+ } catch (IOException ex)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.couldnt_read_pasted_text", new String[]
+ { ex.toString() }), MessageManager
+ .getString("label.error_parsing_text"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+
+ if (al != null && al.hasValidSequence())
+ {
+ String title = MessageManager.formatMessage(
+ "label.input_cut_paste_params",
+ new String[] { format.getName() });
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+
+ /*
+ * if the view panel was closed its alignment is nulled
+ * and this is an orphaned cut and paste window
+ */
+ if (viewport != null && viewport.getAlignment() != null)
+ {
+ if (proxyColourScheme != null)
+ {
+ viewport.applyFeaturesStyle(proxyColourScheme);
+ }
+ ((AlignViewport) viewport).addAlignment(al, title);
+ }
+ else
+ {
+
+ AlignFrame af;
+ if (source instanceof ComplexAlignFile)