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2014-10-21	Jim Procter	JAL-1216 update to VARNA 3.91	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 remove any spurious PDBEntrys generated by...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 methods and test for PDB derived annotation...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 store ID in MCview.PDBfile calcId string, not...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 don't create multiple secondary structure lines...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test for the test for presence of annotation...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test for presence of annotation derived from...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 patch for duplicate row bug	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test for duplicate alignment annotation rows...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 patch to ensure existing annotation is properly...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 test to ensure sequence and annotation on sequence...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 source formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 JAL-207 getTers for aligned sequences in dataset...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 refactor method to match and transfer annotation...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'features/JAL-1264_showHideAnnotations...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 crlf changes	commit \| commitdiff \| tree
2014-10-16	Jim Procter	Merge branch 'feature/JAL-674_dssp' into features/JAL...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	Merge branch 'jims_crlf_hell_JAL-1551' of https://source...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-1551 crlf changes due to checkout with text=auto	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-1551 crlf changes due to checkout with text=auto	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 always try to extract secondary structure when...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 support preservation of any annotation created...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 make transferAnnotation method static	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-348 JAL-674 JAL-1564 TODO and implementation error...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 patch logic to test whether old and new sequence...	commit \| commitdiff \| tree
2014-10-15	Jim Procter	JAL-674 JAL-1305 JAL-348 new liftOver method and test...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 employ new signature in Annotate3D service...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 disable secondary structure annotation when...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 typo	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 new constructors to pass flags about annotating...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 parser flag to control secondary structure...	commit \| commitdiff \| tree
2014-10-10	Jim Procter	JAL-674 change jalview.io.AlignFile to allow parsing...	commit \| commitdiff \| tree
2014-10-09	Jim Procter	Merge branch 'bug/JAL-1558' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-09	Jim Procter	patch fixes JAL-1558	commit \| commitdiff \| tree
2014-10-07	Jim Procter	Merge branch 'bugs/JAL-1151' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-07	Jim Procter	JAL-1557 partial implementation - need to think about...	commit \| commitdiff \| tree
2014-10-07	Jim Procter	patch for JAL-1151 - select whole sequence when double...	commit \| commitdiff \| tree
2014-10-07	Jim Procter	JAL-1421 remove Vector and pass a list	commit \| commitdiff \| tree
2014-10-07	Jim Procter	JAL-1151 source tidy	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'JAL-429_phylip-file-support' into Release_2_8_...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'patch/JAL-848' into JAL-429_phylip-file...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'patch/JAL-848' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-848 reinstate netbeans files from Phylip patch...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'JAL-429_phylip-file-support' into Release_2_8_...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'Release_2_8_2_Branch' into JAL-429_phylip...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'patch/JAL-1286_JAL-1265' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-1286 missing file for testcase where file ends...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-1500 JAL-1265 patch to parse PDB database refs...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	Merge branch 'feature/JAL-654_dssp' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 remove any annotation rows for chain specific...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 updated pdb db fetcher test to verify the number...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 JAL-1264 sequence associated annotation is...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 format and refactor test demonstrating PDB...	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-1115 TODO remove use of java.util.Vector	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654 javadoc createDatasetSequence and transferAnnotation	commit \| commitdiff \| tree
2014-10-06	Jim Procter	JAL-654_dssp formatting and javadoc	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'Release_2_8_2_Branch_i18n' into Release_2_8_2_...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	JAL-1355 removed all top level html tags from message...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'Release_2_8_2_Branch' into Release_2_8_2_Branc...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-03	Jim Procter	JAL-1338 note added #fridaycommits not actually connected...	commit \| commitdiff \| tree
2014-10-03	Jim Procter	Merge branch 'bugs/JAL-1138_osgi' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-03	Jim Procter	JAL-1499 simple test to check JABA client can	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	Merge branch 'Release_2_8_2_Branch' of https://source...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	Merge branch 'bug/JAL-1486_flatfile' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1486 JAL-1543 pushed alignment viewport->view-...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	formatting and organise imports	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1486 fix: pass selected region to jalview.io via...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1199 add stockholm output to list of AppletFormatAdapter...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1486 JAL-535 refactor code for trimming alignment...	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-535 tidy interface definition and documentation	commit \| commitdiff \| tree
2014-09-12	j.procter@dundee...	JAL-1516 Annotation row score output script for jalview...	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	Merge branch 'features/JAL-1333' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 fix imports	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	Merge branch 'features/JAL-1333' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 log4j/slf additional jars	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 add log4j-slf4j bridge	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	Merge branch 'features/JAL-1333' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 finessing log4j and slf dependencies for strucviz...	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 JAL-1533 todo to get Chimera superposing properly...	commit \| commitdiff \| tree
2014-07-22	j.procter@dundee...	JAL-1333 more superposition debugging and deadlock...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1379 Jpred JABA client test harness	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1333 allow reuse of existing chimera for new or...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1333 more refinements - deadlocks still possible...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-674 futzing with bugs	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-795 take colour from annotation if colour is present	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	ensure the dataset is instantiated before materialising...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1379 new look JPred results	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1520 switch between Protein and non-canonical RNA...	commit \| commitdiff \| tree
2014-07-18	j.procter@dundee...	JAL-1028 JAL-1142 refactor test to allow reuse of secondary...	commit \| commitdiff \| tree
2014-07-08	j.procter@dundee...	JAL-1333 allow reuse of existing viewers (of a specified...	commit \| commitdiff \| tree
2014-07-08	j.procter@dundee...	JAL-1333 more efficient color statement	commit \| commitdiff \| tree
2014-07-04	j.procter@dundee...	JAL-1333 more abstraction and refactoring and working...	commit \| commitdiff \| tree
2014-07-03	j.procter@dundee...	Merge branch 'Release_2_8_2_Branch' into features/JAL...	commit \| commitdiff \| tree
2014-07-03	j.procter@dundee...	Merge branch 'hotfix/JAL-1530' into Release_2_8_2_Branch	commit \| commitdiff \| tree

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