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Bio::Search::Result::HUserRContributed PerlBio::Search::Result::HMMERResult(3)

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)

perl v5.24.1			  2017-07-0Bio::Search::Result::HMMERResult(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | APPENDIX

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