Bio::SearchIO FastHitEventBuilder
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Summary
Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Search::HSP::HSPFactory
Bio::Search::Hit::HitFactory
Bio::Search::Result::ResultFactory
Bio::SearchIO::EventHandlerI
Inherit
Bio::Root::Root Bio::SearchIO::EventHandlerI
Synopsis
  # Do not use this object directly, this object is part of the SearchIO
# event based parsing system.
# to use the FastHitEventBuilder do this use Bio::SearchIO::FastHitEventBuilder; my $searchio = new Bio::SearchIO(-format => $format, -file => $file); $searchio->attach_EventHandler(new Bio::SearchIO::FastHitEventBuilder); while( my $r = $searchio->next_result ) { while( my $h = $r->next_hit ) { # note that Hits will NOT have HSPs } }
Description
This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them. This object
is intended for lightweight parsers which only want Hits and not deal
with the overhead of HSPs. It is a lot faster than the standard
parser event handler but of course you are getting less information
and less objects out.
Methods
end_hitDescriptionCode
end_resultDescriptionCode
factoryDescriptionCode
newDescriptionCode
register_factoryDescriptionCode
start_hitDescriptionCode
start_resultDescriptionCode
will_handleDescriptionCode
Methods description
end_hitcode    nextTop
 Title   : end_hit
Usage : $handler->end_hit()
Function: Ends a Hit event cycle
Returns : Bio::Search::Hit::HitI object
Args : type of event and associated hashref
end_resultcodeprevnextTop
 Title   : end_result
Usage : my @results = $parser->end_result
Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI
Args : none
factorycodeprevnextTop
 Title   : factory
Usage : my $f = $handler->factory('TYPE');
Function: Retrieves the associated factory for requested 'TYPE'
Returns : a Bio::Factory::ObjectFactoryI or undef if none registered
Args : name of factory class to retrieve
See Bio::Factory::ObjectFactoryI for more information
newcodeprevnextTop
 Title   : new
Usage : my $obj = new Bio::SearchIO::FastHitEventBuilder();
Function: Builds a new Bio::SearchIO::FastHitEventBuilder object
Returns : Bio::SearchIO::FastHitEventBuilder
Args : -hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
See Bio::Factory::ObjectFactoryI for more information
register_factorycodeprevnextTop
 Title   : register_factory
Usage : $handler->register_factory('TYPE',$factory);
Function: Register a specific factory for a object type class
Returns : none
Args : string representing the class and
Bio::Factory::ObjectFactoryI
See Bio::Factory::ObjectFactoryI for more information
start_hitcodeprevnextTop
 Title   : start_hit
Usage : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args : type of event and associated hashref
start_resultcodeprevnextTop
 Title   : start_result
Usage : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args : Type of Report
will_handlecodeprevnextTop
 Title   : will_handle
Usage : if( $handler->will_handle($event_type) ) { ... }
Function: Tests if this event builder knows how to process a specific event
Returns : boolean
Args : event type name
Methods code
end_hitdescriptionprevnextTop
sub end_hit {
    my ($self,$type,$data) = @_;   
    my %args = map { my $v = $data->{$_}; s/HIT//; ($_ => $v); } grep { /^HIT/ } keys %{$data};
    $args{'-algorithm'} =  uc( $args{'-algorithm_name'} || $type);
    $args{'-query_len'} =  $data->{'RESULT-query_length'};
    my ($hitrank) = scalar @{$self->{'_hits'}} + 1;
    $args{'-rank'} = $hitrank;
    my $hit = $self->factory('hit')->create(%args);
    push @{$self->{'_hits'}}, $hit;
    $self->{'_hsps'} = [];
    return $hit;
}
end_resultdescriptionprevnextTop
sub end_result {
    my ($self,$type,$data) = @_;    
    if( defined $data->{'runid'} &&
	$data->{'runid'} !~ /^\s+$/ ) {	
	
	if( $data->{'runid'} !~ /^lcl\|/) { 
	    $data->{"RESULT-query_name"}= $data->{'runid'};
	} else { 
	    ($data->{"RESULT-query_name"},$data->{"RESULT-query_description"}) = split(/\s+/,$data->{"RESULT-query_description"},2);
	}
	
	if( my @a = split(/\|/,$data->{'RESULT-query_name'}) ) {
	    my $acc = pop @a ; # this is for accession |1234|gb|AAABB1.1|AAABB1
# this is for |123|gb|ABC1.1|
$acc = pop @a if( ! defined $acc || $acc =~ /^\s+$/); $data->{"RESULT-query_accession"}= $acc; } delete $data->{'runid'}; } my %args = map { my $v = $data->{$_}; s/RESULT//; ($_ => $v); } grep { /^RESULT/ } keys %{$data}; $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $type); $args{'-hits'} = $self->{'_hits'}; my $result = $self->factory('result')->create(%args); $self->{'_hits'} = []; return $result;
}
factorydescriptionprevnextTop
sub factory {
   my ($self,$type) = @_;
   return $self->{'_factories'}->{lc($type)} || $self->throw("No factory registered for $type");
}

1;
}
newdescriptionprevnextTop
sub new {
     my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($hspF,$hitF,$resultF) = $self->_rearrange([qw(HIT_FACTORY
						      RESULT_FACTORY)],@args);
    $self->register_factory('hit', $hitF || Bio::Search::Hit::HitFactory->new());
    $self->register_factory('result', $resultF || Bio::Search::Result::ResultFactory->new());

    return $self;
}

# new comes from the superclass
}
register_factorydescriptionprevnextTop
sub register_factory {
   my ($self, $type,$f) = @_;
   if( ! defined $f || ! ref($f) || 
       ! $f->isa('Bio::Factory::ObjectFactoryI') ) { 
       $self->throw("Cannot set factory to value $f".ref($f)."\n");
   }
   $self->{'_factories'}->{lc($type)} = $f;
}
start_hitdescriptionprevnextTop
sub start_hit {
    my ($self,$type) = @_;
    return;
}
start_resultdescriptionprevnextTop
sub start_result {
   my ($self,$type) = @_;
   $self->{'_resulttype'} = $type;
   $self->{'_hits'} = [];
   return;
}
will_handledescriptionprevnextTop
sub will_handle {
   my ($self,$type) = @_;
   # these are the events we recognize
return ( $type eq 'hit' || $type eq 'result' );
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Reporting BugsTop
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/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
SAX methodsTop
Factory methodsTop