Bio::Search::Result::GenericResult.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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
            -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.
 
 

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