Bio::Search::Result
ResultI
Summary
Bio::Search::Result::ResultI - Abstract interface to Search Result objects
Package variables
No package variables defined.
Included modules
Inherit
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.
Methods
Methods description
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 |
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 |
Title : query_accession
Usage : $id = $result->query_accession();
Function: Get the accession (if available) for the query sequence
Returns : a string
Args : none |
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 |
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 |
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 |
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 |
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 |
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) |
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 |
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) |
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 |
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 |
Title : algorithm_version
Usage : my $r_version = $hsp->algorithm_version
Function: Obtain the version of the algorithm used to obtain the Result
Returns : string (e.g., 2.1.2)
Args : [optional] scalar string to set algorithm version value |
Methods code
sub next_hit
{ my ($self,@args) = @_;
$self->throw_not_implemented;} | sub query_name
{ my ($self,@args) = @_;
$self->throw_not_implemented;} | sub query_accession
{ my ($self,@args) = @_;
$self->throw_not_implemented;} | sub query_length
{ my ($self,@args) = @_;
$self->throw_not_implemented;} | sub query_description
{ my ($self,@args) = @_;
$self->throw_not_implemented;} | sub database_name
{ my ($self,@args) = @_;
$self->throw_not_implemented;} | sub database_letters
{ my ($self,@args) = @_;
$self->throw_not_implemented();} | sub database_entries
{ my ($self,@args) = @_;
$self->throw_not_implemented();} | sub get_parameter
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub available_parameters
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub get_statistic
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub available_statistics
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub algorithm
{ return ''; } | sub algorithm_version
{ return ''; } | General documentation
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
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/
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.
This software is provided "as is" without warranty of any kind.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _