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# $Id: hmmer.pm,v 1.34.4.1 2006/10/02 23:10:26 sendu Exp $
#
# BioPerl module for Bio::SearchIO::hmmer
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 55 lines of Pod
=head1 NAME
Bio::SearchIO::hmmer - A parser for HMMER output (hmmpfam, hmmsearch)
=head1 SYNOPSIS
    # do not use this class directly it is available through Bio::SearchIO
    use Bio::SearchIO;
    my $in = new Bio::SearchIO(-format => 'hmmer',
                               -file   => 't/data/L77119.hmmer');
    while( my $result = $in->next_result ) {
        # this is a Bio::Search::Result::HMMERResult object
        print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
        while( my $hit = $result->next_hit ) {
            print $hit->name(), "\n";
            while( my $hsp = $hit->next_hsp ) {
                print "length is ", $hsp->length(), "\n";
            }
        }
    }
=head1 DESCRIPTION
This object implements a parser for HMMER output.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list.  Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SearchIO::hmmer;
use strict;
use Bio::Factory::ObjectFactory;
use vars qw(%MAPPING %MODEMAP
);
use base qw(Bio::SearchIO);
BEGIN {
    # mapping of HMMER items to Bioperl hash keys
    %MODEMAP = (
        'HMMER_Output' => 'result',
        'Hit'          => 'hit',
        'Hsp'          => 'hsp'
    );
    %MAPPING = (
        'Hsp_bit-score'   => 'HSP-bits',
        'Hsp_score'       => 'HSP-score',
        'Hsp_evalue'      => 'HSP-evalue',
        'Hsp_query-from'  => 'HSP-query_start',
        'Hsp_query-to'    => 'HSP-query_end',
        'Hsp_hit-from'    => 'HSP-hit_start',
        'Hsp_hit-to'      => 'HSP-hit_end',
        'Hsp_positive'    => 'HSP-conserved',
        'Hsp_identity'    => 'HSP-identical',
        'Hsp_gaps'        => 'HSP-hsp_gaps',
        'Hsp_hitgaps'     => 'HSP-hit_gaps',
        'Hsp_querygaps'   => 'HSP-query_gaps',
        'Hsp_qseq'        => 'HSP-query_seq',
        'Hsp_hseq'        => 'HSP-hit_seq',
        'Hsp_midline'     => 'HSP-homology_seq',
        'Hsp_align-len'   => 'HSP-hsp_length',
        'Hsp_query-frame' => 'HSP-query_frame',
        'Hsp_hit-frame'   => 'HSP-hit_frame',
        'Hit_id'        => 'HIT-name',
        'Hit_len'       => 'HIT-length',
        'Hit_accession' => 'HIT-accession',
        'Hit_desc'      => 'HIT-description',
        'Hit_signif'    => 'HIT-significance',
        'Hit_score'     => 'HIT-score',
        'HMMER_program'   => 'RESULT-algorithm_name',
        'HMMER_version'   => 'RESULT-algorithm_version',
        'HMMER_query-def' => 'RESULT-query_name',
        'HMMER_query-len' => 'RESULT-query_length',
        'HMMER_query-acc' => 'RESULT-query_accession',
        'HMMER_querydesc' => 'RESULT-query_description',
        'HMMER_hmm'       => 'RESULT-hmm_name',
        'HMMER_seqfile'   => 'RESULT-sequence_file',
        'HMMER_db'        => 'RESULT-database_name',
    );
}
HideShow 11 lines of Pod
=head2 new
 Title   : new
 Usage   : my $obj = new Bio::SearchIO::hmmer();
 Function: Builds a new Bio::SearchIO::hmmer object 
 Returns : Bio::SearchIO::hmmer
 Args    : -fh/-file => HMMER filename
           -format   => 'hmmer'
=cut
sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my $handler = $self->_eventHandler;
    $handler->register_factory(
        'result',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::Result::HMMERResult',
            -interface => 'Bio::Search::Result::ResultI'
        )
    );
    $handler->register_factory(
        'hit',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::Hit::HMMERHit',
            -interface => 'Bio::Search::Hit::HitI'
        )
    );
    $handler->register_factory(
        'hsp',
        Bio::Factory::ObjectFactory->new(
            -type      => 'Bio::Search::HSP::HMMERHSP',
            -interface => 'Bio::Search::HSP::HSPI'
        )
    );
    $self->{'_hmmidline'} = 'HMMER 2.2g (August 2001)';
}
HideShow 10 lines of Pod
=head2 next_result
 Title   : next_result
 Usage   : my $hit = $searchio->next_result;
 Function: Returns the next Result from a search
 Returns : Bio::Search::Result::ResultI object
 Args    : none
=cut
sub next_result {
    my ($self) = @_;
    my $seentop = 0;
    my $reporttype;
    my ( $last, @hitinfo, @hspinfo, %hspinfo, %hitinfo );
    local $/ = "\n";
    local $_;
    my $verbose = $self->verbose;    # cache for speed?
