Summary

Bio::SearchIO::FastHitEventBuilder - Event Handler for SearchIO events.

Package variables

Included modules

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

Methods description

 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

 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

 Title   : start_result
 Usage   : $handler->start_result($resulttype)
 Function: Begins a result event cycle
 Returns : none 
 Args    : Type of Report

 Title   : end_result
 Usage   : my @results = $parser->end_result
 Function: Finishes a result handler cycle Returns : A Bio::Search::Result::ResultI
 Args    : none

 Title   : start_hit
 Usage   : $handler->start_hit()
 Function: Starts a Hit event cycle
 Returns : none
 Args    : type of event and associated hashref

 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

 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

 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

Methods code

sub new {

     my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($hitF,$resultF) = $self->_rearrange([qw(HIT_FACTORY
						      RESULT_FACTORY)],@args);
    $self->register_factory('hit', $hitF ||
                            Bio::Factory::ObjectFactory->new(
                                      -type      => 'Bio::Search::Hit::GenericHit',
                                      -interface => 'Bio::Search::Hit::HitI'));

    $self->register_factory('result', $resultF ||
                            Bio::Factory::ObjectFactory->new(
                                      -type      => 'Bio::Search::Result::GenericResult',
                                      -interface => 'Bio::Search::Result::ResultI'));

    return $self;

}

sub will_handle {

   my ($self,$type) = @_;
   # these are the events we recognize
   return ( $type eq 'hit' || $type eq 'result' );

}

sub start_result {

   my ($self,$type) = @_;
   $self->{'_resulttype'} = $type;
   $self->{'_hits'} = [];
   return;

}

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;

}

sub start_hit {

    my ($self,$type) = @_;
    return;

}

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;

}

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;

}

sub factory {

   my ($self,$type) = @_;
   return $self->{'_factories'}->{lc($type)} || $self->throw("No factory registered for $type");

}

sub inclusion_threshold {

    my $self = shift;
    return $self->{'_inclusion_threshold'} = shift if @_;
    return $self->{'_inclusion_threshold'};

}

General documentation

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

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/

Email jason-at-bioperl.org

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _