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    return $self->next_prediction(@args);
}

=head2 next_prediction

 Title   : next_prediction
 Usage   : while($gene = $mzef->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the MZEF result
           file. Call this method repeatedly until FALSE is returned.

           Note that with the present version of MZEF there will only be one
           object returned, because MZEF does not predict individual genes
           but just potential internal exons.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

=cut

sub next_prediction {
    my ($self) = @_;
    my $gene;

    # if the prediction section hasn't been parsed yet, we do this now
    $self->_parse_predictions() unless $self->_predictions_parsed();

    # return the next gene structure (transcript)
    return $self->_prediction();
}

=head2 _parse_predictions

 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns : 

=cut

sub _parse_predictions {
    my ($self) = @_;
    my ($method); # set but not used presently
    my $exon_tag = "InternalExon";
    my $gene;
    # my $seqname; # name given in output is poorly formatted
    my $seqlen;
    my $prednr = 1;

    while(defined($_ = $self->_readline())) {
	if(/^\s*(\d+)\s*-\s*(\d+)\s+/) {
	    # exon or signal
	    if(! defined($gene)) {
		$gene = Bio::Tools::Prediction::Gene->new(
                                       '-primary' => "GenePrediction$prednr",
				       '-source' => 'MZEF');
	    }
	    # we handle start-end first because may not be space delimited
	    # for large numbers
	    my ($start,$end) = ($1,$2);
	    s/^\s*(\d+)\s*-\s*(\d+)\s+//;
	    # split the rest into fields
	    chomp();
	    # format: Coordinates P Fr1 Fr2 Fr3 Orf 3ss Cds 5ss
	    # index:              0   1   2   3   4   5   6   7
	    my @flds = split(' ', $_);
	    # create the feature object depending on the type of signal --
	    # which is always an (internal) exon for MZEF
	    my $predobj = Bio::Tools::Prediction::Exon->new();
	    # set common fields
	    $predobj->source_tag('MZEF');
	    $predobj->significance($flds[0]);
	    $predobj->score($flds[0]); # what shall we set as overall score?
	    $predobj->strand($self->{'_strand'}); # MZEF searches only one
	    if($predobj->strand() == 1) {
		$predobj->start($start);
		$predobj->end($end);
	    } else {
		$predobj->start($seqlen-$end+1);
		$predobj->end($seqlen-$start+1);
	    }
	    # set scores
	    $predobj->start_signal_score($flds[5]);
	    $predobj->end_signal_score($flds[7]);
	    $predobj->coding_signal_score($flds[6]);
	    # frame -- we simply extract the one with highest score from the
	    # orf field, and store the individual scores for now
	    my $frm = index($flds[4], "1");
	    $predobj->frame(($frm < 0) ? undef : $frm);
	    $predobj->primary_tag($exon_tag);
	    $predobj->is_coding(1);
	    # add to gene structure (should be done only when start and end
	    # are set, in order to allow for proper expansion of the range)
	    $gene->add_exon($predobj);		
	    next;
	}
	if(/^\s*Internal .*(MZEF)/) {
	    $self->analysis_method($1);
	    next;
	}
	if(/^\s*File_Name:\s+(\S+)\s+Sequence_length:\s+(\d+)/) {
	    # $seqname = $1; # this is too poor currently (file name truncated
                             # to 10 chars) in order to be sensible enough
	    $seqlen = $2;
	    next;
	}
    }
    # $gene->seq_id($seqname);
    $self->_add_prediction($gene) if defined($gene);
    $self->_predictions_parsed(1);
}

=head2 _prediction

 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :