Bio::SearchIO SearchResultEventBuilder
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Summary
Bio::SearchIO::SearchResultEventBuilder - Event Handler for SearchIO events.
Package variables
No package variables defined.
Included modules
Bio::Factory::ObjectFactory
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
newDescriptionCode
will_handleDescriptionCode
start_resultDescriptionCode
end_resultDescriptionCode
start_hspDescriptionCode
end_hspDescriptionCode
start_hitDescriptionCode
end_hitDescriptionCode
_add_hit
No description
Code
register_factoryDescriptionCode
factoryDescriptionCode
inclusion_thresholdDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::SearchIO::SearchResultEventBuilder->new();
Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object
Returns : Bio::SearchIO::SearchResultEventBuilder
Args : -hsp_factory => Bio::Factory::ObjectFactoryI
-hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
See Bio::Factory::ObjectFactoryI for more information
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
start_resultcodeprevnextTop
 Title   : start_result
Usage : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args : Type of Report
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
start_hspcodeprevnextTop
 Title   : start_hsp
Usage : $handler->start_hsp($name,$data)
Function: Begins processing a HSP event
Returns : none
Args : type of element
associated data (hashref)
end_hspcodeprevnextTop
 Title   : end_hsp
Usage : $handler->end_hsp()
Function: Finish processing a HSP event
Returns : none
Args : type of event and associated hashref
start_hitcodeprevnextTop
 Title   : start_hit
Usage : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args : type of event and associated hashref
end_hitcodeprevnextTop
 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
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
factorycodeprevnextTop
 Title   : factory
Usage : my $f = $handler->factory('TYPE');
Function: Retrieves the associated factory for requested 'TYPE'
Returns : a Bio::Factory::ObjectFactoryI
Throws : Bio::Root::BadParameter if none registered for the supplied type
Args : name of factory class to retrieve
See Bio::Factory::ObjectFactoryI for more information
inclusion_thresholdcodeprevnextTop
See Bio::SearchIO::blast::inclusion_threshold.
Methods code
newdescriptionprevnextTop
sub new {
     my ($class,@args) = @_;
    my $self = $class->SUPER::new(@args);
    my ($hspF,$hitF,$resultF) = $self->_rearrange([qw(HSP_FACTORY
                                                      HIT_FACTORY
                                                      RESULT_FACTORY)],@args);
    $self->register_factory('hsp', $hspF || 
                            Bio::Factory::ObjectFactory->new(
                                     -type      => 'Bio::Search::HSP::GenericHSP',
                                     -interface => 'Bio::Search::HSP::HSPI'));

