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BioPerl-1.7.8
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Search::Result::PullResultI

NAME

Bio::Search::Result::PullResultI - Bio::Search::Result::ResultI interface for 'pull' parsers

SYNOPSIS

# This is an interface and cannot be instantiated

# typically one gets Results from a SearchIO stream
use Bio::SearchIO;
my $io = Bio::SearchIO->new(-format => 'hmmer_pull',
                            -file   => 't/data/hmmpfam.out');

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.

PullResultI is for fast implementations that only do parsing work on the result data when you actually request information by calling one of the ResultI methods.

Many methods of ResultI are implemented in a way suitable for inheriting classes that use Bio::PullParserI. It only really makes sense for PullResult modules to be created by (and have as a -parent) SearchIO modules written using PullParserI.

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:

https://github.com/bioperl/bioperl-live/issues

AUTHOR Sendu Bala

Email bix@sendu.me.uk

COPYRIGHT

Copyright (c) 2006 Sendu Bala.

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 _

_setup

Title   : _setup
Usage   : $self->_setup(@args)
Function: Implementers should call this to setup common fields and deal with
          common arguments to new().
Returns : n/a
Args    : @args received in new().

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);

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

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();
Function  : 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
Args      : none

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

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

add_parameter

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

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

add_statistic

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