def annotate_file(self, cu, analysis):
        """Annotate a single file.

        `cu` is the CodeUnit for the file to annotate.

        """
        if not cu.relative:
            return

        filename = cu.filename
        source = cu.source_file()
        if self.directory:
            dest_file = os.path.join(self.directory, cu.flat_rootname())
            dest_file += ".py,cover"
        else:
            dest_file = filename + ",cover"
        dest = open(dest_file, 'w')

        statements = sorted(analysis.statements)
        missing = sorted(analysis.missing)
        excluded = sorted(analysis.excluded)

        lineno = 0
        i = 0
        j = 0
        covered = True
        while True:
            line = source.readline()
            if line == '':
                break
            lineno += 1
            while i < len(statements) and statements[i] < lineno:
                i += 1
            while j < len(missing) and missing[j] < lineno:
                j += 1
            if i < len(statements) and statements[i] == lineno:
                covered = j >= len(missing) or missing[j] > lineno
            if self.blank_re.match(line):
                dest.write('  ')
            elif self.else_re.match(line):
                # Special logic for lines containing only 'else:'.
                if i >= len(statements) and j >= len(missing):
                    dest.write('! ')
                elif i >= len(statements) or j >= len(missing):
                    dest.write('> ')
                elif statements[i] == missing[j]:
                    dest.write('! ')
                else:
                    dest.write('> ')
            elif lineno in excluded:
                dest.write('- ')
            elif covered:
                dest.write('> ')
            else:
                dest.write('! ')
            dest.write(line)
        source.close()
        dest.close()
Annotate a single file.

        `cu` is the CodeUnit for the file to annotate.