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

NAME

       Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for
                                         'pull' parsers

SYNOPSIS

           # This is an interface and cannot be instantiated

           # typically one gets Results from a SearchIO stream
           use Bio::SearchIO;
           my $io = Bio::SearchIO->new(-format => 'hmmer_pull',
                                       -file   => 't/data/hmmpfam.out');

           my $result = $io->next_result;

           while( $hit = $result->next_hit()) {
               # enter code here for hit processing
           }

           my $id = $result->query_name();
           my $desc = $result->query_description();
           my $dbname = $result->database_name();
           my $size = $result->database_letters();
           my $num_entries = $result->database_entries();
           my $gap_ext = $result->get_parameter('gapext');
           my @params = $result->available_parameters;
           my $kappa = $result->get_statistic('kappa');
           my @statnames = $result->available_statistics;

DESCRIPTION

       Bio::Search::Result::ResultI objects are data structures containing the results from the
       execution of a search algorithm.  As such, it may contain various algorithm specific
       information as well as details of the execution, but will contain a few fundamental
       elements, including the ability to return Bio::Search::Hit::HitI objects.

       PullResultI is for fast implementations that only do parsing work on the result data when
       you actually request information by calling one of the ResultI methods.

       Many methods of ResultI are implemented in a way suitable for inheriting classes that use
       Bio::PullParserI. It only really makes sense for PullResult modules to be created by (and
       have as a -parent) SearchIO modules written using PullParserI.

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 one of the Bioperl mailing lists.  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 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

COPYRIGHT

       Copyright (c) 2006 Sendu Bala.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   _setup
        Title   : _setup
        Usage   : $self->_setup(@args)
        Function: Implementers should call this to setup common fields and deal with
                  common arguments to new().
        Returns : n/a
        Args    : @args received in new().

   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

   sort_hits
        Title          : sort_hits
        Usage          : $result->sort_hits(\&sort_function)
        Function       : Sorts the available hit objects by a user-supplied function.
                     Defaults to sort by descending score.
        Returns        : n/a
        Args           : A coderef for the sort function. See the documentation on the Perl
                     sort() function for guidelines on writing sort functions.
        Note           : To access the special variables $a and $b used by the Perl sort()
                     function the user function must access Bio::Search::Result::ResultI namespace.
                     For example, use :
                     $result->sort_hits(sub{$Bio::Search::Result::ResultI::a->length <=>
                                                                $Bio::Search::Result::ResultI::b->length});
                     NOT $result->sort_hits($a->length <=>$b->length);

   query_name
        Title   : query_name
        Usage   : $id = $result->query_name();
        Function: Get the string identifier of the query used by the
                  algorithm that performed the search.
        Returns : a string.
        Args    : none

   query_accession
        Title   : query_accession
        Usage   : $id = $result->query_accession();
        Function: Get the accession (if available) for the query sequence
        Returns : a string
        Args    : none

   query_length
        Title   : query_length
        Usage   : $id = $result->query_length();
        Function: Get the length of the query sequence used in the search.
        Returns : a number
        Args    : none

   query_description
        Title   : query_description
        Usage   : $id = $result->query_description();
        Function: Get the description of the query sequence
                  used in the search.
        Returns : a string
        Args    : none

   database_name
        Title   : database_name
        Usage   : $name = $result->database_name()
        Function: Used to obtain the name of the database that the query was searched
                  against by the algorithm.
        Returns : a scalar string
        Args    : none

   database_letters
        Title   : database_letters
        Usage   : $size = $result->database_letters()
        Function: Used to obtain the size of database that was searched against.
        Returns : a scalar integer (units specific to algorithm, but probably the
                  total number of residues in the database, if available) or undef if
                  the information was not available to the Processor object.
        Args    : none

   database_entries
        Title   : database_entries
        Usage   : $num_entries = $result->database_entries()
        Function: Used to obtain the number of entries contained in the database.
        Returns : a scalar integer representing the number of entities in the database
                  or undef if the information was not available.
        Args    : none

   algorithm
        Title   : algorithm
        Usage   : my $r_type = $result->algorithm
        Function: Obtain the name of the algorithm used to obtain the Result
        Returns : string (e.g., BLASTP)
        Args    : [optional] scalar string to set value

   algorithm_version
        Title   : algorithm_version
        Usage   : my $r_version = $result->algorithm_version
        Function: Obtain the version of the algorithm used to obtain the Result
        Returns : string (e.g., 2.1.2)
        Args    : [optional] scalar string to set algorithm version value

   algorithm_reference
        Title   : algorithm_reference
        Usage   : $obj->algorithm_reference($newval)
        Function:
        Returns : value of the literature reference for the algorithm
        Args    : newvalue (optional)
        Comments: The default implementation in ResultI returns an empty string
                  rather than throwing a NotImplemented exception, since
                  the ref may not always be available and is not critical.

   num_hits
        Title   : num_hits
        Usage   : my $hitcount= $result->num_hits
        Function: returns the number of hits for this query result
        Returns : integer
        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

   no_hits_found
        Usage     : $nohits = $blast->no_hits_found();
        Function  : Get boolean indicator indicating whether or not any hits
                    were present in the report.

                    This is NOT the same as determining the number of hits via
                    the hits() method, which will return zero hits if there were no
                    hits in the report or if all hits were filtered out during the
                    parse.

                    Thus, this method can be used to distinguish these possibilities
                    for hitless reports generated when filtering.

        Returns   : Boolean
        Args      : none

   rewind
        Title   : rewind
        Usage   : $result->rewind;
        Function: Allow one to reset the Hit iterator to the beginning
                  Since this is an in-memory implementation
        Returns : none
        Args    : none

   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)

   available_parameters
        Title   : available_parameters
        Usage   : my @params = $result->available_parameters
        Function: Returns the names of the available parameters
        Returns : Return list of available parameters used for this result
        Args    : none

   add_parameter
        Title   : add_parameter
        Usage   : $result->add_parameter('gapext', 11);
        Function: Adds a parameter
        Returns : none
        Args    : key  - key value name for this parama
                  value - value for this parameter

   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)

   available_statistics
        Title   : available_statistics
        Usage   : my @statnames = $result->available_statistics
        Function: Returns the names of the available statistics
        Returns : Return list of available statistics used for this result
        Args    : none

   add_statistic
        Title   : add_statistic
        Usage   : $result->add_statistic('lambda', 2.3);
        Function: Adds a statistic
        Returns : none
        Args    : key  - key value name for this statistic
                  value - value for this statistic