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

NAME

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

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 hit 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://github.com/bioperl/bioperl-live/issues

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::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)

   next_hsp
        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

   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

   hsps
        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

   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

   hsp
        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()

   rewind
        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

   strand
        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')

   frac_aligned_query
        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