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

NAME

       Bio::Search::Result::BlastPullResult - A parser and result object for BLASTN
                                            results

SYNOPSIS

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

           while (my $result = $in->next_result) {
                       print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
           }

DESCRIPTION

       This object implements a parser for NCBI BLASTN result output.

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

CONTRIBUTORS

       Additional contributors names and emails here

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

   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

   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.
                                 By default the sort order is ascending significance value (ie.
                                 most significant hits first).
                                 *** example

   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

   get_statistic
        Title   : get_statistic
        Usage   : my $gap_ext = $result->get_statistic('kappa')
        Function: Returns the value for a specific statistic available
                  from this result
        Returns : string
        Args    : name of statistic (string)

   get_parameter
        Title   : get_parameter
        Usage   : my $gap_ext = $result->get_parameter('gapext')
        Function: Returns the value for a specific parameter used
                  when running this result
        Returns : string
        Args    : name of parameter (string)