Calculate alignment errors from the alignment and add it to the profile.

def add_alignment(self,align):
    """Calculate alignment errors from the alignment and add it to the profile."""
    self._target_context_errors = None
    self._query_context_errors = None
    ae = AlignmentErrors(align)
    self._alignment_errors.append(ae)
    self._general_errors.add_alignment_errors(ae)