Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::Search::Hit::HmmpfamHit - A parser and hit object for hmmpfam hits


           # 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 hit 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::Hit::HmmpfamHit->new();
        Function: Builds a new Bio::Search::Hit::HmmpfamHit object.
        Returns : Bio::Search::Hit::HmmpfamHit
        Args    : -chunk    => [Bio::Root::IO, $start, $end] (required if no -parent)
                  -parent   => Bio::PullParserI object (required if no -chunk)
                  -hit_data => array ref with [name description score significance
                                                       num_hsps rank]

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

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

        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

        Usage     : $hit_object->hsps();
        Purpose   : Get a list containing all HSP objects.
        Example   : @hsps = $hit_object->hsps();
        Returns   : list of L<Bio::Search::HSP::BlastHSP> objects.
        Argument  : 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

        Usage     : $hit_object->hsp( [string] );
        Purpose   : Get a single HSPI object for the present HitI object.
        Example   : $hspObj  = $hit_object->hsp;  # same as 'best'
                  : $hspObj  = $hit_object->hsp('best');
                  : $hspObj  = $hit_object->hsp('worst');
        Returns   : Object reference for a L<Bio::Search::HSP::HSPI> object.
        Argument  : String (or no argument).
                  :   No argument (default) = highest scoring HSP (same as 'best').
                  :   'best'  = highest scoring HSP.
                  :   'worst' = lowest scoring HSP.
        Throws    : Exception if an unrecognized argument is used.

       See Also   : hsps(), num_hsps()

        Title   : rewind
        Usage   : $result->rewind;
        Function: Allow one to reset the Hit iterator to the beginning, so that
                  next_hit() will subsequently return the first hit and so on.
        Returns : n/a
        Args    : none

        Usage     : $sbjct->strand( [seq_type] );
        Purpose   : Gets the strand(s) for the query, sbjct, or both sequences.
                  : For hmmpfam, the answers are always 1 (forward strand).
        Example   : $qstrand = $sbjct->strand('query');
                  : $sstrand = $sbjct->strand('hit');
                  : ($qstrand, $sstrand) = $sbjct->strand();
        Returns   : scalar context: integer '1'
                  : array context without args: list of two strings (1, 1)
                  : Array context can be "induced" by providing an argument of 'list'
                          : or 'array'.
        Argument  : In scalar context: seq_type = 'query' or 'hit' or 'sbjct' (default
                  : = 'query') ('sbjct' is synonymous with 'hit')

        Usage     : $hit_object->frac_aligned_query();
        Purpose   : Get the fraction of the query sequence which has been aligned
                  : across all HSPs (not including intervals between non-overlapping
                  : HSPs).
        Example   : $frac_alnq = $hit_object->frac_aligned_query();
        Returns   : undef (the length of query sequences is unknown in Hmmpfam reports)
        Argument  : none