Raw content of Bio::SearchIO::FastHitEventBuilder
<![CDATA[# $Id: FastHitEventBuilder.pm,v 1.6 2002/12/05 13:46:35 heikki Exp $
#
# BioPerl module for Bio::SearchIO::FastHitEventBuilder
#
# 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::FastHitEventBuilder - Event Handler for SearchIO events.
=head1 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
}
}
=head1 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.
=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::FastHitEventBuilder;
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 $obj = new Bio::SearchIO::FastHitEventBuilder();
Function: Builds a new Bio::SearchIO::FastHitEventBuilder object
Returns : Bio::SearchIO::FastHitEventBuilder
Args : -hit_factory => Bio::Factory::ObjectFactoryI
-result_factory => Bio::Factory::ObjectFactoryI
See L<Bio::Factory::ObjectFactoryI> for more information
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($hspF,$hitF,$resultF) = $self->_rearrange([qw(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
=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 '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'} = [];
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'} || $type);
$args{'-hits'} = $self->{'_hits'};
my $result = $self->factory('result')->create(%args);
$self->{'_hits'} = [];
return $result;
}
=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) = @_;
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};
$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;
}
=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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