- protected void openLinkedAlignmentAs(AlignmentI al, String title,
- boolean newWindowOrSplitPane)
+ /**
+ * link given alignment to the alignment in this viewport and open
+ * @param al - alignment containing sequences to link to this alignment
+ * @param title
+ * @param newWindowOrSplitPane
+ * @param alignAs TODO
+ * @param alignAs - 0 - don't modify either alignment, 1 - align al according to us, 2- align us according to al
+ * @return alignFrame holding al
+ */
+ protected AlignFrame openLinkedAlignmentAs(AlignmentI al, String title,
+ boolean newWindowOrSplitPane, int alignAs)