    $self->start_document();
    local ($_);
    while ( defined( $_ = $self->_readline ) ) {
        my $lineorig = $_;
        chomp;
        if (/^HMMER\s+(\S+)\s+\((.+)\)/o) {
            my ( $prog, $version ) = split;
            if ($seentop) {
                $self->_pushback($_);
                $self->end_element( { 'Name' => 'HMMER_Output' } );
                return $self->end_document();
            }
            $self->{'_hmmidline'} = $_;
            $self->start_element( { 'Name' => 'HMMER_Output' } );
            $self->{'_result_count'}++;
            $seentop = 1;
            if ( defined $last ) {
                ($reporttype) = split( /\s+/, $last );
                $self->element(
                    {
                        'Name' => 'HMMER_program',
                        'Data' => uc($reporttype)
                    }
                );
            }
            $self->element(
                {
                    'Name' => 'HMMER_version',
                    'Data' => $version
                }
            );
        }
        elsif (s/^HMM file:\s+//o) {
            $self->{'_hmmfileline'} = $lineorig;
            $self->element(
                {
                    'Name' => 'HMMER_hmm',
                    'Data' => $_
                }
            );
        }
        elsif (s/^Sequence\s+(file|database):\s+//o) {
            $self->{'_hmmseqline'} = $lineorig;
            if ( $1 eq 'database' ) {
                $self->element(
                    {
                        'Name' => 'HMMER_db',
                        'Data' => $_
                    }
                );
            }
            $self->element(
                {
                    'Name' => 'HMMER_seqfile',
                    'Data' => $_
                }
            );
        }
        elsif (s/^Query(\s+(sequence|HMM))?(?:\s+\d+)?:\s+//o) {
            if ( !$seentop ) {
                # we're in a multi-query report
                $self->_pushback( $self->{'_hmmidline'} );
                $self->_pushback( $self->{'_hmmfileline'} );
                $self->_pushback( $self->{'_hmmseqline'} );
                $self->_pushback($lineorig);
                next;
            }
            s/\s+$//;
            $self->element(
                {
                    'Name' => 'HMMER_query-def',
                    'Data' => $_
                }
            );
        }
        elsif (s/^Accession:\s+//o) {
            s/\s+$//;
            $self->element(
                {
                    'Name' => 'HMMER_query-acc',
                    'Data' => $_
                }
            );
        }
        elsif (s/^Description:\s+//o) {
            s/\s+$//;
            $self->element(
                {
                    'Name' => 'HMMER_querydesc',
                    'Data' => $_
                }
            );
        }
        elsif ( defined $self->{'_reporttype'}
            && $self->{'_reporttype'} eq 'HMMSEARCH' )
        {
            # PROCESS HMMSEARCH RESULTS HERE
            if (/^Scores for complete sequences/o) {
                while ( defined( $_ = $self->_readline ) ) {
                    last if (/^\s+$/);
                    next if ( /^Sequence\s+Description/o || /^\-\-\-/o );
                    my @line = split;
                    my ( $name, $n, $evalue, $score ) =
                      ( shift @line, pop @line, pop @line, pop @line );
                    my $desc = join( ' ', @line );
                    push @hitinfo, [ $name, $desc, $evalue, $score ];
                    $hitinfo{$name} = $#hitinfo;
                }
            }
            elsif (/^Parsed for domains:/o) {
                @hspinfo = ();
                while ( defined( $_ = $self->_readline ) ) {
                    last if (/^\s+$/);
                    if (m!^//!) {
                        $self->_pushback($_);
                        last;
                    }
                    next if ( /^(Model|Sequence)\s+Domain/ || /^\-\-\-/ );
                    chomp;
                    if (
                        my ( $n, $domainnum, $domainct, @vals ) = (
                            m!^(\S+)\s+      # host name
                        (\d+)/(\d+)\s+   # num/num (ie 1 of 2) 
                        (\d+)\s+(\d+).+? # sequence start and end
                        (\d+)\s+(\d+)\s+ # hmm start and end
                        \S+\s+           # []
                        (\S+)\s+         # score
                        (\S+)            # evalue
                        \s*$!ox
                        )
                      )
                    {
                        # array lookup so that we can get rid of things
                        # when they've been processed
                        my $info = $hitinfo[ $hitinfo{$n} ];
                        if ( !defined $info ) {
                            $self->warn(
"Incomplete Sequence information, can't find $n hitinfo says $hitinfo{$n}"
                            );
                            next;
                        }
                        push @hspinfo, [ $n, @vals ];
                    }
                }
            }
            elsif (/^Alignments of top/o) {
                my ( $prelength, $lastdomain, $count, $width );
                $count = 0;
                my %domaincounter;
                my $second_tier = 0;
                while ( defined( $_ = $self->_readline ) ) {
                    next if ( /^Align/o
                        || /^\s+RF\s+[x\s]+$/o );
                    if ( /^Histogram/o || m!^//!o ) {
