Bio::Search::Result::PullResultI(3pm) User Contributed Perl Documentation Bio::Search::Result::PullResultI(3pm)
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://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::Search::Result::PullResultI(3pm)