Raw content of Bio::Search::Result::HMMERResult
<![CDATA[# $Id: HMMERResult.pm,v 1.3 2002/10/22 07:45:18 lapp Exp $
#
# BioPerl module for Bio::Search::Result::HMMERResult
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Search::Result::HMMERResult - A Result object for HMMER results
=head1 SYNOPSIS
use Bio::Search::Result::HMMERResult;
my $result = new Bio::Search::Result::HMMERResult
( -hmm_name => 'pfam',
-sequence_file => 'roa1.pep',
-hits => \@hits);
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = new Bio::SearchIO(-format => 'hmmer',
-file => 'result.hmmer');
while( my $result = $in->next_result ) {
print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
}
=head1 DESCRIPTION
This is a specialization of L<Bio::Search::Result::GenericResult>.
There are a few extra methods, specifically L<sequence_file>,
L<hmm_name>, L<next_models>, and L<models>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Search::Result::HMMERResult;
use vars qw(@ISA);
use strict;
use Bio::Search::Result::GenericResult;
@ISA = qw(Bio::Search::Result::GenericResult );
=head2 new
Title : new
Usage : my $obj = new Bio::Search::Result::HMMERResult();
Function: Builds a new Bio::Search::Result::HMMERResult object
Returns : Bio::Search::Result::HMMERResult
Args : -hmm_name => string, name of hmm file
-sequence_file => name of the sequence file
plus Bio::Search::Result::GenericResult parameters
-query_name => Name of query Sequence
-query_accession => Query accession number (if available)
-query_description => Description of query sequence
-query_length => Length of query sequence
-database_name => Name of database
-database_letters => Number of residues in database
-database_entries => Number of entries in database
-parameters => hash ref of search parameters (key => value)
-statistics => hash ref of search statistics (key => value)
-algorithm => program name (blastx)
-algorithm_version => version of the algorithm (2.1.2)
-program_reference => literature reference string for this algorithm
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($hmm,$seqfile) = $self->_rearrange([qw(HMM_NAME SEQUENCE_FILE)],
@args);
defined( $seqfile) && $self->sequence_file($seqfile);
defined( $hmm) && $self->hmm_name($hmm);
return $self;
}
=head2 hmm_name
Title : hmm_name
Usage : $obj->hmm_name($newval)
Function: Get/Set the value of hmm_name
Returns : value of hmm_name
Args : newvalue (optional)
=cut
sub hmm_name{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_hmm_name'} = $value;
}
return $self->{'_hmm_name'};
}
=head2 sequence_file
Title : sequence_file
Usage : $obj->sequence_file($newval)
Function: Get/Set the value of sequence_file
Returns : value of sequence_file
Args : newvalue (optional)
=cut
sub sequence_file{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_sequence_file'} = $value;
}
return $self->{'_sequence_file'};
}
=head2 next_model
Title : next_model
Usage : my $domain = $result->next_model
Function: Returns the next domain - this
is an alias for next_hit
Returns : L<Bio::Search::Hit::HitI> object
Args : none
=cut
sub next_model{ shift->next_hit }
=head2 models
Title : models
Usage : my @domains = $result->models;
Function: Returns the list of HMM models seen - this
is an alias for hits()
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : none
=cut
sub models{ shift->hits }
=head2 Bio::Search::Result::GenericResult inherited methods
=cut
=head2 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
=cut
=head2 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
=cut
=head2 Bio::Search::Result::ResultI interface methods
Bio::Search::Result::ResultI implementation
=head2 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
=cut
=head2 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 : [optional] new string value for query name
=cut
=head2 query_accession
Title : query_accession
Usage : $id = $result->query_accession();
Function: Get the accession (if available) for the query sequence
Returns : a string
Args : [optional] new string value for accession
=cut
=head2 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 : [optional] new integer value for query length
=cut
=head2 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 : [optional] new string for the query description
=cut
=head2 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 : [optional] new string for the db name
=cut
=head2 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 : [optional] new scalar integer for number of letters in db
=cut
=head2 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 : [optional] new integer for the number of sequence entries in the db
=cut
=head2 get_parameter
Title : get_parameter
Usage : my $gap_ext = $report->get_parameter('gapext')
Function: Returns the value for a specific parameter used
when running this report
Returns : string
Args : name of parameter (string)
=cut
=head2 available_parameters
Title : available_parameters
Usage : my @params = $report->available_paramters
Function: Returns the names of the available parameters
Returns : Return list of available parameters used for this report
Args : none
=cut
=head2 get_statistic
Title : get_statistic
Usage : my $gap_ext = $report->get_statistic('kappa')
Function: Returns the value for a specific statistic available
from this report
Returns : string
Args : name of statistic (string)
=cut
=head2 available_statistics
Title : available_statistics
Usage : my @statnames = $report->available_statistics
Function: Returns the names of the available statistics
Returns : Return list of available statistics used for this report
Args : none
=cut
=head2 Bio::Search::Result::GenericResult specific methods
=cut
=head2 add_hit
Title : add_hit
Usage : $report->add_hit($hit)
Function: Adds a HitI to the stored list of hits
Returns : Number of HitI currently stored
Args : Bio::Search::Hit::HitI
=cut
=head2 rewind
Title : rewind
Usage : $result->rewind;
Function: Allow one to reset the Hit iteration to the beginning
Since this is an in-memory implementation
Returns : none
Args : none
=cut
sub rewind{
my ($self) = @_;
$self->{'_hitindex'} = 0;
}
=head2 add_parameter
Title : add_parameter
Usage : $report->add_parameter('gapext', 11);
Function: Adds a parameter
Returns : none
Args : key - key value name for this parama
value - value for this parameter
=cut
=head2 add_statistic
Title : add_statistic
Usage : $report->add_statistic('lambda', 2.3);
Function: Adds a parameter
Returns : none
Args : key - key value name for this parama
value - value for this parameter
=cut
=head2 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
=cut
=head2 hits
Title : hits
Usage : my @hits = $result->hits
Function: Returns the available hits for this Result
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args : none
=cut
=head2 program_reference
Title : program_reference
Usage : $obj->program_reference($newval)
Function:
Returns : value of the literature reference for the algorithm
Args : newvalue (optional)
=cut
1;
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