                        if ( $self->in_element('hsp') ) {
                            $self->end_element( { 'Name' => 'Hsp' } );
                        }
                        if ( $self->within_element('hit') ) {
                            $self->end_element( { 'Name' => 'Hit' } );
                        }
                        last;
                    }
                    chomp;
                    if (
                        m/^\s*(.+):\s+domain\s+(\d+)\s+of\s+(\d+)\,\s+
                        from\s+(\d+)\s+to\s+(\d+)/x
                      )
                    {
                        my ( $name, $domainct, $domaintotal, $from, $to ) =
                          ( $1, $2, $3, $4, $5 );
                        $domaincounter{$name}++;
                        if ( $self->within_element('hit') ) {
                            if ( $self->within_element('hsp') ) {
                                $self->end_element( { 'Name' => 'Hsp' } );
                            }
                            $self->end_element( { 'Name' => 'Hit' } );
                        }
                        $self->start_element( { 'Name' => 'Hit' } );
                        my $info = [
                            @{
                                $hitinfo[ $hitinfo{$name} ] || $self->throw(
"Could not find hit info for $name: Insure that your database contains only unique sequence names"
                                )
                              }
                        ];
                        if ( $info->[0] ne $name ) {
                            $self->throw(
"Somehow the Model table order does not match the order in the domains (got "
                                  . $info->[0]
                                  . ", expected $name)" );
                        }
                        $self->element(
                            {
                                'Name' => 'Hit_id',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hit_desc',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hit_signif',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hit_score',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->start_element( { 'Name' => 'Hsp' } );
                        $self->element(
                            {
                                'Name' => 'Hsp_identity',
                                'Data' => 0
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_positive',
                                'Data' => 0
                            }
                        );
                        my $HSPinfo = shift @hspinfo;
                        my $id      = shift @$HSPinfo;
                        if ( $id ne $name ) {
                            $self->throw(
"Somehow the domain list details do not match the table (got $id, expected $name)"
                            );
                        }
                        if ( $domaincounter{$name} == $domaintotal ) {
                            $hitinfo[ $hitinfo{$name} ] = undef;
                        }
                        $self->element(
                            {
                                'Name' => 'Hsp_hit-from',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_hit-to',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_query-from',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_query-to',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_score',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_evalue',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $lastdomain = $name;
                    }
                    else {
                        # Might want to change this so that it
                        # accumulates all the of the alignment lines into
                        # three array slots and then tests for the
                        # end of the line
                        if (/^(\s+\*\-\>)(\S+)/o) {    # start of domain
                            $prelength = CORE::length($1);
                            $width     = 0;
                            # $width = CORE::length($2);
                            $self->element(
                                {
                                    'Name' => 'Hsp_qseq',
                                    'Data' => $2
                                }
                            );
                            $count       = 0;
                            $second_tier = 0;
                        }
                        elsif (/^(\s+)(\S+)\<\-\*\s*$/o) {    #end of domain
                            $self->element(
                                {
                                    'Name' => 'Hsp_qseq',
                                    'Data' => $2
                                }
                            );
                            $width = CORE::length($2);
                            $count = 0;
                        }
                        elsif (( $count != 1 && /^\s+$/o )
                            || CORE::length($_) == 0
                            || /^\s+\-?\*\s*$/ )
                        {
                            next;
                        }
                        elsif ( $count == 0 ) {
                            $prelength -= 3 unless ( $second_tier++ );
                            unless ( defined $prelength ) {
                                # $self->warn("prelength not set");
                                next;
                            }
                            $self->element(
                                {
                                    'Name' => 'Hsp_qseq',
