Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Search::Hit::hmmer3Hit - DESCRIPTION of Object

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Describe the object here

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AUTHOR - Thomas Sharpton

       Email thomas.sharpton@gmail.com

       Describe contact details here

CONTRIBUTORS

       Additional contributors names and emails here

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $obj = Bio::Search::Hit::HMMERHit->new();
        Function: Builds a new Bio::Search::Hit::HMMERHit object
        Returns : Bio::Search::Hit::HMMERHit
        Args    :

        Plus the Bio::Search::Hit::GenericHit inherited params
                  -name         => Name of Hit (required)
                  -description  => Description (optional)
                  -accession    => Accession number (optional)
                  -length       => Length of the Hit (optional)
                  -score        => Raw Score for the Hit (optional)
                  -significance => Significance value for the Hit (optional)
                  -algorithm    => Algorithm used (BLASTP, FASTX, etc...)
                  -hsps         => Array ref of HSPs for this Hit.

   next_domain
        Title   : next_domain
        Usage   : my $domain = $hit->next_domain();
        Function: An alias for L<next_hsp()>, this will return the next HSP
        Returns : L<Bio::Search::HSP::HSPI> object
        Args    : none

   domains
        Title   : domains
        Usage   : my @domains = $hit->domains();
        Function: An alias for L<hsps()>, this will return the full list of hsps
        Returns : array of L<Bio::Search::HSP::HSPI> objects
        Args    : none

   bits
        Usage     : $hit_object->bits();
        Purpose   : Gets the bit score of the best HSP for the current hit.
        Example   : $bits = $hit_object->bits();
        Returns   : Integer or undef if bit score is not set
        Argument  : n/a

       See Also   : score()

   iteration
        Title   : iteration
        Usage   : $obj->iteration($newval)
        Function: PSI-BLAST iteration
        Returns : value of iteration
        Args    : newvalue (optional)