | tree | snapshot
2013-02-11 jprocterupgrade to latest paradise services model using JSon... commit | commitdiff | tree | snapshot
2013-02-06 jprocterMerge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing commit | commitdiff | tree | snapshot
2013-02-06 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-02-06 jprocterJAL-1265 basic support for parsing database accessions... commit | commitdiff | tree | snapshot
2013-02-06 jprocterJAL-1199 added test for Rfam Stockholm file example commit | commitdiff | tree | snapshot
2013-02-06 jprocterJAL-1199 refactored stockholm test code from main class... commit | commitdiff | tree | snapshot
2013-02-05 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-02-05 jprocterformatting commit | commitdiff | tree | snapshot
2013-02-05 jprocterMerge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-01-20 jprocterMerge branch 'Dbfetch_hotfix-JAL-1238' into develop commit | commitdiff | tree | snapshot
2013-01-20 jprocterMerge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8... commit | commitdiff | tree | snapshot
2013-01-18 jprocterJAL-1238 test to see if the primary Uniprot source... commit | commitdiff | tree | snapshot
2013-01-18 jprocterJAL-1238 order to place primary sources before lower... commit | commitdiff | tree | snapshot
2013-01-18 jprocterJAL-1238 method to test if DAS source is a primary... commit | commitdiff | tree | snapshot
2013-01-18 jprocterJAL-1238 tier index indicating distance of a source... commit | commitdiff | tree | snapshot
2013-01-18 jprocterMerge branch 'JAL-1254-hotfix' into develop commit | commitdiff | tree | snapshot
2013-01-18 jprocterMerge branch 'JAL-1254-hotfix' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2013-01-18 jprocterJAL-1255 don't show 'Right click to add annotations... commit | commitdiff | tree | snapshot
2013-01-18 jprocterJAL-1254 patch for NPE in annotation renderer when... commit | commitdiff | tree | snapshot
2012-12-17 Natashatest for output a file in Stockholm format commit | commitdiff | tree | snapshot
2012-12-12 NatashaOutput accession number for file in stockholm format commit | commitdiff | tree | snapshot
2012-12-11 jprocterJAL-1217 check and avoid NPE if no datastore object... commit | commitdiff | tree | snapshot
2012-12-11 jprocterJAL-1217 report exception for service when no datastore... commit | commitdiff | tree | snapshot
2012-12-07 jprocterrevised renderer and annotation model to support differ... commit | commitdiff | tree | snapshot
2012-12-07 jprocterconvenience function to get the RNA model for an annota... commit | commitdiff | tree | snapshot
2012-12-07 jprocteruse new secstructure process algorithm commit | commitdiff | tree | snapshot
2012-12-07 jprocterAnne's refined RNAML parser. Seems to have some bugs... commit | commitdiff | tree | snapshot
2012-12-07 jprocterAnne reinstated general stockholm parser code but exten... commit | commitdiff | tree | snapshot
2012-12-07 jproctertyping commit | commitdiff | tree | snapshot
2012-12-07 jprocterconsensus secondary structure algorithm (possibly came... commit | commitdiff | tree | snapshot
2012-12-07 jprocterrevised RNA stem/loop processing code that copes with... commit | commitdiff | tree | snapshot
2012-12-07 jprocterupdate authors for RNA processing routines commit | commitdiff | tree | snapshot
2012-12-07 jproctermenu for choosing between 'protein' and 'RNA' mode... commit | commitdiff | tree | snapshot
2012-12-07 jprocterformatting and error report cleanup commit | commitdiff | tree | snapshot
2012-12-07 jproctergui hooks for contrafold and RNAfold services. commente... commit | commitdiff | tree | snapshot
2012-12-07 jprocterException signature change (will be overwritten by... commit | commitdiff | tree | snapshot
2012-12-07 jprocterformatting commit | commitdiff | tree | snapshot
2012-12-07 jproctertidy import commit | commitdiff | tree | snapshot
2012-12-07 jprocterremove mentions of non-functional RNAInteraction colour... commit | commitdiff | tree | snapshot
2012-12-07 jproctertidy debug messages commit | commitdiff | tree | snapshot
2012-12-07 jprocterproxy commit for Anne Menard <menard.annec@gmail.com... commit | commitdiff | tree | snapshot
2012-12-04 jprocterbogus source dir for jmol (only for jim - fix for yours... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1140 - handled VARNA specific RNA exceptions within... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1140 - handle VARNA specific RNA exceptions within... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1140 - IO classes should only raise generic IOExcep... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1216 switch to official release of VARNA 3.9 commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1213 JAL-674 robust test with an existing structure... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1214 todo commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1213 JAL-674 - import a PDB file using Jmol data... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-674 commented out annotate3d calling code for Jmol... commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1028 JAL-674 hooks to call external processing... commit | commitdiff | tree | snapshot
2012-12-04 jprocterMerge branch 'menard' into develop commit | commitdiff | tree | snapshot
2012-12-04 jprocterJAL-1028 tidy and refactor external processing and... commit | commitdiff | tree | snapshot
2012-11-23 Natashastockholm file output code developed by Natasha Sherstneva commit | commitdiff | tree | snapshot
2012-11-21 jproctervalid URLs in website menu frame and fixed GA code commit | commitdiff | tree | snapshot
2012-11-19 jprocterbugfix commit | commitdiff | tree | snapshot
2012-11-18 jprocterJAL-1205 JAL-1140 generalised exception for Anne's... commit | commitdiff | tree | snapshot
2012-11-17 jprocterMerge branch 'develop' into menard commit | commitdiff | tree | snapshot
2012-11-17 jprocterMerge branch 'Release_2_8_Branch' into develop commit | commitdiff | tree | snapshot
2012-11-17 jprocterMerge branch 'master' into Release_2_8_Branch commit | commitdiff | tree | snapshot
2012-11-17 jprocterFileParse adapter for reading directly from inputstreams commit | commitdiff | tree | snapshot
2012-11-17 jprocterreturn alignmentI created from pdbfile class directly... commit | commitdiff | tree | snapshot
2012-11-17 jprocterreturn annotated rna sequences from rnaml returned... commit | commitdiff | tree | snapshot
2012-11-17 jprocterstore chainid on pdbentry commit | commitdiff | tree | snapshot
2012-11-17 jprocterformat adapter should return AlignmentI commit | commitdiff | tree | snapshot
2012-11-17 jprocterformatting commit | commitdiff | tree | snapshot
2012-11-17 jproctercall annotate3d service and parse rnaml to alignment commit | commitdiff | tree | snapshot
2012-11-17 jprocterformatting commit | commitdiff | tree | snapshot
2012-11-17 jproctersequence numbering from 1 commit | commitdiff | tree | snapshot
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