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

NAME

       Bio::Search::Result::HmmpfamResult - A parser and result object for hmmpfam
                                            results

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) {
                       print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
           }

DESCRIPTION

       This object implements a parser for hmmpfam result 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::SearchIO::Result::hmmpfam->new();
        Function: Builds a new Bio::SearchIO::Result::hmmpfam object
        Returns : Bio::SearchIO::Result::hmmpfam
        Args    : -chunk  => [Bio::Root::IO, $start, $end] (required if no -parent)
                  -parent => Bio::PullParserI object (required if no -chunk)
                  -parameters => hash ref of search parameters (key => value), optional
                  -statistics => hash ref of search statistics (key => value), optional

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

   next_hit
        Title   : next_hit
        Usage   : while( $hit = $result->next_hit()) { ... }
        Function: Returns the next available Hit object, representing potential
                  matches between the query and various entities from the database.
        Returns : a Bio::Search::Hit::HitI object or undef if there are no more.
        Args    : none

   next_model
        Title   : next_model
        Usage   : my $domain = $result->next_model
        Function: Returns the next domain - this is an alias for next_hit()
        Returns : L<Bio::Search::Hit::HitI> object
        Args    : none

   hits
        Title   : hits
        Usage   : my @hits = $result->hits
        Function: Returns the HitI objects contained within this Result
        Returns : Array of Bio::Search::Hit::HitI objects
        Args    : none

       See Also: Bio::Search::Hit::HitI

   models
        Title   : models
        Usage   : my @domains = $result->models;
        Function: Returns the list of HMM models seen - this is an alias for hits()
        Returns : Array of L<Bio::Search::Hit::HitI> objects
        Args    : none

   sort_hits
        Title          : sort_hits
        Usage          : $result->sort_hits('<score')
        Function       : Sorts the hits so that they come out in the desired order when
                     hits() or next_hit() is called.
        Returns        : n/a
        Args           : A coderef for the sort function. See the documentation on the Perl
                     sort() function for guidelines on writing sort functions.
                                 You will be sorting array references, not HitI objects. The
                                 references contain name as element 0, description as element 1,
                                 score as element 2, significance as element 3 and number of hsps
                                 as element 4.
                                 By default the sort order is ascending significance value (ie.
                                 most significant hits first).
        Note           : To access the special variables $a and $b used by the Perl sort()
                     function the user function must access
                                 Bio::Search::Result::HmmpfamResult namespace.
                     For example, use :
                     $result->sort_hits(
                                       sub{$Bio::Search::Result::HmmpfamResult::a->[2]
                                                                <=>
                                               $Bio::Search::Result::HmmpfamResult::b->[2]});
                     NOT $result->sort_hits($a->[2] <=> $b->[2]);

   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