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Bio::Search::Result::RUsertContributed Perl DocBio::Search::Result::ResultI(3)

NAME
       Bio::Search::Result::ResultI - Abstract interface to Search Result
       objects

SYNOPSIS
       # Bio::Search::Result::ResultI objects cannot be	instantiated since
       this # module defines a pure interface.

       # Given an object that implements the Bio::Search::Result::ResultI
       interface, # you	can do the following things with it:

	   use Bio::SearchIO;
	   my $io = Bio::SearchIO->new(-format => 'blast',
				       -file   => 't/data/HUMBETGLOA.tblastx');
	   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.

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

AUTHOR
       Aaron Mackey <amackey@virginia.edu>  (original author)

       Steve Chervitz <sac@bioperl.org>

       See the FEEDBACK	section	 for where to send bug reports and comments.

COPYRIGHT
       Copyright (c) 1999-2001 Aaron Mackey, Steve Chervitz. All Rights
       Reserved.

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 _

   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);

   _default sort_hits
	 Title : _default_sort_hits
	 Usage : Do not	call directly.
	 Function: Sort	hits in	descending order by score
	 Args  : None
	 Returns: 1 on success
	 Note  : Used by $result->sort_hits()

   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

   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

   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

   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.

   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

   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();
	Purpose	  : 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
	Argument  : none

   set_no_hits_found
	Usage	  : $blast->set_no_hits_found();
	Purpose	  : Set	boolean	indicator indicating whether or	not any	hits
		    were present in the	report.
	Returns	  : n/a
	Argument  : none

perl v5.24.1			  2017-07-08   Bio::Search::Result::ResultI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | COPYRIGHT | DISCLAIMER | APPENDIX

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