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Bio::AnalysisResultI(3User Contributed Perl DocumentatiBio::AnalysisResultI(3)

NAME
       Bio::AnalysisResultI - Interface	for analysis result objects

SYNOPSIS
       Bio::AnalysisResultI defines an interface that must be implemented by a
       subclass. So you	cannot create Bio::AnalysisResultI objects, only
       objects that inherit from Bio::AnalysisResultI.

DESCRIPTION
       The AnalysisResultI module provides an interface	for modules
       encapsulating the result	of an analysis that was	carried	out with a
       query sequence and an optional subject dataset.

       The notion of an	analysis represented by	this base class	is that	of a
       unary or	binary operator, taking	either one query or a query and	a
       subject and producing a result. The query is e.g. a sequence, and a
       subject is either a sequence, too, or a database	of sequences.

       This interface defines methods to access	analysis result	data and does
       not impose any constraints on how the analysis result data is acquired.

       Note that this module does not provide support for running an analysis.
       Rather, it is positioned	in the subsequent parsing step (concerned with
       turning raw results into	BioPerl	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 - Steve Chervitz, Hilmar	Lapp
       Email sac@bioperl.org Email hlapp@gmx.net (author of
       Bio::Tools::AnalysisResult on which this	module is based)

COPYRIGHT
       Copyright (c) 2001 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 _

   analysis_query
	Usage	  : $query_obj = $result->analysis_query();
	Purpose	  : Get	a Bio::PrimarySeqI-compatible object representing the entity
		    on which the analysis was performed. Lacks sequence	information.
	Argument  : n/a
	Returns	  : A Bio::PrimarySeqI-compatible object without sequence information.
		    The	sequence will have display_id, description, moltype, and length	data.

   analysis_subject
	Usage	  : $obj = $result->analyis_subject();
	Purpose	  : Get	the subject of the analysis against which it was
		    performed. For similarity searches it will probably	be a database,
		    and	for sequence feature predictions (exons, promoters, etc) it
		    may	be a collection	of models or homologous	sequences that were
		    used, or undefined.
	Returns	  : An object of a type	the depends on the implementation
		    May	also return undef for analyses that don\'t involve subjects.
	Argument  : n/a
	Comments  : Implementation of this method is optional.
		    AnalysisResultI provides a default behavior	of returning undef.

   analysis_subject_version
	Usage	  : $vers = $result->analyis_subject_version();
	Purpose	  : Get	the version string of the subject of the analysis.
	Returns	  : String or undef for	analyses that don\'t involve subjects.
	Argument  : n/a
	Comments  : Implementation of this method is optional.
		    AnalysisResultI provides a default behavior	of returning undef.

   analysis_date
	Usage	  : $date = $result->analysis_date();
	Purpose	  : Get	the date on which the analysis was performed.
	Returns	  : String
	Argument  : n/a

   analysis_method
	Usage	  : $meth = $result->analysis_method();
	Purpose	  : Get	the name of the	sequence analysis method that was used
		    to produce this result (BLASTP, FASTA, etc.). May also be the
		    actual name	of a program.
	Returns	  : String
	Argument  : n/a

   analysis_method_version
	Usage	  : $vers = $result->analysis_method_version();
	Purpose	  : Get	the version string of the analysis program.
		  : (e.g., 1.4.9MP, 2.0a19MP-WashU).
	Returns	  : String
	Argument  : n/a

   next_feature
	Title	: next_feature
	Usage	: $seqfeature =	$obj->next_feature();
	Function: Returns the next feature available in	the analysis result, or
		  undef	if there are no	more features.
	Example	:
	Returns	: A Bio::SeqFeatureI implementing object, or undef if there are	no
		  more features.
	Args	: none

perl v5.24.1			  2017-07-08	       Bio::AnalysisResultI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Steve Chervitz, Hilmar Lapp | COPYRIGHT | DISCLAIMER | APPENDIX

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