                                    'Data' => substr( $_, $prelength )
                                }
                            );
                        }
                        elsif ( $count == 1 ) {
                            if ( !defined $prelength ) {
                                $self->warn("prelength not set");
                            }
                            if ($width) {
                                $self->element(
                                    {
                                        'Name' => 'Hsp_midline',
                                        'Data' =>
                                          substr( $_, $prelength, $width )
                                    }
                                );
                            }
                            else {
                                $self->debug("midline is $_\n")
                                  if ( $verbose > 0
                                    && CORE::length($_) <= $prelength );
                                $self->element(
                                    {
                                        'Name' => 'Hsp_midline',
                                        'Data' => substr( $_, $prelength )
                                    }
                                );
                            }
                        }
                        elsif ( $count == 2 ) {
                            if (/^\s+(\S+)\s+(\d+|\-)\s+(\S*)\s+(\d+|\-)/o) {
                                $self->element(
                                    {
                                        'Name' => 'Hsp_hseq',
                                        'Data' => $3
                                    }
                                );
                            }
                            else {
                                $self->warn("unrecognized line: $_\n");
                            }
                        }
                        $count = 0 if $count++ >= 2;
                    }
                }
            }
            elsif ( /^Histogram/o || m!^//!o ) {
                while ( my $HSPinfo = shift @hspinfo ) {
                    my $id   = shift @$HSPinfo;
                    my $info = [ @{ $hitinfo[ $hitinfo{$id} ] } ];
                    next unless defined $info;
                    $self->start_element( { 'Name' => 'Hit' } );
                    $self->element(
                        {
                            'Name' => 'Hit_id',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hit_desc',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hit_signif',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hit_score',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->start_element( { 'Name' => 'Hsp' } );
                    $self->element(
                        {
                            'Name' => 'Hsp_query-from',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_query-to',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_hit-from',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_hit-to',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_score',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_evalue',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_identity',
                            'Data' => 0
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_positive',
                            'Data' => 0
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_positive',
                            'Data' => 0
                        }
                    );
                    $self->end_element( { 'Name' => 'Hsp' } );
                    $self->end_element( { 'Name' => 'Hit' } );
                }
                @hitinfo = ();
                %hitinfo = ();
                last;
            }
        }
        elsif ( defined $self->{'_reporttype'}
            && $self->{'_reporttype'} eq 'HMMPFAM' )
        {
            # process HMMPFAM results here
            if (/^Scores for sequence family/o) {
                while ( defined( $_ = $self->_readline ) ) {
                    last if (/^\s+$/);
                    next if ( /^Model\s+Description/o || /^\-\-\-/o );
                    chomp;
                    my @line = split;
                    my ( $model, $n, $evalue, $score ) =
                      ( shift @line, pop @line, pop @line, pop @line );
                    my $desc = join( ' ', @line );
                    push @hitinfo, [ $model, $desc, $score, $evalue, $n ];
                    $hitinfo{$model} = $#hitinfo;
                }
            }
            elsif (/^Parsed for domains:/o) {
                @hspinfo = ();
                while ( defined( $_ = $self->_readline ) ) {
                    last if (/^\s+$/);
                    if (m!^//!) {
                        $self->_pushback($_);
                        last;
                    }
                    next if ( /^Model\s+Domain/o || /^\-\-\-/o );
                    chomp;
                    if (
                        my ( $n, $domainnum, $domainct, @vals ) = (
                            m!^(\S+)\s+         # domain name
                            (\d+)/(\d+)\s+      # domain num out of num
                            (\d+)\s+(\d+).+?    # seq start, end
                            (\d+)\s+(\d+)\s+    # hmm start, end
                            \S+\s+              # []
                            (\S+)\s+            # score       
                            (\S+)               # evalue
                            \s*$!ox
                        )
                      )
