view.setWidth(size.width);
view.setHeight(size.height);
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
+ view.setStartRes(av.getStartRes());
+ view.setStartSeq(av.getStartSeq());
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
.getGlobalColourScheme()));
}
- ResidueShaderI vcs = av.getViewportColourScheme();
+ ResidueShaderI vcs = av.getResidueShading();
ColourSchemeI cs = av.getGlobalColourScheme();
if (cs != null)
}
af.viewport.setGlobalColourScheme(cs);
- 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);
if (view.getConservationSelected() && cs != null)
{
- af.viewport.getViewportColourScheme().setConservationInc(
+ af.viewport.getResidueShading().setConservationInc(
view.getConsThreshold());
}