NAME

       Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps

SYNOPSIS

           # generally we use Bio::SearchIO to build these objects
           use Bio::SearchIO;
           my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
                                                                  -file   => 'result.hmmer');

           while (my $result = $in->next_result) {
                       while (my $hit = $result->next_hit) {
                               print $hit->name, "\n";
                               print $hit->score, "\n";
                               print $hit->significance, "\n";

                               while (my $hsp = $hit->next_hsp) {
                                       # process HSPI objects
                               }
                       }
           }

DESCRIPTION

       This object implements a parser for hmmpfam hsp output, a program in the HMMER package.

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 - Sendu Bala

       Email bix@sendu.me.uk

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::HSP::HmmpfamHSP->new();
        Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
        Returns : Bio::Search::HSP::HmmpfamHSP
        Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
                  -parent => Bio::PullParserI object (required if no -chunk)
                  -hsp_data => array ref with [rank query_start query_end hit_start
                                                                                       hit_end score evalue]

                  where the array ref provided to -chunk contains an IO object
                  for a filehandle to something representing the raw data of the
                  hsp, and $start and $end define the tell() position within the
                  filehandle that the hsp data starts and ends (optional; defaults
                  to start and end of the entire thing described by the filehandle)

   query
        Title   : query
        Usage   : my $query = $hsp->query
        Function: Returns a SeqFeature representing the query in the HSP
        Returns : L<Bio::SeqFeature::Similarity>
        Args    : none

   hit
        Title   : hit
        Usage   : my $hit = $hsp->hit
        Function: Returns a SeqFeature representing the hit in the HSP
        Returns : L<Bio::SeqFeature::Similarity>
        Args    : [optional] new value to set

   gaps
        Title    : gaps
        Usage    : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
        Function : Get the number of gaps in the query, hit, or total alignment.
        Returns  : Integer, number of gaps or 0 if none
        Args     : 'query' = num conserved / length of query seq (without gaps)
                   'hit'   = num conserved / length of hit seq (without gaps)
                   'total' = num conserved / length of alignment (with gaps)
                   default = 'total'

   pvalue
        Title   : pvalue
        Usage   : my $pvalue = $hsp->pvalue();
        Function: Returns the P-value for this HSP
        Returns : undef (Hmmpfam reports do not have p-values)
        Args    : none