                    {
                        my $hindex = $hitinfo{$n};
                        if ( !defined $hindex ) {
                            push @hitinfo,
                              [ $n, '', $vals[5], $vals[6], $domainct ];
                            $hitinfo{$n} = $#hitinfo;
                            $hindex = $#hitinfo;
                        }
                        my $info = $hitinfo[$hindex];
                        if ( !defined $info ) {
                            $self->warn(
"incomplete Domain information, can't find $n hitinfo says $hitinfo{$n}"
                            );
                            next;
                        }
                        push @hspinfo, [ $n, @vals ];
                    }
                }
            }
            elsif (/^Alignments of top/o) {
                my ( $prelength, $lastdomain, $count, $width );
                $count = 0;
                my $second_tier = 0;
                while ( defined( $_ = $self->_readline ) ) {
                    next
                      if (
                        /^Align/o
                        || ( $count != 1
                            && /^\s+RF\s+[x\s]+$/o )
                      );
                    $self->debug("$count $_") if $verbose > 0;
                    if ( /^Histogram/o || m!^//!o || /^Query sequence/o ) {
                        if ( $self->in_element('hsp') ) {
                            $self->end_element( { 'Name' => 'Hsp' } );
                        }
                        if ( $self->in_element('hit') ) {
                            $self->end_element( { 'Name' => 'Hit' } );
                        }
                        $self->_pushback($_);
                        last;
                    }
                    chomp;
                    if (m/(\S+):.*from\s+(\d+)\s+to\s+(\d+)/o) {
                        my ( $name, $from, $to ) = ( $1, $2, $3 );
                        if ( $self->within_element('hit') ) {
                            if ( $self->in_element('hsp') ) {
                                $self->end_element( { 'Name' => 'Hsp' } );
                            }
                            $self->end_element( { 'Name' => 'Hit' } );
                        }
                        my $info = [ @{ $hitinfo[ $hitinfo{$name} ] } ];
                        if ( !defined $info
                            || $info->[0] ne $name )
                        {
                            $self->warn(
"Somehow the Model table order does not match the order in the domains (got "
                                  . $info->[0]
                                  . ", expected $name). We're back loading this from the alignment information instead"
                            );
                            $info = [
                                $name, '',
                                /score\s+([^,\s]+),\s+E\s+=\s+(\S+)/ox
                            ];
                            push @hitinfo, $info;
                            $hitinfo{$name} = $#hitinfo;
                        }
                        $self->start_element( { 'Name' => 'Hit' } );
                        $self->element(
                            {
                                'Name' => 'Hit_id',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hit_desc',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hit_score',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hit_signif',
                                'Data' => shift @{$info}
                            }
                        );
                        $self->start_element( { 'Name' => 'Hsp' } );
                        $self->element(
                            {
                                'Name' => 'Hsp_identity',
                                'Data' => 0
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_positive',
                                'Data' => 0
                            }
                        );
                        my $HSPinfo = shift @hspinfo;
                        my $id      = shift @$HSPinfo;
                        if ( $id ne $name ) {
                            $self->throw(
"Somehow the domain list details do not match the table (got $id, expected $name)"
                            );
                        }
                        $self->element(
                            {
                                'Name' => 'Hsp_query-from',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_query-to',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_hit-from',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_hit-to',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_score',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $self->element(
                            {
                                'Name' => 'Hsp_evalue',
                                'Data' => shift @$HSPinfo
                            }
                        );
                        $lastdomain = $name;
                    }
                    else {
                        if (/^(\s+\*\-\>)(\S+)/o) {
                            # start of domain
                            $prelength = CORE::length($1);
                            $width     = 0;
                            # $width = CORE::length($2);
                            $self->element(
                                {
                                    'Name' => 'Hsp_hseq',
                                    'Data' => $2
                                }
                            );
                            $count       = 0;
