+ updateJalview(cdoc);
+
+ }
+ /**
+ * this will close all windows currently in Jalview.
+ *
+ */
+ protected void closeWindows() {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+
+ try
+ {
+ for (int i = frames.length - 1; i > -1; i--) {
+ frames[i].dispose();
+ }
+ } catch (Exception e) {
+ Cache.log.error("Whilst closing windows",e);
+ }