+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
+
+ public void setSavedUpToDate(boolean s)
+ {
+ setSavedUpToDate(s, QuitHandler.Message.UNSAVED_CHANGES);
+ }
+
+ public void setSavedUpToDate(boolean s, QuitHandler.Message m)
+ {
+ Console.debug(
+ "Setting " + this.getViewId() + " setSavedUpToDate to " + s);
+ savedUpToDate = s;
+ QuitHandler.setMessage(m);
+ }
+
+ public boolean savedUpToDate()
+ {
+ Console.debug("Returning " + this.getViewId() + " savedUpToDate value: "
+ + savedUpToDate);
+ return savedUpToDate;
+ }