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package Algorithm::HMM::Hit::Domain;
use strict;
use 5.006;
use Carp;
use Algorithm::HMM::Hit;
our @ISA = qw(Algorithm::HMM::Hit);
=head1 NAME
Algorithm::HMM::Hit::Domain - Object encapsulating information about a Hidden Markov Model domain hit.
=head1 DESCRIPTION
The Algorithm::HMM::Hit::Domain object encapsulates information about a domain hit in the Hidden Markov Model. Unlike global hits which attempt to match the provided sequence against the entire model, a domain hit indicates a match against a smaller subsequence in the model.
=head1 METHODS
$dhit->pvalue()
$dhit->evalue()
$dhit->score()
Returns the pvalue, evalue and score values respectively for the hit.
$dhit->seq_from()
$dhit->seq_to()
$dhit->seq_length()
Returns the starting and ends points in the sequence that matched the model. seq_length returns the length of the hit.
$dhit->hmm_from()
$dhit->hmm_to()
Returns the starting and end points in the model.
$dhit->parent_pvalue()
$dhit->parent_evalue()
$dhit->parent_score()
Returns the parent pvalue, evalue and score values respectively.
=head1 AUTHOR
The Algorithm::HMM package was originally written by Cory Spencer <cspencer@sfu.ca> of the Simon Fraser University Brinkman Laboratory. It is currently maintained by Matthew Laird <matt@brinkman.mbb.sfu.ca>.
=head1 SEE ALSO
Algorithm::HMM, Algorithm::HMM::Hit::Global, Algorithm::HMM::Report
=cut
sub new {
my ($class, %args) = @_;
my $self = $class->SUPER::new(%args);
return $self;
}
sub seq_from {
my $self = shift;
return (@_) ? $self->_setSeqFrom(shift(@_)) : $self->_getSeqFrom();
}
sub seq_to {
my $self = shift;
return (@_) ? $self->_setSeqTo(shift(@_)) : $self->_getSeqTo();
}
sub seq_length {
my $self = shift;
return (@_) ? $self->_setSeqLength(shift(@_)) : $self->_getSeqLength();
}
sub hmm_from {
my $self = shift;
return (@_) ? $self->_setHMMFrom(shift(@_)) : $self->_getHMMFrom();
}
sub hmm_to {
my $self = shift;
return (@_) ? $self->_setHMMTo(shift(@_)) : $self->_getHMMTo();
}
sub parent_pvalue {
my $self = shift;
return (@_) ? $self->_setParentPValue(shift(@_)) : $self->_getParentPValue();
}
sub parent_evalue {
my $self = shift;
return (@_) ? $self->_setParentEValue(shift(@_)) : $self->_getParentEValue();
}
sub parent_score {
my $self = shift;
return (@_) ? $self->_setParentScore(shift(@_)) : $self->_getParentScore();
}
1;
__END__
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