jmolpopup = JmolPopup.newJmolPopup(viewer);
viewer.evalStringQuiet(command);
+
+ colourBySequence = true;
}
SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer();
boolean showFeatures = false;
+
if (ap.av.showSequenceFeatures)
{
showFeatures = true;
if (fr == null)
{
- fr = new jalview.gui.FeatureRenderer(ap.av);
+ fr = new jalview.gui.FeatureRenderer(ap);
}
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
{
for (int m = 0; m < mapping.length; m++)
{
- if (mapping[m].getSequence() == sequence[s])
+ if (mapping[m].getSequence() == sequence[s]
+ && ap.av.alignment.findIndex(sequence[s])>-1)
{
for (int r = 0; r < sequence[s].getLength(); r++)
{