NAME

       Bio::Search::Hit::HMMERHit - A Hit module for HMMER hits

SYNOPSIS

           use Bio::Search::Hit::HMMERHit;
           my $hit = Bio::Search::Hit::HMMERHit->new();
           # use it in the same way as Bio::Search::Hit::GenericHit

DESCRIPTION

       This is a specialization of Bio::Search::Hit::GenericHit.  There are a few news methods
       next_domain and domains.  Note that bits and iteration make no sense for this object and
       will return 0.

FEEDBACK

   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/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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 the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich

       Email jason@bioperl.org

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

   inherited Bio::Search::Hit::GenericHit methods
   add_hsp
        Title   : add_hsp
        Usage   : $hit->add_hsp($hsp)
        Function: Add a HSP to the collection of HSPs for a Hit
        Returns : number of HSPs in the Hit
        Args    : Bio::Search::HSP::HSPI object

   Bio::Search::Hit::HitI methods
   name
        Title   : name
        Usage   : $hit_name = $hit->name();
        Function: returns the name of the Hit sequence
        Returns : a scalar string
        Args    : [optional] scalar string to set the name

   accession
        Title   : accession
        Usage   : $acc = $hit->accession();
        Function: Retrieve the accession (if available) for the hit
        Returns : a scalar string (empty string if not set)
        Args    : none

   description
        Title   : description
        Usage   : $desc = $hit->description();
        Function: Retrieve the description for the hit
        Returns : a scalar string
        Args    : [optional] scalar string to set the descrition

   length
        Title   : length
        Usage   : my $len = $hit->length
        Function: Returns the length of the hit
        Returns : integer
        Args    : [optional] integer to set the length

   algorithm
        Title   : algorithm
        Usage   : $alg = $hit->algorithm();
        Function: Gets the algorithm specification that was used to obtain the hit
                  For BLAST, the algorithm denotes what type of sequence was aligned
                  against what (BLASTN: dna-dna, BLASTP prt-prt, BLASTX translated
                  dna-prt, TBLASTN prt-translated dna, TBLASTX translated
                  dna-translated dna).
        Returns : a scalar string
        Args    : [optional] scalar string to set the algorithm

   raw_score
        Title   : raw_score
        Usage   : $score = $hit->raw_score();
        Function: Gets the "raw score" generated by the algorithm.  What
                  this score is exactly will vary from algorithm to algorithm,
                  returning undef if unavailable.
        Returns : a scalar value
        Args    : [optional] scalar value to set the raw score

   significance
        Title   : significance
        Usage   : $significance = $hit->significance();
        Function: Used to obtain the E or P value of a hit, i.e. the probability that
                  this particular hit was obtained purely by random chance.  If
                  information is not available (nor calculatable from other
                  information sources), return undef.
        Returns : a scalar value or undef if unavailable
        Args    : [optional] scalar value to set the significance

   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()

   next_hsp
        Title    : next_hsp
        Usage    : while( $hsp = $obj->next_hsp()) { ... }
        Function : Returns the next available High Scoring Pair
        Example  :
        Returns  : Bio::Search::HSP::HSPI object or null if finished
        Args     : none

   hsps
        Usage     : $hit_object->hsps();
        Purpose   : Get a list containing all HSP objects.
                  : Get the numbers of HSPs for the current hit.
        Example   : @hsps = $hit_object->hsps();
                  : $num  = $hit_object->hsps();  # alternatively, use num_hsps()
        Returns   : Array context : list of Bio::Search::HSP::BlastHSP.pm objects.
                  : Scalar context: integer (number of HSPs).
                  :                 (Equivalent to num_hsps()).
        Argument  : n/a. Relies on wantarray
        Throws    : Exception if the HSPs have not been collected.

       See Also   : hsp(), num_hsps()

   num_hsps
        Usage     : $hit_object->num_hsps();
        Purpose   : Get the number of HSPs for the present Blast hit.
        Example   : $nhsps = $hit_object->num_hsps();
        Returns   : Integer
        Argument  : n/a
        Throws    : Exception if the HSPs have not been collected.

       See Also   : hsps()

   rewind
        Title   : rewind
        Usage   : $hit->rewind;
        Function: Allow one to reset the HSP iteration to the beginning
                  Since this is an in-memory implementation
        Returns : none
        Args    : none

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