+
+ // now update any complementary alignment (its viewport ranges object
+ // is different so does not get automatically updated)
+ if (isSetToScrollComplementPanel())
+ {
+ setToScrollComplementPanel(false);
+ av.scrollComplementaryAlignment();
+ setToScrollComplementPanel(true);
+ }
+ }
+
+ /**
+ * Set the reference to the PCA/Tree chooser dialog for this panel. This
+ * reference should be nulled when the dialog is closed.
+ *
+ * @param calculationChooser
+ */
+ public void setCalculationDialog(CalculationChooser calculationChooser)
+ {
+ calculationDialog = calculationChooser;
+ }
+
+ /**
+ * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+ * if none is open)
+ */
+ public CalculationChooser getCalculationDialog()
+ {
+ return calculationDialog;
+ }
+
+ /**
+ * Constructs and sets the title for the Overview window (if there is one),
+ * including the align frame's title, and view name (if applicable). Returns
+ * the title, or null if this panel has no Overview window open.
+ *
+ * @param alignFrame
+ * @return
+ */
+ public String setOverviewTitle(AlignFrame alignFrame)
+ {
+ if (this.overviewPanel == null)
+ {
+ return null;
+ }
+ String overviewTitle = MessageManager
+ .formatMessage("label.overview_params", new Object[]
+ { alignFrame.getTitle() });
+ String viewName = getViewName();
+ if (viewName != null)
+ {
+ overviewTitle += (" " + viewName);
+ }
+ overviewPanel.setTitle(overviewTitle);
+ return overviewTitle;
+ }
+
+ /**
+ * If this alignment panel has an Overview panel open, closes it
+ */
+ public void closeOverviewPanel()
+ {
+ if (overviewPanel != null)
+ {
+ overviewPanel.close();
+ overviewPanel = null;
+ }