Raw content of Bio::SearchIO::SearchResultEventBuilder
<![CDATA[# $Id: SearchResultEventBuilder.pm,v 1.25.2.1 2003/01/17 20:32:54 jason Exp $
#
# BioPerl module for Bio::SearchIO::SearchResultEventBuilder
#
# 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::SearchResultEventBuilder - Event Handler for SearchIO events.
=head1 SYNOPSIS
# Do not use this object directly, this object is part of the SearchIO
# event based parsing system.
=head1 DESCRIPTION
This object handles Search Events generated by the SearchIO classes
and build appropriate Bio::Search::* objects from them.
=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
# Let the code begin...
package Bio::SearchIO::SearchResultEventBuilder;
use vars qw(@ISA %KNOWNEVENTS);
use strict;
use Bio::Root::Root;
use Bio::SearchIO::EventHandlerI;
use Bio::Search::HSP::HSPFactory;
use Bio::Search::Hit::HitFactory;
use Bio::Search::Result::ResultFactory;
@ISA = qw(Bio::Root::Root Bio::SearchIO::EventHandlerI);
=head2 new
Title : new
Usage : my $obj = new Bio::SearchIO::SearchResultEventBuilder();
Function: Builds a new Bio::SearchIO::SearchResultEventBuilder object
Returns : Bio::SearchIO::SearchResultEventBuilder
Args : -hsp_factory => Bio::Factory::ObjectFactoryI
-hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
See L<Bio::Factory::ObjectFactoryI> for more information
=cut
sub new {
my ($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::Search::HSP::HSPFactory->new());
$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
=head2 will_handle
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
=cut
sub will_handle{
my ($self,$type) = @_;
# these are the events we recognize
return ( $type eq 'hsp' || $type eq 'hit' || $type eq 'result' );
}
=head2 SAX methods
=cut
=head2 start_result
Title : start_result
Usage : $handler->start_result($resulttype)
Function: Begins a result event cycle
Returns : none
Args : Type of Report
=cut
sub start_result {
my ($self,$type) = @_;
$self->{'_resulttype'} = $type;
$self->{'_hits'} = [];
$self->{'_hsps'} = [];
return;
}
=head2 end_result
Title : end_result
Usage : my @results = $parser->end_result
Function: Finishes a result handler cycle
Returns : A Bio::Search::Result::ResultI
Args : none
=cut
sub end_result {
my ($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(%args);
$self->{'_hits'} = [];
return $result;
}
=head2 start_hsp
Title : start_hsp
Usage : $handler->start_hsp($name,$data)
Function: Begins processing a HSP event
Returns : none
Args : type of element
associated data (hashref)
=cut
sub start_hsp {
my ($self,@args) = @_;
return;
}
=head2 end_hsp
Title : end_hsp
Usage : $handler->end_hsp()
Function: Finish processing a HSP event
Returns : none
Args : type of event and associated hashref
=cut
sub end_hsp {
my ($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->{'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
$data->{'HSP-query_length'} ||= length ($data->{'HSP-query_seq'} || '');
$data->{'HSP-hit_length'} ||= length ($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;
my $hsp = $self->factory('hsp')->create(%args);
push @{$self->{'_hsps'}}, $hsp;
return $hsp;
}
=head2 start_hit
Title : start_hit
Usage : $handler->start_hit()
Function: Starts a Hit event cycle
Returns : none
Args : type of event and associated hashref
=cut
sub start_hit{
my ($self,$type) = @_;
$self->{'_hsps'} = [];
return;
}
=head2 end_hit
Title : end_hit
Usage : $handler->end_hit()
Function: Ends a Hit event cycle
Returns : Bio::Search::Hit::HitI object
Args : type of event and associated hashref
=cut
sub end_hit{
my ($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( $args{'-name'} =~ /BL_ORD_ID/ ) {
($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'} = $data->{'RESULT-query_length'};
my ($hitrank) = scalar @{$self->{'_hits'}} + 1;
$args{'-rank'} = $hitrank;
my $hit = $self->factory('hit')->create(%args);
push @{$self->{'_hits'}}, $hit;
$self->{'_hsps'} = [];
return $hit;
}
=head2 Factory methods
=cut
=head2 register_factory
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 L<Bio::Factory::ObjectFactoryI> for more information
=cut
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;
}
=head2 factory
Title : factory
Usage : my $f = $handler->factory('TYPE');
Function: Retrieves the associated factory for requested 'TYPE'
Returns : a Bio::Factory::ObjectFactoryI or undef if none registered
Args : name of factory class to retrieve
See L<Bio::Factory::ObjectFactoryI> for more information
=cut
sub factory{
my ($self,$type) = @_;
return $self->{'_factories'}->{lc($type)} || $self->throw("No factory registered for $type");
}
1;
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