Raw content of Bio::SearchIO::hmmer # $Id: hmmer.pm,v 1.13.2.3 2003/08/07 15:40:36 jason 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 =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/MailList.shtml - 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 email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut package Bio::SearchIO::hmmer; use vars qw(@ISA); use strict; use vars qw(@ISA %MAPPING %MODEMAP $DEFAULT_HSP_FACTORY_CLASS $DEFAULT_HIT_FACTORY_CLASS $DEFAULT_RESULT_FACTORY_CLASS ); use Bio::SearchIO; use Bio::Factory::ObjectFactory; @ISA = 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', ); $DEFAULT_HIT_FACTORY_CLASS = 'Bio::Factory::HMMERHitFactory'; $DEFAULT_HSP_FACTORY_CLASS = 'Bio::Factory::HMMERHSPFactory'; $DEFAULT_RESULT_FACTORY_CLASS = 'Bio::Factory::HMMERResultFactory'; } =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; # new object initialization code $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)'; } =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); my @alignemnt_lines; $self->start_document(); while( defined ($_ = $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; $self->element({'Name' => 'HMMER_seqfile', 'Data' => $_}); } elsif( s/^Query(\s+(sequence|HMM))?:\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} = $#hitinfo; } } elsif( /^Parsed for domains:/o ) { @hspinfo = (); while( defined($_ = $self->_readline) ) { last if( /^\s+$/); next if( /^(Model|Sequence)\s+Domain/o || /^\-\-\-/o ); 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')) { $self->end_element({'Name' => 'Hit'}); } last; } chomp; if( /^\s*(.+):\s+domain\s+(\d+)\s+of\s+(\d+)\,\s+from\s+(\d+)\s+to\s+(\d+)/o ) { my ($name,$domainct,$domaintotal, $from,$to) = ($1,$2,$3,$4,$5); $domaincounter{$name}++; if( ! defined $lastdomain || $lastdomain ne $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->end_element({'Name' => 'Hsp'}) if $self->in_element('hsp'); $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 $_\n") if( CORE::length($_) <= $prelength && $self->verbose > 0); $self->element({'Name' => 'Hsp_midline', 'Data' => substr($_, $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'} && $self->{'_reporttype'} eq 'HMMPFAM' ) { if( /^Scores for sequence family/o ) { while( defined($_ = $self->_readline) ) { last if( /^\s+$/); 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} = $#hitinfo; } } elsif( /^Parsed for domains:/o ) { @hspinfo = (); while( defined($_ = $self->_readline) ) { last if( /^\s+$/); next if( /^Model\s+Domain/o || /^\-\-\-/o ); chomp; if( my ($n,$domainnum,$domainct,@vals) = (m!^(\S+)\s+ # domain name \s+(\d+)/(\d+)\s+ # domain num out of num (\d+)\s+(\d+).+? # seq start, end (\d+)\s+(\d+)\s+ # hmm start, end \S+\s+ # [] (\S+)\s+ # score (\S+) # evalue \s*$!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 $second_tier=0; while( defined($_ = $self->_readline) ) { next if( /^Align/o || /^\s+RF\s+[x\s]+$/o); 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->end_element({'Name' => 'HMMER_Output'}); if( /^Query sequence/o ) { $self->_pushback($_); } return $self->end_document(); last; } chomp; if( m/(\S+):.*from\s+(\d+)\s+to\s+(\d+)/o ) { my ($name,$from,$to) = ($1,$2,$3); if( ! defined $lastdomain || $lastdomain ne $name ) { if( $self->within_element('hit') ) { if( $self->in_element('hsp') ) { $self->end_element({'Name' => 'Hsp'}); } $self->end_element({'Name' => 'Hit'}); } $self->start_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; } $self->element({'Name' => 'Hit_id', 'Data' => shift @{$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}}); } if( $self->within_element('hsp') ) { #if( defined $lastdomain ) { $self->end_element({'Name' => 'Hsp'}); } $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 { $self->warn("unrecognized line ($count): $_\n"); } } $count = 0 if $count++ >= 2; } } } else { $self->debug($_); } } $last = $_; } $self->end_element({'Name' => 'HMMER_Output'}) unless ! $seentop; return $self->end_document(); } =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; } } =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; } =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); } =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'}; } =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; } =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) } =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'} = []; } =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'}; } =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;