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2014-11-28	Jim Procter	JAL-1583 javadoc and fix constructor signature	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1342 document argument to specify preferred JABA...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1604 formatting	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1604 revised wording and internationalised dialog	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 back out original fix and simply check MSAWSThread...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 formatting	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 new validInput flag set according to validity...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1583 refactored addInternalFrame to allow webservice...	commit \| commitdiff \| tree
2014-11-28	Jim Procter	JAL-1517 formatting/tidy	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-1517 svg==scalable :)	commit \| commitdiff \| tree
2014-11-27	Jim Procter	Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 add sequence associated annotation rows to...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-1177 JAL-905 cannot recover sequences from dataset...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 avoid writing \0 for chain code	commit \| commitdiff \| tree
2014-11-27	Jim Procter	Merge branch 'patchJAL-674_offset' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 patch to fix bug with showing reference annotation...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 formatting	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 unused variable	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 bug in test	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 test that PDB annotation created when importing...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 patch NPE bug when test run in isolation	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 fix test properties path and add properties...	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-674 JAL-966 new method to retrieve all views	commit \| commitdiff \| tree
2014-11-27	Jim Procter	organise imports	commit \| commitdiff \| tree
2014-11-27	Jim Procter	JAL-966 promote getName to an api method	commit \| commitdiff \| tree
2014-11-26	Jim Procter	Merge branch 'JAL-674_fixannotlabels' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 make RNAML-extracted secondary structure lines...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-1578 fix logic for showing score when no description...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 JAL-1578 commented code for displaying annotation...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 friendly name for PDB file included in secondary...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 employ the provided DNA/Protein matrix string...	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 disable addition of PDBRESNUM annotation line	commit \| commitdiff \| tree
2014-11-26	Jim Procter	JAL-674 nicer temperature factor labelling and include...	commit \| commitdiff \| tree
2014-11-25	Jim Procter	Merge branch 'bug/JAL-689' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-25	Jim Procter	fix for JAL-689 ensure fastpainting flag set only when...	commit \| commitdiff \| tree
2014-11-25	Jim Procter	formatting	commit \| commitdiff \| tree
2014-11-25	Jim Procter	patch for JAL-1599 - annotation row constructed by...	commit \| commitdiff \| tree
2014-11-25	Jim Procter	Merge branch 'patch_JAL-689' into Release_2_8_2_Branch	commit \| commitdiff \| tree
2014-11-25	Jim Procter	back out duplicate jfree classpath entry	commit \| commitdiff \| tree
2014-11-24	Jim Procter	Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1593 refactor rna helix colours to static singleton...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1264 update annotation panel dimensions before...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1595 update annotation sort on opening of the ...	commit \| commitdiff \| tree
2014-11-24	Jim Procter	JAL-1595 annotation score is total number of rna helices	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 interactive editing of secondary structure...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	Merge branch 'JAL-1569_wuss_vienna_broke' into Release_2_8_2...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	employ test and secondary structure character for determinin...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1593 allow per-sequence shading of RNA helix (stored...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 test for open/close RNA parenthesis character	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 refactoring of stockholm test	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 consistent handling of sequence and alignment...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 revise tests to count number and type of annotation...	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 formatting	commit \| commitdiff \| tree
2014-11-23	Jim Procter	JAL-1569 preserve input ordering for stockholm files...	commit \| commitdiff \| tree
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
2014-11-18	Jim Procter	Merge branch 'JAL-1587_promotedisorder' into Release_2_8_2_B...	commit \| commitdiff \| tree
2014-11-18	Jim Procter	JAL-674 make temperature factor, local secondary structure...	commit \| commitdiff \| tree
2014-11-18	Jim Procter	JAL-674 JAL-1512 JAL-1333 documentation	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1517 JAL-1587 JAL-674 secondary structure and annotation...	commit \| commitdiff \| tree
2014-11-17	Jim Procter	JAL-1517 release notes for 2.8.2	commit \| commitdiff \| tree
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	Merge branch 'Release_2_8_2_Branch' of https://source...	commit \| commitdiff \| tree
2014-11-17	Jim Procter	Merge branch 'r282_portforward' into Release_2_8_2_Branch	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
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