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package Algorithm::HMM::Report;
use strict;
use 5.006;
use Carp;
use Algorithm::HMM::Hit;
=head1 NAME
Algorithm::HMM::Report - Report object for the Algorithm::HMM package.
=head1 DESCRIPTION
The Algorithm::HMM::Report object is returned by the Algorithm::HMM search method. It contains the sets of global and domain hits returned by the model.
=head1 SYNOPSIS
# Search the HMM model. An Algorithm::HMM::Report object is returned.
my $rep = $hmm->search("AAIELKBPOWELKQJPASDLKJIGE");
# Get all the global hits from the report object.
my @ghits = $rep->global_hits();
# Get all the domain hits from the report object.
my @dhits = $rep->domain_hits();
=head1 METHODS
my @ghits = $rep->global_hits();
my @dhits = $rep->domain_hits();
The global_hits() and domain_hits() methods return lists of Algorithm::HMM::Hit::Global and Algorithm::HMM::Hit::Domain objects respectively. A global hit is a match across the entire model, while a domain hit is a match on a smaller subsequence of the model.
=head1 AUTHOR
The Algorithm::HMM package was originally written by Cory Spencer <cspencer@sfu.ca> of the Simon Fraser University Brinkman Laboratory. It is currently maintained by Matthew Laird <matt@brinkman.mbb.sfu.ca>.
=head1 SEE ALSO
Algorithm::HMM, Algorithm::HMM::Hit::Global, Algorithm::HMM::Hit::Domain
=cut
sub new {
my ($class, %args) = @_;
my $self = bless({ }, $class);
# Get the list of global hits and make sure it's an array ref.
croak("Global hits must be array ref")
if(defined($args{Global}) && (ref($args{Global}) ne "ARRAY"));
$self->{global} = $args{Global} || [ ];
# Get the list of global hits and make sure it's an array ref.
croak("Domain hits must be array ref")
if(defined($args{Domain}) && (ref($args{Domain}) ne "ARRAY"));
$self->{domain} = $args{Domain} || [ ];
return $self;
}
sub global_hits {
my $self = shift;
my @hits;
push(@hits, $self->_getGlobalHit($_)) for(0..($self->_numGlobalHits() - 1));
return @hits;
}
sub domain_hits {
my $self = shift;
my @hits;
push(@hits, $self->_getDomainHit($_)) for(0..($self->_numDomainHits() - 1));
return @hits;
}
1;
__END__
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