/ 
bioperl-1.0.2
/ Bio::Search::Result::ResultI

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 = new Bio::SearchIO(-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://bio.perl.org/MailList.html  - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

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

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

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 = $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