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2013-05-21	Jim Procter	JAL-1231 add chain ID	commit \| commitdiff \| tree
2013-05-21	Jim Procter	JAL-1231 allow Jmol file handler to read from a stream	commit \| commitdiff \| tree
2013-05-21	Jim Procter	Merge branch 'JAL-1199-Stk_writing' into rnaml_test	commit \| commitdiff \| tree
2013-05-21	Jim Procter	split test for general Stockholm IO consistency (JAL...	commit \| commitdiff \| tree
2013-05-21	Jim Procter	JAL-1199 JAL-1272 remove main() method from test class	commit \| commitdiff \| tree
2013-05-21	Jim Procter	formatting	commit \| commitdiff \| tree
2013-05-21	Jim Procter	JAL-1199 JAL-1272 refactored Natasha's test to a generic...	commit \| commitdiff \| tree
2013-02-15	Jim Procter	JAL-1140 JAL-1215 JAL-1272 test import of RNAML and...	commit \| commitdiff \| tree
2013-02-15	Jim Procter	split test for general Stockholm IO consistency (JAL...	commit \| commitdiff \| tree
2013-02-15	Jim Procter	JAL-1199 JAL-1272 remove main() method from test class	commit \| commitdiff \| tree
2013-02-15	Jim Procter	formatting	commit \| commitdiff \| tree
2013-02-15	Jim Procter	JAL-1199 JAL-1272 refactored Natasha's test to a generic...	commit \| commitdiff \| tree
2013-02-14	Jim Procter	Merge branch 'JAL-1199-Stk_writing' into rnaml_test	commit \| commitdiff \| tree
2013-02-14	Jim Procter	JAL-1140 reinstate the simpler version of parsing code...	commit \| commitdiff \| tree
2013-02-14	Jim Procter	patch for bizarre ConcurrentModificationException that...	commit \| commitdiff \| tree
2013-02-13	Jim Procter	Merge branch 'jims_annotate3d_update' into menard_finalsep2012	commit \| commitdiff \| tree
2013-02-13	jprocter	fix merge conflicts for finess on JAL-1140 (introduced...	commit \| commitdiff \| tree
2013-02-13	jprocter	JAL-1216 switch to official release of VARNA 3.9	commit \| commitdiff \| tree
2013-02-13	jprocter	JAL-1213 JAL-674 robust test with an existing structure...	commit \| commitdiff \| tree
2013-02-13	jprocter	JAL-1214 todo	commit \| commitdiff \| tree
2013-02-13	jprocter	JAL-1213 JAL-674 - import a PDB file using Jmol data...	commit \| commitdiff \| tree
2013-02-13	jprocter	JAL-674 commented out annotate3d calling code for Jmol...	commit \| commitdiff \| tree
2013-02-13	jprocter	JAL-1028 JAL-674 hooks to call external processing...	commit \| commitdiff \| tree
2013-02-11	jprocter	patch for 'This parser does not support specification...	commit \| commitdiff \| tree
2013-02-11	jprocter	json simple library	commit \| commitdiff \| tree
2013-02-11	jprocter	upgrade to latest paradise services model using JSon...	commit \| commitdiff \| tree
2013-02-06	jprocter	Merge branch 'Release_2_8_Branch' into JAL-1199-Stk_writing	commit \| commitdiff \| tree
2013-02-06	jprocter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-02-06	jprocter	JAL-1265 basic support for parsing database accessions...	commit \| commitdiff \| tree
2013-02-06	jprocter	JAL-1199 added test for Rfam Stockholm file example	commit \| commitdiff \| tree
2013-02-06	jprocter	JAL-1199 refactored stockholm test code from main class...	commit \| commitdiff \| tree
2013-02-05	jprocter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-02-05	jprocter	formatting	commit \| commitdiff \| tree
2013-02-05	jprocter	Merge branch 'JAL-1199-Stk_writing' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-01-20	jprocter	Merge branch 'Dbfetch_hotfix-JAL-1238' into develop	commit \| commitdiff \| tree
2013-01-20	jprocter	Merge branch 'Dbfetch_hotfix-JAL-1238' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 test to see if the primary Uniprot source...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 order to place primary sources before lower...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 method to test if DAS source is a primary...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1238 tier index indicating distance of a source...	commit \| commitdiff \| tree
2013-01-18	jprocter	Merge branch 'JAL-1254-hotfix' into develop	commit \| commitdiff \| tree
2013-01-18	jprocter	Merge branch 'JAL-1254-hotfix' into Release_2_8_Branch	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1255 don't show 'Right click to add annotations...	commit \| commitdiff \| tree
2013-01-18	jprocter	JAL-1254 patch for NPE in annotation renderer when...	commit \| commitdiff \| tree
2012-12-11	jprocter	JAL-1217 check and avoid NPE if no datastore object...	commit \| commitdiff \| tree
2012-12-11	jprocter	JAL-1217 report exception for service when no datastore...	commit \| commitdiff \| tree
2012-12-07	jprocter	revised renderer and annotation model to support different...	commit \| commitdiff \| tree