                            $second_tier = 0;
                        }
                        elsif (/^(\s+)(\S+)\<\-?\*?\s*$/o) {
                            #end of domain
                            $prelength -= 3 unless ( $second_tier++ );
                            $self->element(
                                {
                                    'Name' => 'Hsp_hseq',
                                    'Data' => $2
                                }
                            );
                            $width = CORE::length($2);
                            $count = 0;
                        }
                        elsif (CORE::length($_) == 0
                            || ( $count != 1 && /^\s+$/o )
                            || /^\s+\-?\*\s*$/ )
                        {
                            next;
                        }
                        elsif ( $count == 0 ) {
                            $prelength -= 3 unless ( $second_tier++ );
                            unless ( defined $prelength ) {
                                # $self->warn("prelength not set");
                                next;
                            }
                            $self->element(
                                {
                                    'Name' => 'Hsp_hseq',
                                    'Data' => substr( $_, $prelength )
                                }
                            );
                        }
                        elsif ( $count == 1 ) {
                            if ( !defined $prelength ) {
                                $self->warn("prelength not set");
                            }
                            if ($width) {
                                $self->element(
                                    {
                                        'Name' => 'Hsp_midline',
                                        'Data' =>
                                          substr( $_, $prelength, $width )
                                    }
                                );
                            }
                            else {
                                $self->element(
                                    {
                                        'Name' => 'Hsp_midline',
                                        'Data' => substr( $_, $prelength )
                                    }
                                );
                            }
                        }
                        elsif ( $count == 2 ) {
                            if (   /^\s+(\S+)\s+(\d+)\s+(\S+)\s+(\d+)/o
                                || /^\s+(\S+)\s+(\-)\s+(\S*)\s+(\-)/o )
                            {
                                $self->element(
                                    {
                                        'Name' => 'Hsp_qseq',
                                        'Data' => $3
                                    }
                                );
                            }
                            else {
                                $self->throw(
                                    "unrecognized line ($count): $_\n");
                            }
                        }
                        $count = 0 if $count++ >= 2;
                    }
                }
            }
            elsif ( /^Histogram/o || m!^//!o ) {
                while ( my $HSPinfo = shift @hspinfo ) {
                    my $id   = shift @$HSPinfo;
                    my $info = [ @{ $hitinfo[ $hitinfo{$id} ] } ];
                    next unless defined $info;
                    $self->start_element( { 'Name' => 'Hit' } );
                    $self->element(
                        {
                            'Name' => 'Hit_id',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hit_desc',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hit_signif',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hit_score',
                            'Data' => shift @{$info}
                        }
                    );
                    $self->start_element( { 'Name' => 'Hsp' } );
                    $self->element(
                        {
                            'Name' => 'Hsp_query-from',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_query-to',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_hit-from',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_hit-to',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_score',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_evalue',
                            'Data' => shift @$HSPinfo
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_identity',
                            'Data' => 0
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_positive',
                            'Data' => 0
                        }
                    );
                    $self->element(
                        {
                            'Name' => 'Hsp_positive',
                            'Data' => 0
                        }
                    );
                    $self->end_element( { 'Name' => 'Hsp' } );
                    $self->end_element( { 'Name' => 'Hit' } );
                }
                @hitinfo = ();
                %hitinfo = ();
                last;
            }
            else {
                $self->debug($_) if $verbose > 0;
            }
        }
        $last = $_;
    }
    $self->end_element( { 'Name' => 'HMMER_Output' } ) unless !$seentop;
    return $self->end_document();
}
HideShow 11 lines of Pod
=head2 start_element
