Bio::Search::Result::ResultI.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Search::Result::ResultI - Abstract interface to Search Result objects

SYNOPSIS

# Bio::Search::Result::ResultI objects cannot be instantiated since this # module defines a pure interface.

# Given an object that implements the Bio::Search::Result::ResultI interface, # you can do the following things with it:

     use Bio::SearchIO;
     my $io = Bio::SearchIO->new(-format => 'blast',
                                 -file   => 't/data/HUMBETGLOA.tblastx');
     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.

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

AUTHOR

Aaron Mackey <amackey@virginia.edu> (original author)

Steve Chervitz <sac@bioperl.org>

See the FEEDBACK section for where to send bug reports and comments.

Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights Reserved.

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 _

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);
 
 

_default sort_hits

   Title : _default_sort_hits
   Usage : Do not call directly.
   Function: Sort hits in descending order by score
   Args  : None
   Returns: 1 on success
   Note  : Used by $result->sort_hits()
 
 

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
 
 

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
 
 

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
 
 

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();
  Purpose   : 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
  Argument  : none
 
 

set_no_hits_found

  Usage     : $blast->set_no_hits_found(); 
  Purpose   : Set boolean indicator indicating whether or not any hits
              were present in the report.
  Returns   : n/a
  Argument  : none