import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
initTreePanel(alignPanel, null, null, newtree, inputData);
}
+ /**
+ * columnwise tree associated with positions in aa
+ *
+ * @param alignPanel
+ * @param fin
+ * @param title
+ * @param aa
+ */
+ public TreePanel(AlignmentPanel alignPanel, NewickFile fin,
+ AlignmentAnnotation aa, String title)
+ {
+ this(alignPanel, fin, title, null);
+ columnWise=true;
+ assocAnnotation = aa;
+
+
+ }
+ boolean columnWise=false;
+ AlignmentAnnotation assocAnnotation=null;
+ public boolean getColumnWise()
+ {
+ return columnWise;
+ }
+
public AlignmentI getAlignment()
{
return getTreeCanvas().getViewport().getAlignment();