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2014-11-17	Jim Procter	JAL-1587 distinct calc IDs for JPredMSA and Jpred single...	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1587 propagate results of JABA sequence based predictors...	commit \| commitdiff \| tree
2014-11-17	Jim Procter	imports and formatting	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1587 propagate JPred annotation from legacy jpred...	commit \| commitdiff \| tree
2014-11-17	Jim Procter	formatting	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1587 JAL-407 instrument setDataset to add dataset...	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1469 help documentation	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1469 help documentation	commit \| commitdiff \| tree
2014-11-17	Jim Procter	Merge branch 'mrg_dev_282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-17	Jim Procter	Merge branch 'Release_2_8_2_Branch' into mrg_dev_282	commit \| commitdiff \| tree
2014-11-17	Jim Procter	Merge branch 'mrg_dev_282' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-17	Jim Procter	Merge commit '1d9e1c80fb6c0e32313a976ae0065fd32639f2bc...	commit \| commitdiff \| tree
2014-11-13	Jim Procter	Merge branch 'features/JAL-1469_svg-output-for-figure...	commit \| commitdiff \| tree
2014-11-13	Jim Procter	JAL-1469 added jfreesvg to desktop dependencies	commit \| commitdiff \| tree
2014-11-12	Jim Procter	Merge branch 'features/typed_annotations_calcId' into...	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-974 fix class contamination for jalviewLite build	commit \| commitdiff \| tree
2014-11-12	Jim Procter	Merge branch 'features/typed_annotations_calcId' into...	commit \| commitdiff \| tree
2014-11-12	Jim Procter	javadoc	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-674 use the getMapping/transfer to transfer annotation...	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-674 patch broken getMapping function	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-674 switch from .transfer to .liftOver for transfer...	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-674 note about broken .transfer method (expect...	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-674 javadoc	commit \| commitdiff \| tree
2014-11-12	Jim Procter	JAL-674 new tests and deprecated tests for PDB mapping...	commit \| commitdiff \| tree
2014-11-06	Jim Procter	Merge branch 'features/JAL-1152annotationSorting' into...	commit \| commitdiff \| tree
2014-11-04	Jim Procter	JAL-1213 normalise sequence extracted from Jmol in...	commit \| commitdiff \| tree
2014-11-04	Jim Procter	JAL-1213 test to ensure JMol extracted sequences are...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	Merge branch 'develop' into features/JAL-1152annotationSorting	commit \| commitdiff \| tree
2014-11-03	Jim Procter	Merge branch 'bug/JAL-1250_redundance-removal' into...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	Merge branch 'develop' into features/JAL-1152annotationSorting	commit \| commitdiff \| tree
2014-11-03	Jim Procter	Merge branch 'features/ssFromPDBEntry' into develop	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-795 JAL-674 tweaked logic to avoid black annotation...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	fix for JAL-1579 create threshold object for annotation...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1578 test property accessors/copy constructor	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1578 JAL-674 store/restore alignment annotation...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1578 formatting and imports	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-674 peptide structure input so test is not dependent...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-1551 formatting	commit \| commitdiff \| tree
2014-11-03	Jim Procter	JAL-674 JAL-961 JAL-1578 accessors and copy constructor...	commit \| commitdiff \| tree
2014-11-03	Jim Procter	javadoc	commit \| commitdiff \| tree
2014-10-31	Jim Procter	JAL-674 JAL-961 pass row reference to handler to check...	commit \| commitdiff \| tree
2014-10-31	Jim Procter	JAL-674 JAL-961 properties to stash additional information...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	Merge branch 'develop' into features/ssFromPDBEntry	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 hang on to sequences created by secondary parsiing...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 count number of annotation transferred in test	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 propagate annotation onto mapped sequence and...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 register PDB IDs when ever they are resolved...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 use PDB ID<>File registry to look up correct...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 return original and replacement sequences and...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 helpful javadoc for remap method	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 flag and proxy method to distinguish setMapping...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 map on StructureSelectionManager to record...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	patch for JAL-795 - use base secondary structure colour...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-674 patch test to verify presence of annotation...	commit \| commitdiff \| tree
2014-10-30	Jim Procter	JAL-1551 format and tidy	commit \| commitdiff \| tree
2014-10-29	Jim Procter	JAL-1264 JAL-674 test to exercise the AlignmentAnnotation...	commit \| commitdiff \| tree
2014-10-29	Jim Procter	JAL-1264 JAL-674 method to copy annotation on structure...	commit \| commitdiff \| tree
2014-10-29	Jim Procter	JAL-674 JAL-1264 remap method to allow annotation positions...	commit \| commitdiff \| tree
2014-10-27	Jim Procter	Merge branch 'develop' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-27	Jim Procter	Merge branch 'Release_2_8_2_Branch' into merge_r282_dev	commit \| commitdiff \| tree
2014-10-23	Jim Procter	Merge branch 'hotfix/JAL-1521' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-10-23	Jim Procter	Merge branch 'hotfix/JAL-1521' into develop	commit \| commitdiff \| tree
2014-10-23	unknown	JAL-1521 updated xerces to 2.11 along with xml-apis	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 develop	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 develop	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 develop	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...	Merge branch 'features/JAL-1333' into develop	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...	Merge branch 'features/JAL-1333' into develop	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 develop	commit \| commitdiff \| tree
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