FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);
FeaturesDisplayedI fd = ((ComplexAlignFile) source)
.getDisplayedFeatures();
af = new AlignFrame(al, hiddenSeqs, colSel,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
af.getViewport().setShowSequenceFeatures(showSeqFeatures);
af.getViewport().setFeaturesDisplayed(fd);