    $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;
}

# new comes from the superclass
}
will_handledescriptionprevnextTop
sub will_handle {
   my ($self,$type) = @_;
   # these are the events we recognize
return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' );
}
start_resultdescriptionprevnextTop
sub start_result {
   my ($self,$type) = @_;
   $self->{'_resulttype'} = $type;
   $self->{'_hits'} = [];   
   $self->{'_hsps'} = [];
   $self->{'_hitcount'} = 0;
   return;
}
end_resultdescriptionprevnextTop
sub end_result {
    my ($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'} || $data->{'RESULT-algorithm_name'} || $type); $args{'-hits'} = $self->{'_hits'}; my $result = $self->factory('result')->create_object(%args); $result->hit_factory($self->factory('hit')); $self->{'_hits'} = []; return $result;
}
start_hspdescriptionprevnextTop
sub start_hsp {
    my ($self,@args) = @_;
    return;
}
end_hspdescriptionprevnextTop
sub end_hsp {
    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'}; } # 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->{'HSP-query_frame'} && # this is here to protect from undefs
(( $data->{'HSP-query_frame'} < 0 && $data->{'HSP-query_start'} < $data->{'HSP-query_end'} ) || $data->{'HSP-query_frame'} > 0 && ( $data->{'HSP-query_start'} > $data->{'HSP-query_end'} ) ) ) { # swap
($data->{'HSP-query_start'}, $data->{'HSP-query_end'}) = ($data->{'HSP-query_end'}, $data->{'HSP-query_start'}); } if( defined $data->{'HSP-hit_frame'} && # this is here to protect from undefs
((defined $data->{'HSP-hit_frame'} && $data->{'HSP-hit_frame'} < 0 && $data->{'HSP-hit_start'} < $data->{'HSP-hit_end'} ) || defined $data->{'HSP-hit_frame'} && $data->{'HSP-hit_frame'} > 0 && ( $data->{'HSP-hit_start'} > $data->{'HSP-hit_end'} ) ) ) { # swap
($data->{'HSP-hit_start'}, $data->{'HSP-hit_end'}) = ($data->{'HSP-hit_end'}, $data->{'HSP-hit_start'}); } $data->{'HSP-query_frame'} ||= 0; $data->{'HSP-hit_frame'} ||= 0; # handle Blast 2.1.2 which did not support data member: hsp_align-len
$data->{'HSP-query_length'} ||= $data->{'RESULT-query_length'}; $data->{'HSP-query_length'} ||= length ($data->{'HSP-query_seq'} || ''); $data->{'HSP-hit_length'} ||= $data->{'HIT-length'}; $data->{'HSP-hit_length'} ||= length ($data->{'HSP-hit_seq'} || ''); $data->{'HSP-hsp_length'} ||= length ($data->{'HSP-homology_seq'} || ''); my %args = map { my $v = $data->{$_}; s/HSP//; ($_ => $v) } grep { /^HSP/ } keys %{$data}; $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $data->{'RESULT-algorithm_name'} || $type); # copy this over from result
$args{'-query_name'} = $data->{'RESULT-query_name'}; $args{'-hit_name'} = $data->{'HIT-name'}; my ($rank) = scalar @{$self->{'_hsps'} || []} + 1; $args{'-rank'} = $rank; $args{'-hit_desc'} = $data->{'HIT-description'}; $args{'-query_desc'} = $data->{'RESULT-query_description'}; my $bits = $args{'-bits'}; my $hsp =\% args; push @{$self->{'_hsps'}}, $hsp; return $hsp;
}
start_hitdescriptionprevnextTop
sub start_hit {
    my ($self,$type) = @_;
    $self->{'_hsps'} = [];
    return;
}
end_hitdescriptionprevnextTop
sub end_hit {
    my ($self,$type,$data) = @_;   
    my %args = map { my $v = $data->{$_}; s/HIT//; ($_ => $v); } grep { /^HIT/ } keys %{$data};

    # I hate special cases, but this is here because NCBI BLAST XML
# doesn't play nice and is undergoing mutation -jason
if(exists $args{'-name'} && $args{'-name'} =~ /BL_ORD_ID/ ) { ($args{'-name'}, $args{'-description'}) = split(/\s+/,$args{'-description'},2); } $args{'-algorithm'} = uc( $args{'-algorithm_name'} || $data->{'RESULT-algorithm_name'} || $type); $args{'-hsps'} = $self->{'_hsps'}; $args{'-query_len'} = $data->{'RESULT-query_length'}; $args{'-rank'} = $self->{'_hitcount'} + 1; unless( defined $args{'-significance'} ) { if( defined $args{'-hsps'} && $args{'-hsps'}->[0] ) { # use pvalue if present (WU-BLAST), otherwise evalue (NCBI BLAST)
$args{'-significance'} = $args{'-hsps'}->[0]->{'-pvalue'} || $args{'-hsps'}->[0]->{'-evalue'}; } } my $hit =\% args; $hit->{'-hsp_factory'} = $self->factory('hsp'); $self->_add_hit($hit); $self->{'_hsps'} = []; return $hit; } # TODO: Optionally impose hit filtering here
}
_add_hitdescriptionprevnextTop
sub _add_hit {
    my ($self, $hit) = @_;
    push @{$self->{'_hits'}}, $hit;
    $self->{'_hitcount'} = scalar @{$self->{'_hits'}};
}
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)} = $f;
}
factorydescriptionprevnextTop
sub factory {
   my ($self,$type) = @_;
   return $self->{'_factories'}->{lc($type)} || 
       $self->throw(-class=>'Bio::Root::BadParameter',
                    -text=>"No factory registered for $type");
}
inclusion_thresholddescriptionprevnextTop
sub inclusion_threshold {
    my $self = shift;
    return $self->{'_inclusion_threshold'} = shift if @_;
    return $self->{'_inclusion_threshold'};
}

1;
}
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/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl.org
CONTRIBUTORSTop
Sendu Bala, bix@sendu.me.uk
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
SAX methodsTop
Factory methodsTop