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2014-11-23	Jim Procter	JAL-1569 remove stdout on parsing RNA	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1152 avoid NPE on null alignment annotation vector	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-674 add RNA sequence associated annotation to alignment...	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-1140 sensible name for seuqences in RNAML files...	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-1489 change initial value to distinguish non-rna...	commit \| commitdiff \| tree
2014-11-21	Jim Procter	JAL-1592 JAL-1489 avoid invalid RNA structure and distinguis...	commit \| commitdiff \| tree
2014-11-20	Jim Procter	JAL-1569 rna pair code in secondary structure character...	commit \| commitdiff \| tree
2014-11-20	Jim Procter	JAL-674 JAL-1569 mark RNA helix number in the value...	commit \| commitdiff \| tree
2014-11-20	Jim Procter	JAL-1569 remove log output during RNA secondary structure...	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	Charles Ofoegbu	comand line support for svg generation	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	gmungoc	JAL-1528 Chimera Help doc + fixes to setting colours	commit \| commitdiff \| tree
2014-11-17	gmungoc	JAL-1528 new Preference CHIMERA_PATH (Preferences ...	commit \| commitdiff \| tree
2014-11-17	gmungoc	JAL-1528 Chimera tidy errors, focus after align, close...	commit \| commitdiff \| tree
2014-11-17	gmungoc	JAL-1528 bug fixes and adjustments to Chimera interface	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	Jim Procter	JAL-1521 patch is to remove xerces from classpath....	commit \| commitdiff \| tree
2014-10-23	Jim Procter	JAL-1521 test to check registry is returning sources	commit \| commitdiff \| tree
2014-10-23	Jim Procter	patch fixes JAL-1558	commit \| commitdiff \| tree
2014-10-23	Jim Procter	JAL-1503 tag 2.8.1b1 hotfix - last in 2.8.1 line	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'forpush/JAL-674_dssp' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 check for null vector before ...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'patch_sjf4j_typo' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1216 update varna dependency string in jalviewLite...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'patch_sjf4j_typo' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JWS-59 JAL-1216 patch broken InstallAnywhere build	commit \| commitdiff \| tree
2014-10-21	Jim Procter	Merge branch 'forpush/JAL-674_dssp' into develop	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 reinstate missing import	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 initial implementation - only need to extract...	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-1551 crlf	commit \| commitdiff \| tree
2014-10-21	Jim Procter	JAL-674 JAL-1551 imports dropped during merge	commit \| commitdiff \| tree
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
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