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BioPerl-1.007000_006
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Search::Result::HMMERResult

NAME

Bio::Search::Result::HMMERResult - A Result object for HMMER results

SYNOPSIS

    use Bio::Search::Result::HMMERResult;
    my $result = Bio::Search::Result::HMMERResult->new
    ( -hmm_name => 'pfam',
      -sequence_file => 'roa1.pep',
      -hits => \@hits);

    # generally we use Bio::SearchIO to build these objects
    use Bio::SearchIO;
    my $in = Bio::SearchIO->new(-format => 'hmmer',
			       -file   => 'result.hmmer');
    while( my $result = $in->next_result ) {
	print $result->query_name, " ", $result->algorithm, " ", $result->num_hits(), " hits\n";
    }

DESCRIPTION

This is a specialization of Bio::Search::Result::GenericResult. There are a few extra methods, specifically sequence_file, hmm_name, next_models, and models.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = Bio::Search::Result::HMMERResult->new();
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

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)

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)

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

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

Bio::Search::Result::GenericResult inherited methods

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

Bio::Search::Result::ResultI interface methods

Bio::Search::Result::ResultI implementation

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    : [optional] new string value for query name

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

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

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

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

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

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

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)

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

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)

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

Bio::Search::Result::GenericResult specific methods

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

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

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

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

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 available hits for this Result
Returns : Array of L<Bio::Search::Hit::HitI> objects
Args    : none

program_reference

Title   : program_reference
Usage   : $obj->program_reference($newval)
Function: 
Returns : value of the literature reference for the algorithm
Args    : newvalue (optional)