Summary

Bio::SearchIO::SearchResultEventBuilder - 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.

Description

This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::SearchIO::SearchResultEventBuilder();
 Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object 
 Returns : Bio::SearchIO::SearchResultEventBuilder
 Args    :

 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_hsp
 Usage   : $handler->start_hsp($name,$data)
 Function: Begins processing a HSP event
 Returns : none
 Args    : type of element 
           associated data (hashref)

 Title   : end_hsp
 Usage   : $handler->end_hsp()
 Function: Finish processing a HSP event
 Returns : none
 Args    : type of event and associated hashref

 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

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  return $self;

}

sub will_handle {

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

}

sub start_result {

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

}

sub end_result {

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

    my $result = new Bio::Search::Result::GenericResult
	('-database_name'           => $data->{'dbname'},
	 '-database_letters'        => $data->{'dblets'},
	 '-database_entries'        => $data->{'dbsize'},
	 '-query_name'              => $data->{'queryname'},
	 '-query_length'            => $data->{'querylen'},
	 '-query_accession'         => $data->{'queryacc'},
	 '-query_description'       => $data->{'querydesc'},
	 
#	 '-program_name'            => $data->{'programname'},
#	 '-program_version'         => $data->{'programver'},
	 '-algorithm'              => $type,
	 '-algorithm_version'      => $data->{'programver'},	 
	 '-parameters'        => $data->{'param'},
	 '-statistics'        => $data->{'stat'},
	 '-hits'              => $self->{'_hits'});

    $self->{'_hits'} = [];
    return $result;

}

sub start_hsp {

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

}

sub end_hsp {

    my ($self,$type,$data) = @_;
    
    # this code is to deal with the fact that Blast XML data
    # always has start < end and one has to infer strandedness
    # from the frame which is a problem for the Search::HSP object
    # which expect to be able to infer strand from the order of 
    # of the begin/end of the query and hit coordinates

    if( defined $data->{'queryframe'} && # this is here to protect from undefs
	(( $data->{'queryframe'} < 0 && 
	   $data->{'querystart'} < $data->{'queryend'} ) ||       
	 $data->{'queryframe'} > 0 && 
	 ( $data->{'querystart'} > $data->{'queryend'} ) ) 
	)
    { 
	# swap
	($data->{'querystart'},
	 $data->{'queryend'}) = ($data->{'queryend'},				 $data->{'querystart'});
    } 
    if( defined $data->{'hitframe'} && # this is here to protect from undefs
	((defined $data->{'hitframe'} && $data->{'hitframe'} < 0 && 
	  $data->{'hitstart'} < $data->{'hitend'} ) ||       
	 defined $data->{'hitframe'} && $data->{'hitframe'} > 0 && 
	 ( $data->{'hitstart'} > $data->{'hitend'} ) )
	) 
    { 
	# swap
	($data->{'hitstart'},
	 $data->{'hitend'}) = ($data->{'hitend'},
			       $data->{'hitstart'});
    }
    $data->{'queryframe'} ||= 0;
    $data->{'hitframe'} ||= 0;
    # handle Blast 2.1.2 which did not support data member: hsp_align-len
    
    $data->{'querylen'} ||= length $data->{'queryseq'};
    $data->{'hitlen'}   ||= length $data->{'hitseq'};
    $data->{'hsplen'}   ||= length $data->{'homolseq'};
    

    my $hsp = new Bio::Search::HSP::GenericHSP
	(
	 '-algorithm'     => $type,
	 '-score'         => $data->{'score'} || $data->{'swscore'},
	 '-bits'          => $data->{'bits'},
	 '-identical'     => $data->{'identical'},
	 '-hsp_length'    => $data->{'hsplen'},
	 '-conserved'     => $data->{'conserved'},
	 '-hsp_gaps'      => $data->{'gaps'},
	 '-hit_gaps'      => $data->{'hitgaps'},
	 '-query_gaps'    => $data->{'querygaps'},
	 '-evalue'        => $data->{'evalue'},
	 '-pvalue'        => $data->{'pvalue'},
	 '-query_start'   => $data->{'querystart'},
	 '-query_end'     => $data->{'queryend'},
	 '-hit_start'     => $data->{'hitstart'},
	 '-hit_end'       => $data->{'hitend'},
	 '-query_seq'     => $data->{'queryseq'},
	 '-hit_seq'       => $data->{'hitseq'},
	 '-homology_seq'  => $data->{'homolseq'},
	 '-query_length'  => $data->{'querylen'},
	 '-hit_length'    => $data->{'hitlen'},
	 '-query_name'    => $data->{'queryname'},
	 '-hit_name'      => $data->{'hitname'},
	 '-query_frame'   => $data->{'queryframe'},
	 '-hit_frame'     => $data->{'hitframe'},
	 );
    push @{$self->{'_hsps'}}, $hsp;
    return $hsp;

}

sub start_hit {

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

}

sub end_hit {

   my ($self,$type,$data) = @_;   
    my $hit = new Bio::Search::Hit::GenericHit
	( '-algorithm' => $type,
	  '-name'        => $data->{'hitname'}, 
	  '-length'      => $data->{'hitlen'},
	  '-accession'   => $data->{'hitacc'},
	  '-description' => $data->{'hitdesc'},
	  '-significance'=> $data->{'hitsignif'},
	  '-score'       => $data->{'hitscore'},
	  '-hsps'        => $self->{'_hsps'});
   push @{$self->{'_hits'}}, $hit;
   $self->{'_hsps'} = [];
   return $hit;

}

General documentation

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Email jason@bioperl.org
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Additional contributors names and emails here

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