# 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) {
		print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
    }

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
	
	$self->_setup(@args);
	
	foreach my $field (qw( header hit_table hsp_table alignments next_model models query_length )) {
		$self->_fields->{$field} = undef;
	}
	
	$self->_dependencies( { ( query_name => 'header',
                              query_accession => 'header',
                              query_description => 'header',
                              hit_table => 'header',
							  num_hits => 'hit_table',
							  no_hits_found => 'hit_table',
                              hsp_table => 'hit_table',
                              next_alignment => 'hsp_table' ) } );
    
    return $self;

	my $self = shift;
	$self->_chunk_seek(0);
	my $header = $self->_get_chunk_by_end("all domains):\n");
	$self->{_after_header} = $self->_chunk_tell;
	
	$header || $self->throw("Could not find hmmer header, is file really hmmer format?");
	
	($self->_fields->{query_name}) = $header =~ /^Query(?:\s+sequence)?:\s+(\S+)/m;
	($self->_fields->{query_accession}) = $header =~ /^Accession:\s+(\S+)/m;
	($self->_fields->{query_description}) = $header =~ /^Description:\s+(\S.+)/m;
	$self->_fields->{query_accession} ||= '';
	$self->_fields->{query_description} ||= '';
	
	$self->_fields->{header} = 1; # stop this method being called again

	my $self = shift;
	
	$self->_chunk_seek($self->{_after_header});
	my $table = $self->_get_chunk_by_end("for domains:\n");
	$self->{_after_hit_table} = $self->_chunk_tell;
	
	my $evalue_cutoff = $self->get_field('evalue_cutoff');
	undef $evalue_cutoff if $evalue_cutoff eq '[unset]';
	my $score_cutoff = $self->get_field('score_cutoff');
	undef $score_cutoff if $score_cutoff eq '[unset]';
	my $hsps_cutoff = $self->get_field('hsps_cutoff');
	undef $hsps_cutoff if $hsps_cutoff eq '[unset]';
	
	my @table;
	my $no_hit = 1;
	while ($table =~ /^(\S+)\s+(\S.+?)?\s+(\S+)\s+(\S+)\s+(\d+)\n/gm) {
		$no_hit = 0;
		my $evalue = abs($4); # consistency for tests under Windows
		next if ($evalue_cutoff && $evalue > $evalue_cutoff);
		next if ($score_cutoff && $3 < $score_cutoff);
		next if ($hsps_cutoff && $5 < $hsps_cutoff);
		push(@table, [$1, $2, $3, $evalue, $5]);
	}
	$self->_fields->{hit_table} =\@ table;
	$self->{_next_hit_index} = @table > 0 ? 0 : -1;
	
	$self->_fields->{no_hits_found} = $no_hit;
	$self->_fields->{num_hits} = @table;

	my $self = shift;
	
	$self->_chunk_seek($self->{_after_hit_table});
	my $table = $self->_get_chunk_by_end("top-scoring domains:\n");
	$table ||= $self->_get_chunk_by_end("//\n"); # A0 reports
	$self->{_after_hsp_table} = $self->_chunk_tell;
	
	my %table;
	# can't save this regex work for the hsp object because the hit object needs
	# its length, so may as well just do all the work here
	while ($table =~ /^(\S+)\s+(\d+)\/\d+\s+(\d+)\s+(\d+)\s+\S\S\s+(\d+)\s+(\d+)\s+\S(\S)\s+(\S+)\s+(\S+)/gm) {
		# rank query_start query_end hit_start hit_end score evalue
		my $evalue = abs($9); # consistency for tests under Windows
		push(@{$table{$1}->{hsp_data}}, [$2, $3, $4, $5, $6, $8, $evalue]);
		if ($7 eq ']') {
			$table{$1}->{hit_length} = $6;
		}
	}
	$self->_fields->{hsp_table} =\% table;

	my $self = shift;
	$self->_fields->{alignments} = { };

	my $self = shift;;
	return if $self->{_no_more_alignments};
	
	my $aligns = $self->_fields->{alignments};
	
	unless (defined $self->{_after_previous_alignment}) {
		$self->_chunk_seek($self->{_after_hsp_table});
		my $chunk = $self->_get_chunk_by_end(": domain");
		unless ($chunk) {
			$self->{_no_more_alignments} = 1;
			return;
		}
		
		$self->{_after_previous_alignment} = $self->_chunk_tell;
		$self->{_next_alignment_start_text} = $chunk;
		$self->_next_alignment;
		return;
	}
	
	$self->_chunk_seek($self->{_after_previous_alignment});
	my $chunk = $self->_get_chunk_by_end(": domain");
	unless ($chunk) {
		$self->_chunk_seek($self->{_after_previous_alignment});
		$chunk = $self->_get_chunk_by_end("//");
		
		unless ($chunk) {
			$self->{_no_more_alignments} = 1;
			return;
		}
	}
	
	$self->{_after_previous_alignment} = $self->_chunk_tell;
	
	if (defined $self->{_next_alignment_start_text}) {
		$chunk = $self->{_next_alignment_start_text}.$chunk;
	}
	$chunk =~ s/(\S+: domain)$//;
	$self->{_next_alignment_start_text} = $1;
	
	my ($name, $domain) = $chunk =~ /^(\S+): domain (\d+)/;
	$aligns->{$name.'~~~~'.$domain} = $chunk;
	return 1;

	my $self = shift;
	my @hit_table = @{$self->get_field('hit_table')};
	return if $self->{_next_hit_index} == -1;
	
	#[name description score significance num_hsps rank]
	my @hit_data = (@{$hit_table[$self->{_next_hit_index}++]}, $self->{_next_hit_index});
	
	$self->_fields->{next_hit} = new Bio::Search::Hit::HmmpfamHit(-parent => $self,
																  -hit_data =>\@ hit_data);
	
	if ($self->{_next_hit_index} > $#hit_table) {
		$self->{_next_hit_index} = -1;
	}

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

	my $self = shift;
	my $old = $self->{_next_hit_index} || 0;
	$self->rewind;
	my @hits;
	while (defined(my $hit = $self->next_hit)) {
		push(@hits, $hit);
	}
	$self->{_next_hit_index} = @hits > 0 ? $old : -1;
	return @hits;

    my ($self, $code_ref) = @_;
	$code_ref ||= sub { $a->[3] <=> $b->[3] };
	
	# avoid creating hit objects just to sort, hence force user to sort on
	# the array references in hit table
	my $table_ref = $self->get_field('hit_table');
	@{$table_ref} > 1 || return;
	
	my @sorted = sort $code_ref @{$table_ref};
	@sorted == @{$table_ref} || $self->throw("Your sort routine failed to give back all hits!");
	$self->_fields->{hit_table} =\@ sorted;

	my $self = shift;
	unless ($self->_fields->{hit_table}) {
		$self->get_field('hit_table');
	}
	$self->{_next_hit_index} = @{$self->_fields->{hit_table}} > 0 ? 0 : -1;

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

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

 Title   : next_model
 Usage   : my $domain = $result->next_model
 Function: Returns the next domain - this is an alias for next_hit()
 Returns : Bio::Search::Hit::HitI object
 Args    : none

 Title   : models
 Usage   : my @domains = $result->models;
 Function: Returns the list of HMM models seen - this is an alias for hits()
 Returns : Array of Bio::Search::Hit::HitI objects
 Args    : none