 Title   : start_element
 Usage   : $eventgenerator->start_element
 Function: Handles a start element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub start_element {
    my ( $self, $data ) = @_;
    # we currently don't care about attributes
    my $nm   = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    if ($type) {
        if ( $self->_eventHandler->will_handle($type) ) {
            my $func = sprintf( "start_%s", lc $type );
            $self->_eventHandler->$func( $data->{'Attributes'} );
        }
        unshift @{ $self->{'_elements'} }, $type;
    }
    if ( defined $type
        && $type eq 'result' )
    {
        $self->{'_values'} = {};
        $self->{'_result'} = undef;
    }
}
HideShow 11 lines of Pod
=head2 end_element
 Title   : start_element
 Usage   : $eventgenerator->end_element
 Function: Handles an end element event
 Returns : none
 Args    : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub end_element {
    my ( $self, $data ) = @_;
    my $nm   = $data->{'Name'};
    my $type = $MODEMAP{$nm};
    my $rc;
    if ( $nm eq 'HMMER_program' ) {
        if ( $self->{'_last_data'} =~ /(HMM\S+)/i ) {
            $self->{'_reporttype'} = uc $1;
        }
    }
    # Hsp are sort of weird, in that they end when another
    # object begins so have to detect this in end_element for now
    if ( $nm eq 'Hsp' ) {
        foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq)) {
            $self->element(
                {
                    'Name' => $_,
                    'Data' => $self->{'_last_hspdata'}->{$_}
                }
            );
        }
        $self->{'_last_hspdata'} = {};
    }
    if ($type) {
        if ( $self->_eventHandler->will_handle($type) ) {
            my $func = sprintf( "end_%s", lc $type );
            $rc = $self->_eventHandler->$func( $self->{'_reporttype'},
                $self->{'_values'} );
        }
        my $lastelem = shift @{ $self->{'_elements'} };
    }
    elsif ( $MAPPING{$nm} ) {
        if ( ref( $MAPPING{$nm} ) =~ /hash/i ) {
            my $key = ( keys %{ $MAPPING{$nm} } )[0];
            $self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } =
              $self->{'_last_data'};
        }
        else {
            $self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'};
        }
    }
    else {
        $self->debug("unknown nm $nm, ignoring\n");
    }
    $self->{'_last_data'} = '';    # remove read data if we are at
                                   # end of an element
    $self->{'_result'} = $rc if ( defined $type && $type eq 'result' );
    return $rc;
}
HideShow 11 lines of Pod
=head2 element
 Title   : element
 Usage   : $eventhandler->element({'Name' => $name, 'Data' => $str});
 Function: Convience method that calls start_element, characters, end_element
 Returns : none
 Args    : Hash ref with the keys 'Name' and 'Data'
=cut
sub element {
    my ( $self, $data ) = @_;
    $self->start_element($data);
    $self->characters($data);
    $self->end_element($data);
}
HideShow 11 lines of Pod
=head2 characters
 Title   : characters
 Usage   : $eventgenerator->characters($str)
 Function: Send a character events
 Returns : none
 Args    : string
=cut
sub characters {
    my ( $self, $data ) = @_;
    if (   $self->in_element('hsp')
        && $data->{'Name'} =~ /Hsp\_(qseq|hseq|midline)/o
        && defined $data->{'Data'} )
    {
        $self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'};
    }
    return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/o );
    $self->{'_last_data'} = $data->{'Data'};
}
HideShow 13 lines of Pod
=head2 within_element
 Title   : within_element
 Usage   : if( $eventgenerator->within_element($element) ) {}
 Function: Test if we are within a particular element
           This is different than 'in' because within can be tested
           for a whole block.
 Returns : boolean
 Args    : string element name 
=cut
sub within_element {
    my ( $self, $name ) = @_;
    return 0
      if ( !defined $name
        || !defined $self->{'_elements'}
        || scalar @{ $self->{'_elements'} } == 0 );
    foreach ( @{ $self->{'_elements'} } ) {
        return 1 if ( $_ eq $name );
    }
    return 0;
}
HideShow 13 lines of Pod
=head2 in_element
 Title   : in_element
 Usage   : if( $eventgenerator->in_element($element) ) {}
 Function: Test if we are in a particular element
           This is different than 'within' because 'in' only 
           tests its immediete parent.
 Returns : boolean
 Args    : string element name 
=cut
sub in_element {
    my ( $self, $name ) = @_;
    return 0 if !defined $self->{'_elements'}->[0];
    return ( $self->{'_elements'}->[0] eq $name );
}
HideShow 11 lines of Pod
=head2 start_document
 Title   : start_document
 Usage   : $eventgenerator->start_document
 Function: Handle a start document event
 Returns : none
 Args    : none
=cut
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'}   = {};
    $self->{'_result'}   = undef;
    $self->{'_elements'} = [];
}
HideShow 11 lines of Pod
=head2 end_document
 Title   : end_document
 Usage   : $eventgenerator->end_document
 Function: Handles an end document event
 Returns : Bio::Search::Result::ResultI object
 Args    : none
=cut
sub end_document {
    my ($self) = @_;
    return $self->{'_result'};
}
HideShow 11 lines of Pod
=head2 result_count
 Title   : result_count
 Usage   : my $count = $searchio->result_count
 Function: Returns the number of results we have processed
 Returns : integer
 Args    : none
=cut
sub result_count {
    my $self = shift;
    return $self->{'_result_count'};
}
1;