AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
/**
+ * @return an alignment view, optionally without a complement view
+ * @param selectedOnly
+ * @param markGroups
+ * @param withComplement - false if no complement view required
+ */
+ AlignmentView getAlignmentViewWithComplement(boolean selectedOnly,
+ boolean markGroups, boolean withComplement);
+
+ /**
* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden