Provided by: libbio-perl-perl_1.6.923-1_all bug


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


           # 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


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


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AUTHOR - Sendu Bala



       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::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)

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

        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

        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'

        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