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Merge branch 'JAL-1569_wuss_vienna_broke' into develop
2014-11-24 Jim ProcterMerge branch 'JAL-1569_wuss_vienna_broke' into develop
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2014-11-24 Jim ProcterJAL-1593 refactor rna helix colours to static singleton...
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2014-11-24 Jim ProcterJAL-1264 update annotation panel dimensions before...
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2014-11-24 Jim ProcterJAL-1595 update annotation sort on opening of the ...
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2014-11-24 Jim ProcterJAL-1595 annotation score is total number of rna helices
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2014-11-23 Jim ProcterJAL-1569 interactive editing of secondary structure...
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2014-11-23 Jim ProcterMerge branch 'JAL-1569_wuss_vienna_broke' into develop
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2014-11-23 Jim Procteremploy test and secondary structure character for determinin...
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2014-11-23 Jim ProcterJAL-1569 formatting
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2014-11-23 Jim ProcterJAL-1593 allow per-sequence shading of RNA helix (stored...
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2014-11-23 Jim ProcterJAL-1569 test for open/close RNA parenthesis character
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2014-11-23 Jim ProcterJAL-1569 formatting
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2014-11-23 Jim ProcterJAL-1569 refactoring of stockholm test
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2014-11-23 Jim ProcterJAL-1569 consistent handling of sequence and alignment...
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2014-11-23 Jim ProcterJAL-1569 revise tests to count number and type of annotation...
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2014-11-23 Jim ProcterJAL-1569 formatting
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2014-11-23 Jim ProcterJAL-1569 preserve input ordering for stockholm files...
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2014-11-23 Jim ProcterJAL-1569 remove stdout on parsing RNA
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2014-11-23 Jim ProcterJAL-1152 avoid NPE on null alignment annotation vector
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2014-11-21 Jim ProcterJAL-674 add RNA sequence associated annotation to alignment...
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2014-11-21 Jim ProcterJAL-1569 formatting
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2014-11-21 Jim ProcterJAL-1140 sensible name for seuqences in RNAML files...
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2014-11-21 Jim ProcterJAL-1489 change initial value to distinguish non-rna...
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2014-11-21 Jim ProcterJAL-1592 JAL-1489 avoid invalid RNA structure and distinguis...
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2014-11-20 Jim ProcterJAL-1569 rna pair code in secondary structure character...
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2014-11-20 Jim ProcterJAL-674 JAL-1569 mark RNA helix number in the value...
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2014-11-20 Jim ProcterJAL-1569 remove log output during RNA secondary structure...
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2014-11-18 Jim ProcterMerge branch 'JAL-1587_promotedisorder' into develop
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2014-11-18 Jim ProcterJAL-674 make temperature factor, local secondary structure...
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2014-11-18 Jim ProcterJAL-674 JAL-1512 JAL-1333 documentation
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2014-11-17 Jim ProcterJAL-1517 JAL-1587 JAL-674 secondary structure and annotation...
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2014-11-17 Jim ProcterJAL-1517 release notes for 2.8.2
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2014-11-17 Jim ProcterJAL-1587 distinct calc IDs for JPredMSA and Jpred single...
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2014-11-17 Jim ProcterJAL-1587 propagate results of JABA sequence based predictors...
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2014-11-17 Jim Procterimports and formatting
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2014-11-17 Jim ProcterJAL-1587 propagate JPred annotation from legacy jpred...
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2014-11-17 Jim Procterformatting
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2014-11-17 Jim ProcterJAL-1587 JAL-407 instrument setDataset to add dataset...
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2014-11-17 Jim ProcterMerge branch 'r282_portforward' into develop
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2014-11-17 Jim ProcterJAL-1469 help documentation
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2014-11-17 Jim ProcterJAL-1469 help documentation
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2014-11-17 Jim ProcterMerge branch 'mrg_dev_282' into Release_2_8_2_Branch
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2014-11-17 Jim ProcterMerge branch 'Release_2_8_2_Branch' into mrg_dev_282
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2014-11-17 Jim ProcterMerge branch 'mrg_dev_282' into Release_2_8_2_Branch
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2014-11-17 Jim ProcterMerge commit '1d9e1c80fb6c0e32313a976ae0065fd32639f2bc...
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2014-11-13 Jim ProcterMerge branch 'features/JAL-1469_svg-output-for-figure...
