NAME

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

SYNOPSIS

       Give standard usage here

DESCRIPTION

       Describe the object here

FEEDBACK

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       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
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   Support
       Please direct usage questions or support issues to the mailing list:

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       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
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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)