Provided by: libbio-perl-perl_1.7.2-2_all bug


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


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


       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.


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AUTHOR - Jason Stajich



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

        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.

        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

        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
        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
        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

        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

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

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

        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

        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

        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

        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()

        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

        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 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()

        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()

        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

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