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2014-11-13 Jim ProcterMerge branch 'features/JAL-1469_svg-output-for-figure...
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2014-11-13 Jim ProcterJAL-1469 added jfreesvg to desktop dependencies
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2014-11-12 Jim ProcterMerge branch 'features/JAL-1541_BioJsMSAViewer-export...
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2014-11-12 Jim ProcterJAL-1541 exclude all unnecessary jalview.io classes...
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2014-11-12 Jim ProcterMerge branch 'features/JAL-1541_BioJsMSAViewer-export...
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2014-11-12 Jim ProcterMerge branch 'develop' into features/JAL-1541_BioJsMSAViewer...
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2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into...
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2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into...
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2014-11-12 Jim ProcterJAL-974 fix class contamination for jalviewLite build
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2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into...
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2014-11-12 Jim ProcterMerge branch 'features/typed_annotations_calcId' into...
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2014-11-12 Jim Procterjavadoc
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2014-11-12 Jim ProcterJAL-674 use the getMapping/transfer to transfer annotation...
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2014-11-12 Jim ProcterJAL-674 patch broken getMapping function
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2014-11-12 Jim ProcterJAL-674 switch from .transfer to .liftOver for transfer...
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2014-11-12 Jim ProcterJAL-674 note about broken .transfer method (expect...
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2014-11-12 Jim ProcterJAL-674 javadoc
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2014-11-12 Jim ProcterJAL-674 new tests and deprecated tests for PDB mapping...
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-12 Jim ProcterJAL-1541 added Jsoup to the InstallAnywhere config
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2014-11-06 Jim ProcterMerge branch 'features/JAL-1152annotationSorting' into...
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2014-11-06 Jim ProcterMerge branch 'features/JAL-1541_BioJsMSAViewer-export...
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2014-11-04 Jim ProcterJAL-1213 normalise sequence extracted from Jmol in...
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2014-11-04 Jim ProcterJAL-1213 test to ensure JMol extracted sequences are...
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2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotationSorting
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2014-11-03 Jim ProcterMerge branch 'bug/JAL-1250_redundance-removal' into...
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2014-11-03 Jim ProcterMerge branch 'develop' into features/JAL-1152annotationSorting
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2014-11-03 Jim ProcterMerge branch 'features/ssFromPDBEntry' into develop
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2014-11-03 Jim ProcterJAL-795 JAL-674 tweaked logic to avoid black annotation...
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2014-11-03 Jim Procterfix for JAL-1579 create threshold object for annotation...
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2014-11-03 Jim ProcterJAL-1578 test property accessors/copy constructor
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2014-11-03 Jim ProcterJAL-1578 JAL-674 store/restore alignment annotation...
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2014-11-03 Jim ProcterJAL-1578 formatting and imports
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2014-11-03 Jim ProcterJAL-674 peptide structure input so test is not dependent...
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2014-11-03 Jim ProcterJAL-1551 formatting
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2014-11-03 Jim ProcterJAL-674 JAL-961 JAL-1578 accessors and copy constructor...
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2014-11-03 Jim Procterjavadoc
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2014-10-31 Jim ProcterJAL-674 JAL-961 pass row reference to handler to check...
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2014-10-31 Jim ProcterJAL-674 JAL-961 properties to stash additional information...
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2014-10-30 Jim ProcterMerge branch 'develop' into features/ssFromPDBEntry
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2014-10-30 Jim ProcterJAL-674 hang on to sequences created by secondary parsiing...
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2014-10-30 Jim ProcterJAL-674 count number of annotation transferred in test
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2014-10-30 Jim ProcterJAL-674 propagate annotation onto mapped sequence and...
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2014-10-30 Jim ProcterJAL-674 register PDB IDs when ever they are resolved...
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2014-10-30 Jim ProcterJAL-674 use PDB ID<>File registry to look up correct...
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2014-10-30 Jim ProcterJAL-674 return original and replacement sequences and...
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2014-10-30 Jim ProcterJAL-674 helpful javadoc for remap method
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2014-10-30 Jim ProcterJAL-674 flag and proxy method to distinguish setMapping...
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2014-10-30 Jim ProcterJAL-674 map on StructureSelectionManager to record...
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2014-10-30 Jim Procterpatch for JAL-795 - use base secondary structure colour...
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2014-10-30 Jim ProcterJAL-674 patch test to verify presence of annotation...
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2014-10-30 Jim ProcterJAL-1551 format and tidy
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