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Bio::Search::Result::GUseriContributed PeBio::Search::Result::GenericResult(3)

NAME
       Bio::Search::Result::GenericResult - Generic Implementation of
       Bio::Search::Result::ResultI interface applicable to most search
       results.

SYNOPSIS
	   # typically one gets	Results	from a SearchIO	stream
	   use Bio::SearchIO;
	   my $io = Bio::SearchIO->new(-format => 'blast',
				       -file   => 't/data/HUMBETGLOA.tblastx');
	   while( my $result = $io->next_result	) {
	       # process all search results within the input stream
	       while( my $hit =	$result->next_hit ) {
		   # insert code here for hit processing
	       }
	   }

	   use Bio::Search::Result::GenericResult;
	   my @hits = (); # would be a list of Bio::Search::Hit::HitI objects
	   # typically these are created from a	Bio::SearchIO stream
	   my $result =	Bio::Search::Result::GenericResult->new
	       ( -query_name	    => 'HUMBETGLOA',
		 -query_accession   => ''
		 -query_description => 'Human haplotype	C4 beta-globin gene, complete cds.'
		 -query_length	    => 3002
		 -database_name	    => 'ecoli.aa'
		 -database_letters  => 4662239,
		 -database_entries  => 400,
		 -parameters	    => { 'e' =>	'0.001'	},
		 -statistics	    => { 'kappa' => 0.731 },
		 -algorithm	    => 'blastp',
		 -algorithm_version => '2.1.2',
		 );

	   my $id = $result->query_name();

	   my $desc = $result->query_description();

	   my $name = $result->database_name();

	   my $size = $result->database_letters();

	   my $num_entries = $result->database_entries();

	   my $gap_ext = $result->get_parameter('e');

	   my @params =	$result->available_parameters;

	   my $kappa = $result->get_statistic('kappa');

	   my @statnames = $result->available_statistics;

       # TODO: Show how	to configure a SearchIO	stream so that it generates #
       GenericResult objects.

DESCRIPTION
       This object is an implementation	of the Bio::Search::Result::ResultI
       interface and provides a	generic	place to store results from a sequence
       database	search.

       Unless you're writing a parser, you won't ever need to create a
       GenericResult or	any other ResultI-implementing object. If you use the
       SearchIO	system,	ResultI	objects	are created automatically from a
       SearchIO	stream which returns Bio::Search::Result::ResultI objects.

       For documentation on what you can do with GenericResult (and other
       ResultI objects), please	see the	API documentation in
       Bio::Search::Result::ResultI.

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 and Steve Chervitz
       Email jason@bioperl.org Email sac@bioperl.org

CONTRIBUTORS
       Sendu Bala, bix@sendu.me.uk

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::GenericResult->new();
	Function: Builds a new Bio::Search::Result::GenericResult object
	Returns	: Bio::Search::Result::GenericResult
	Args	: -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
		  -hits		     =>	array ref of Bio::Search::Hit::HitI objects
		  -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)
		  -algorithm_reference => literature reference string for this algorithm
		  -rid		     =>	value of the BLAST Request ID (eg. RID:	ZABJ4EA7014)
		  -hit_factory	     =>	Bio::Factory::ObjectFactoryI capable of	making
					Bio::Search::Hit::HitI objects

   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_gi
	Title	: query_gi
	Usage	: $acc = $hit->query_gi();
	Function: Retrieve the NCBI Unique ID (aka the GI #),
		  if available,	for the	query
	Returns	: a scalar string (empty string	if not set)
	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	:  [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::Report
       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

   hit_factory
	Title	: hit_factory
	Usage	: $hit->hit_factory($hit_factory)
	Function: Get/set the factory used to build HitI objects if necessary.
	Returns	: Bio::Factory::ObjectFactoryI
	Args	: Bio::Factory::ObjectFactoryI

   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

   _nexthitindex
	Title	: _nexthitindex
	Usage	: private

   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

   algorithm_reference
	Title	: algorithm_reference
	Usage	: $obj->algorithm_reference($newval)
	Function:
	Returns	: string containing literature reference for the algorithm
	Args	: newvalue string (optional)
	Comments: Formerly named program_reference(), which is still supported
		  for backwards	compatibility.

   program_reference
	Title	: program_reference
	Usage	: $obj->program_reference()
	Function:
	Returns	: string containing literature reference for the algorithm
	Args	:
	Comments: Deprecated - use algorithm_reference() instead.

   rid
	Title	: rid
	Usage	: $obj->rid($newval)
	Function:
	Returns	: value	of the BLAST Request ID	(eg. RID: ZABJ4EA7014)
	Args	: newvalue (optional)
	Comments: The default implementation in	ResultI	returns	an empty string
		  rather than throwing a NotImplemented	exception, since
		  the RID may not always be available and is not critical.
		  See: (1) https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html
		       (2) https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node63.html

   no_hits_found
       See documentation in Bio::Search::Result::ResultI::no_hits_found()

   set_no_hits_found
       See documentation in Bio::Search::Result::ResultI::set_no_hits_found()

   to_string
	Title	: to_string
	Usage	: print	$blast->to_string;
	Function: Returns a string representation for the Blast	result.
		  Primarily intended for debugging purposes.
	Example	: see usage
	Returns	: A string of the form:
		  [GenericResult] <analysis_method> query=<name> <description> db=<database
		  e.g.:
		  [GenericResult] BLASTP query=YEL060C vacuolar	protease B, db=PDBUNIQ
	Args	: None

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich and Steve Chervitz | CONTRIBUTORS | APPENDIX

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