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

NAME

       Bio::Search::Result::GenericResult - Generic Implementation of
       Bio::Search::Result::ResultI interface applicable to most search results.

SYNOPSIS

           # typically one gets Results from a SearchIO stream
           use Bio::SearchIO;
           my $io = Bio::SearchIO->new(-format => 'blast',
                                       -file   => 't/data/HUMBETGLOA.tblastx');
           while( my $result = $io->next_result ) {
               # process all search results within the input stream
               while( my $hit = $result->next_hit ) {
                   # insert code here for hit processing
               }
           }

           use Bio::Search::Result::GenericResult;
           my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
           # typically these are created from a Bio::SearchIO stream
           my $result = Bio::Search::Result::GenericResult->new
               ( -query_name        => 'HUMBETGLOA',
                 -query_accession   => ''
                 -query_description => 'Human haplotype C4 beta-globin gene, complete cds.'
                 -query_length      => 3002
                 -database_name     => 'ecoli.aa'
                 -database_letters  => 4662239,
                 -database_entries  => 400,
                 -parameters        => { 'e' => '0.001' },
                 -statistics        => { 'kappa' => 0.731 },
                 -algorithm         => 'blastp',
                 -algorithm_version => '2.1.2',
                 );

           my $id = $result->query_name();

           my $desc = $result->query_description();

           my $name = $result->database_name();

           my $size = $result->database_letters();

           my $num_entries = $result->database_entries();

           my $gap_ext = $result->get_parameter('e');

           my @params = $result->available_parameters;

           my $kappa = $result->get_statistic('kappa');

           my @statnames = $result->available_statistics;

       # TODO: Show how to configure a SearchIO stream so that it generates #       GenericResult
       objects.

DESCRIPTION

       This object is an implementation of the Bio::Search::Result::ResultI interface and
       provides a generic place to store results from a sequence database search.

       Unless you're writing a parser, you won't ever need to create a GenericResult or any other
       ResultI-implementing object. If you use the SearchIO system, ResultI objects are created
       automatically from a SearchIO stream which returns Bio::Search::Result::ResultI objects.

       For documentation on what you can do with GenericResult (and other ResultI objects),
       please see the API documentation in Bio::Search::Result::ResultI.

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 - Jason Stajich and Steve Chervitz

       Email jason@bioperl.org Email sac@bioperl.org

CONTRIBUTORS

       Sendu Bala, 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::Result::GenericResult->new();
        Function: Builds a new Bio::Search::Result::GenericResult object
        Returns : Bio::Search::Result::GenericResult
        Args    : -query_name        => Name of query Sequence
                  -query_accession   => Query accession number (if available)
                  -query_description => Description of query sequence
                  -query_length      => Length of query sequence
                  -database_name     => Name of database
                  -database_letters  => Number of residues in database
                  -database_entries  => Number of entries in database
                  -hits              => array ref of Bio::Search::Hit::HitI objects
                  -parameters        => hash ref of search parameters (key => value)
                  -statistics        => hash ref of search statistics (key => value)
                  -algorithm         => program name (blastx)
                  -algorithm_version   => version of the algorithm (2.1.2)
                  -algorithm_reference => literature reference string for this algorithm
                  -rid               => value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
                  -hit_factory       => Bio::Factory::ObjectFactoryI capable of making
                                        Bio::Search::Hit::HitI objects

   algorithm
        Title   : algorithm
        Usage   : my $r_type = $hsp->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 = $hsp->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

   Bio::Search::Result::ResultI interface methods
       Bio::Search::Result::ResultI implementation

   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

   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    : [optional] new string value for query name

   query_accession
        Title   : query_accession
        Usage   : $id = $result->query_accession();
        Function: Get the accession (if available) for the query sequence
        Returns : a string
        Args    : [optional] new string value for accession

   query_gi
        Title   : query_gi
        Usage   : $acc = $hit->query_gi();
        Function: Retrieve the NCBI Unique ID (aka the GI #),
                  if available, for the query
        Returns : a scalar string (empty string if not set)
        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    :  [optional] new integer value for query length

   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    : [optional] new string for the query description

   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    : [optional] new string for the db name

   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    : [optional] new scalar integer for number of letters in db

   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    : [optional] new integer for the number of sequence entries in the db

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

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

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

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

   Bio::Search::Report
       Bio::Search::Result::GenericResult specific methods

   add_hit
        Title   : add_hit
        Usage   : $report->add_hit($hit)
        Function: Adds a HitI to the stored list of hits
        Returns : Number of HitI currently stored
        Args    : Bio::Search::Hit::HitI

   hit_factory
        Title   : hit_factory
        Usage   : $hit->hit_factory($hit_factory)
        Function: Get/set the factory used to build HitI objects if necessary.
        Returns : Bio::Factory::ObjectFactoryI
        Args    : Bio::Factory::ObjectFactoryI

   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

   _nexthitindex
        Title   : _nexthitindex
        Usage   : private

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

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

   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 available hits for this Result
        Returns : Array of L<Bio::Search::Hit::HitI> objects
        Args    : none

   algorithm_reference
        Title   : algorithm_reference
        Usage   : $obj->algorithm_reference($newval)
        Function:
        Returns : string containing literature reference for the algorithm
        Args    : newvalue string (optional)
        Comments: Formerly named program_reference(), which is still supported
                  for backwards compatibility.

   program_reference
        Title   : program_reference
        Usage   : $obj->program_reference()
        Function:
        Returns : string containing literature reference for the algorithm
        Args    :
        Comments: Deprecated - use algorithm_reference() instead.

   rid
        Title   : rid
        Usage   : $obj->rid($newval)
        Function:
        Returns : value of the BLAST Request ID (eg. RID: ZABJ4EA7014)
        Args    : newvalue (optional)
        Comments: The default implementation in ResultI returns an empty string
                  rather than throwing a NotImplemented exception, since
                  the RID may not always be available and is not critical.
                  See: (1) https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html
                       (2) https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html

   no_hits_found
       See documentation in Bio::Search::Result::ResultI::no_hits_found()

   set_no_hits_found
       See documentation in Bio::Search::Result::ResultI::set_no_hits_found()

   to_string
        Title   : to_string
        Usage   : print $blast->to_string;
        Function: Returns a string representation for the Blast result.
                  Primarily intended for debugging purposes.
        Example : see usage
        Returns : A string of the form:
                  [GenericResult] <analysis_method> query=<name> <description> db=<database
                  e.g.:
                  [GenericResult] BLASTP query=YEL060C vacuolar protease B, db=PDBUNIQ
        Args    : None