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        }
        $args->{'chromosome'}    = $chr;
        $args->{'startPosition'} = $start;
        $args->{'endPosition'}   = $end;
    }
    elsif ( $row_identifier_type eq 'Term Source' ) {

        # Term Source Name must be in the $de_namespace (this is in
        # the MAGE-TAB spec).
        unless ( $de_namespace ) {
            croak(qq{Error: Data Matrix Term Source must include Name, e.g. "Term Source REF:embl".\n});
        }
        my $ts_obj = $self->get_builder()->get_term_source({
            'name' => $de_namespace,
        });

        # FIXME consider supporting semicolon-delimited accessions
        # here (not currently part of MAGE-TAB spec).
        my $term = $self->get_builder()->find_or_create_database_entry({
            accession  => $index,
            termSource => $ts_obj,
        });
        $args->{'databaseEntries'} = [ $term ];

        # In such cases this isn't really a namespace, so we get rid of it.
        delete $args->{'namespace'};
    }
    else {

        # Reporter, CompositeElement.
        $args->{'name'} = $index;
    }

    my $element = $self->get_builder()->$method($args);

    return $element;
}

# Make the classes immutable. In theory this speeds up object
# instantiation for a small compilation time cost.
__PACKAGE__->meta->make_immutable();

no Moose;

=head1 NAME

Bio::MAGETAB::Util::Reader::DataMatrix - Data matrix parser class.

=head1 SYNOPSIS

 use Bio::MAGETAB::Util::Reader::DataMatrix;
 my $parser = Bio::MAGETAB::Util::Reader::DataMatrix->new({
     uri => $dm_filename,
 });
 my $data_matrix = $parser->parse();

=head1 DESCRIPTION

This class is used to parse data matrix files. It can be used on its own, but
more often you will want to use the main Bio::MAGETAB::Util::Reader
class which handles extended parsing options more transparently.

=head1 ATTRIBUTES

See the L<TabFile|Bio::MAGETAB::Util::Reader::TabFile> class for superclass attributes.

=over 2

=item magetab_object

A Bio::MAGETAB::DataMatrix object. This can either be set upon
instantiation, or a new object will be created for you. It can be
retrieved at any time using C<get_magetab_object>.

=back

=head1 METHODS

=over 2

=item parse

Parse the data matrix pointed to by C<$self-E<gt>get_uri()>. Returns
the Bio::MAGETAB::DataMatrix object updated with the data matrix
contents.

=back

=head1 SEE ALSO

L<Bio::MAGETAB::Util::Reader::Tabfile>
L<Bio::MAGETAB::Util::Reader>
L<Bio::MAGETAB::DataMatrix>

=head1 AUTHOR

Tim F. Rayner <tfrayner@gmail.com>

=head1 LICENSE

This library is released under version 2 of the GNU General Public
License (GPL).

=cut

1;