2012-12-07	jprocter	convenience function to get the RNA model for an annotation...	commit \| commitdiff \| tree
2012-12-07	jprocter	use new secstructure process algorithm	commit \| commitdiff \| tree
2012-12-07	jprocter	Anne's refined RNAML parser. Seems to have some bugs...	commit \| commitdiff \| tree
2012-12-07	jprocter	Anne reinstated general stockholm parser code but extended...	commit \| commitdiff \| tree
2012-12-07	jprocter	typing	commit \| commitdiff \| tree
2012-12-07	jprocter	consensus secondary structure algorithm (possibly came...	commit \| commitdiff \| tree
2012-12-07	jprocter	revised RNA stem/loop processing code that copes with...	commit \| commitdiff \| tree
2012-12-07	jprocter	update authors for RNA processing routines	commit \| commitdiff \| tree
2012-12-07	jprocter	menu for choosing between 'protein' and 'RNA' mode...	commit \| commitdiff \| tree
2012-12-07	jprocter	formatting and error report cleanup	commit \| commitdiff \| tree
2012-12-07	jprocter	gui hooks for contrafold and RNAfold services. commented...	commit \| commitdiff \| tree
2012-12-07	jprocter	Exception signature change (will be overwritten by...	commit \| commitdiff \| tree
2012-12-07	jprocter	formatting	commit \| commitdiff \| tree
2012-12-07	jprocter	tidy import	commit \| commitdiff \| tree
2012-12-07	jprocter	remove mentions of non-functional RNAInteraction colourscheme	commit \| commitdiff \| tree
2012-12-07	jprocter	tidy debug messages	commit \| commitdiff \| tree
2012-12-07	jprocter	proxy commit for Anne Menard <menard.annec@gmail.com...	commit \| commitdiff \| tree
2012-12-04	jprocter	bogus source dir for jmol (only for jim - fix for yourself!)	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1140 - handled VARNA specific RNA exceptions within...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1140 - handle VARNA specific RNA exceptions within...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1140 - IO classes should only raise generic IOExceptions	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1216 switch to official release of VARNA 3.9	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1213 JAL-674 robust test with an existing structure...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1214 todo	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1213 JAL-674 - import a PDB file using Jmol data...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-674 commented out annotate3d calling code for Jmol...	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1028 JAL-674 hooks to call external processing...	commit \| commitdiff \| tree
2012-12-04	jprocter	Merge branch 'menard' into develop	commit \| commitdiff \| tree
2012-12-04	jprocter	JAL-1028 tidy and refactor external processing and...	commit \| commitdiff \| tree
2012-11-21	jprocter	valid URLs in website menu frame and fixed GA code	commit \| commitdiff \| tree
2012-11-19	jprocter	bugfix	commit \| commitdiff \| tree
2012-11-18	jprocter	JAL-1205 JAL-1140 generalised exception for Anne's...	commit \| commitdiff \| tree
2012-11-17	jprocter	Merge branch 'develop' into menard	commit \| commitdiff \| tree
2012-11-17	jprocter	Merge branch 'Release_2_8_Branch' into develop	commit \| commitdiff \| tree
2012-11-17	jprocter	Merge branch 'master' into Release_2_8_Branch	commit \| commitdiff \| tree
2012-11-17	jprocter	FileParse adapter for reading directly from inputstreams	commit \| commitdiff \| tree
2012-11-17	jprocter	return alignmentI created from pdbfile class directly...	commit \| commitdiff \| tree
2012-11-17	jprocter	return annotated rna sequences from rnaml returned...	commit \| commitdiff \| tree
2012-11-17	jprocter	store chainid on pdbentry	commit \| commitdiff \| tree
2012-11-17	jprocter	format adapter should return AlignmentI	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	call annotate3d service and parse rnaml to alignment	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	sequence numbering from 1	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	store chaincode on pdbentry	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting	commit \| commitdiff \| tree
2012-11-17	jprocter	simple HTTP multipart entity poster - may not be useful	commit \| commitdiff \| tree
2012-11-17	jprocter	tests for jalview.analysis.AlignSeq	commit \| commitdiff \| tree
2012-11-17	jprocter	openjdk7 returns null for default value selected format...	commit \| commitdiff \| tree
2012-11-17	jprocter	method to construct sequence mapping for matching positions...	commit \| commitdiff \| tree
2012-11-17	jprocter	convenience method for performing pairwise alignment	commit \| commitdiff \| tree
2012-11-17	jprocter	formatting and javadoc	commit \| commitdiff \| tree
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