JSONFile bioJsonFile = (JSONFile) formatAdapter.getAlignFile();
AlignFrame alignFrame = new AlignFrame(_alignment,
bioJsonFile.getHiddenSequences(),
- bioJsonFile.getColumnSelection(), AlignFrame.DEFAULT_WIDTH,
+ bioJsonFile.getHiddenColumns(), AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
// Change colour scheme to 'None' and perform round trip
ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(