NAME

       Algorithm::HMM::Hit::Domain - Object encapsulating information about a Hidden Markov Model
       domain hit.

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.

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.

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>.

SEE ALSO

       Algorithm::HMM, Algorithm::HMM::Hit::Global, Algorithm::HMM::Report