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JAL-1486 JAL-1543 pushed alignment viewport->view->flat file logic into jalview.io...

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