af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.getRanges().setStartRes(view.getStartRes());
+ af.viewport.getRanges().setStartSeq(view.getStartSeq());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setColourText(view.getShowColourText());
// }
}
- af.viewport.getViewportColourScheme().setThreshold(
+ af.viewport.getResidueShading().setThreshold(
view.getPidThreshold(), true);
- af.viewport.getViewportColourScheme().setConsensus(
+ af.viewport.getResidueShading().setConsensus(
af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
- af.viewport.getViewportColourScheme().setConservationInc(
+ af.viewport.getResidueShading().setConservationInc(
view.getConsThreshold());
}
Tree tree = jms.getTree(t);
- TreePanel tp = af.ShowNewickTree(
+ TreePanel tp = af.showNewickTree(
new jalview.io.NewickFile(tree.getNewick()),
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());