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Bio::Tools::AnalysisReUser(Contributed Perl DocumBio::Tools::AnalysisResult(3)

NAME
       Bio::Tools::AnalysisResult - Base class for analysis result objects and
       parsers

SYNOPSIS
	   # obtain a AnalysisResult derived object somehow

	   print "Method ", $result->analysis_method(),
		 ", version ", $result->analysis_method_version(),
		 ", performed on ", $result->analysis_date(), "\n";

	   # annotate a	sequence utilizing SeqAnalysisParserI methods
	   while($feat = $result->next_feature()) {
	       $seq->add_SeqFeature($feat);
	   }
	   $result->close();

	   # query object, e.g.	a Bio::SeqI implementing object
	   $queryseq = $result->analysis_query();

	   # Subject of	the analysis --	may be undefined. Refer	to derived module
	   # to	find out what is returned.
	   $subject = $result->analysis_subject();

DESCRIPTION
       The AnalysisResult module is supposed to	be the base class for modules
       encapsulating parsers and interpreters for the result of	a analysis
       that was	carried	out with a query sequence.

       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 module also	implements the Bio::SeqAnalysisParserI interface, and
       thus can	be used	wherever such an object	fits.  See
       Bio::SeqAnalysisParserI.	 Developers will find a	ready-to-use parse()
       method, but need	to implement next_feature() in an inheriting class.
       Support for initialization with input file names	and reading from
       streams is also ready to	use.

       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 - Hilmar	Lapp
       Email hlapp-at-gmx.net

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

   _initialize_state
	Title	: _initialize_state
	Usage	: n/a; usually called by _initialize()
	Function: This method is for BioPerl B<developers> only, as indicated by the
		  leading underscore in	its name.

		  Performs initialization or reset of the state	of this	object.	The
		  difference to	_initialize() is that it may be	called at any time,
		  and repeatedly within	the lifetime of	this object. B<Note>, however,
		  that this is potentially dangerous in	a multi-threading
		  environment. In general, calling this	method twice is	discouraged
		  for this reason.

		  This method is supposed to reset the state such that any 'history'
		  is lost. State information that does not change during object
		  lifetime is not considered as	history, e.g. parent, name, etc	shall
		  not be reset.	An inheriting object should only be concerned with
		  state	information it introduces itself, and for everything else
		  call SUPER::_initialize_state(@args).

		  An example is	parsing	an input file: a state reset implies
		  discarding any unread	input, and the actual input itself, followed
		  by setting the new input.

		  The argument syntax is the same as for L<new()|new> and L<_initialize()|_initialize>,
		  i.e.,	named parameters following the -name=>$value convention.
		  The following	parameters are dealt with by the implementation
		  provided here:
		     -INPUT, -FH, -FILE
		  (tags	are case-insensitive).
	Example	:
	Returns	:
	Args	:

   analysis_query
	Usage	  : $query_obj = $result->analysis_query();
	Purpose	  : Set/Get the	name of	the query used to generate the result, that
		    is,	the entity on which the	analysis was performed.	Will mostly
		    be a sequence object (Bio::PrimarySeq compatible).
	Argument  :
	Returns	  : The	object set before. Mostly a Bio::PrimarySeq compatible object.

   analysis_subject
	Usage	  : $result->analyis_subject();
	Purpose	  : Set/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	  : The	object that was	set before, or undef.
	Argument  :

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

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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp | APPENDIX

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