# generally we use Bio::SearchIO to build these objects
    use Bio::SearchIO;
    my $in = new Bio::SearchIO(-format => 'hmmer_pull',
							   -file   => 'result.hmmer');

    while (my $result = $in->next_result) {
		while (my $hit = $result->next_hit) {
			print $hit->name, "\n";
			print $hit->score, "\n";
			print $hit->significance, "\n";

			while (my $hsp = $hit->next_hsp) {
				# process HSPI objects
			}
		}
    }

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
	
	$self->_setup(@args);
	
	my $fields = $self->_fields;
	foreach my $field (qw( next_domain domains hsp_data )) {
		$fields->{$field} = undef;
	}
	
	my $hit_data = $self->_raw_hit_data;
	if ($hit_data && ref($hit_data) eq 'ARRAY') {
		foreach my $field (qw(name description score significance num_hsps rank)) {
			$fields->{$field} = shift(@{$hit_data});
		}
	}
	$fields->{hit_start} = 1;
	
	delete $self->_fields->{accession};
	
	$self->_dependencies( { ( length => 'hsp_data' ) } );
	
    return $self;

	# this should be set when this object is created, but if it was undef as is
	# possible, this _discover method will be called: just return and keep the
	# return value undef
	return;

	my $self = shift;
	my $hsp_table = $self->get_field('hsp_table');
	my $hsp_data = $hsp_table->{$self->get_field('name')} || undef;
	if ($hsp_data) {
		if (defined $hsp_data->{hit_length}) {
			$self->_fields->{length} = $hsp_data->{hit_length};
		}
		
		# rank query_start query_end hit_start hit_end score evalue
		$self->_fields->{hsp_data} = $hsp_data->{hsp_data};
	}

	my $self = shift;
	my $hsp_data = $self->get_field('hsp_data') || return;
	
	my ($this_hsp) = sort { $a->[1] <=> $b->[1] } @{$hsp_data};
	$self->_fields->{query_start} = $this_hsp->[1];

	my $self = shift;
	my $hsp_data = $self->get_field('hsp_data') || return;
	
	my ($this_hsp) = sort { $b->[2] <=> $a->[2] } @{$hsp_data};
	$self->_fields->{query_end} = $this_hsp->[2];

	my $self = shift;
	my $hsp_data = $self->get_field('hsp_data') || return;
	
	my ($this_hsp) = sort { $a->[3] <=> $b->[3] } @{$hsp_data};
	$self->_fields->{hit_start} = $this_hsp->[3];

	my $self = shift;
	my $hsp_data = $self->get_field('hsp_data') || return;
	
	my ($this_hsp) = sort { $b->[4] <=> $a->[4] } @{$hsp_data};
	$self->_fields->{hit_end} = $this_hsp->[4];

	my $self = shift;
	my $hsp_data = $self->get_field('hsp_data') || return;
	unless (defined $self->{_next_hsp_index}) {
		$self->{_next_hsp_index} = 0;
	}
	return if $self->{_next_hsp_index} == -1;
	
	$self->_fields->{next_hsp} = new Bio::Search::HSP::HmmpfamHSP(-parent => $self,
																  -hsp_data => $hsp_data->[$self->{_next_hsp_index}++]);
	
	if ($self->{_next_hsp_index} > $#{$hsp_data}) {
		$self->{_next_hsp_index} = -1;
	}

    my $self = shift;
    my $hsp = $self->get_field('next_hsp');
	undef $self->_fields->{next_hsp};
	return $hsp;

    my $self = shift;
	my $old = $self->{_next_hsp_index} || 0;
	$self->rewind;
	my @hsps;
	while (defined(my $hsp = $self->next_hsp)) {
		push(@hsps, $hsp);
	}
	$self->{_next_hsp_index} =  @hsps > 0 ? $old : -1;
	return @hsps;

    my ($self, $type) = @_;
	$type ||= 'best';
	my $hsp_data = $self->get_field('hsp_data') || return;
	
	my $sort;
	if ($type eq 'best') {
		$sort = sub { $a->[6] <=> $b->[6] };
	}
	elsif ($type eq 'worst') {
		$sort = sub { $b->[6] <=> $a->[6] };
	}
	else {
		$self->throw("Unknown arg '$type' given to hsp()");
	}
	
	my ($this_hsp) = sort $sort @{$hsp_data};
	return new Bio::Search::HSP::HmmpfamHSP(-parent => $self, -hsp_data => $this_hsp);

	my $self = shift;
	my $hsp_data = $self->get_field('hsp_data') || return;
	$self->{_next_hsp_index} = @{$hsp_data} > 0 ? 0 : -1;

	return shift->significance;

    my ($self, $type) = @_;
	$type ||= (wantarray ? 'list' : 'query');
    $type = lc($type);
	if ($type eq 'list' || $type eq 'array') {
		return (1, 1);
	}
	return 1;

    return undef;

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  http://bugzilla.open-bio.org/

 Title   : next_domain 
 Usage   : my $domain = $hit->next_domain();
 Function: An alias for next_hsp(), this will return the next HSP
 Returns : Bio::Search::HSP::HSPI object
 Args    : none

 Title   : domains
 Usage   : my @domains = $hit->domains();
 Function: An alias for hsps(), this will return the full list of hsps
 Returns : array of Bio::Search::HSP::HSPI objects
 Args    : none