bio::factory::seqanalysisparserfactoryi(3pm) [debian man page]

Bio::Factory::SeqAnalysisParserFactoryI(3pm)		User Contributed Perl Documentation	      Bio::Factory::SeqAnalysisParserFactoryI(3pm)

NAME

       Bio::Factory::SeqAnalysisParserFactoryI - interface describing objects capable
		     of creating SeqAnalysisParserI compliant parsers

SYNOPSIS

	   # initialize an object implementing this interface, e.g.
	   $factory = Bio::Factory::SeqAnalysisParserFactory->new();
	   # obtain a parser object
	   $parser = $factory->get_parser(-input=>$inputobj,
					  -params=>[@params],
					  -method => $method);
	   # $parser is an object implementing Bio::SeqAnalysisParserI
	   # annotate sequence with features produced by parser
	   while(my $feat = $parser->next_feature()) {
	       $seq->add_SeqFeature($feat);
	   }

DESCRIPTION

       This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers.

       The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. See
       Bio::SeqAnalysisParserI for more documentation of this concept.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Hilmar Lapp, Jason Stajich
       Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>

APPENDIX

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

   get_parser
	Title	: get_parser
	Usage	: $factory->get_parser(-input=>$inputobj,
				       [ -params=>[@params] ],
				       -method => $method)
	Function: Creates and returns a parser object for the given input and method.
		  The type of input which is suitable depends on the implementation,
		  but a good-style implementation should allow both file names and
		  streams (filehandles).

		  A particular implementation may not be able to create a parser for
		  the requested method. In this case it shall return undef.

		  Parameters (-params argument) are passed on to the parser object
		  and therefore are specific to the parser to be created. An
		  implementation of this interface should make this argument optional.
	Example :
	Returns : A Bio::SeqAnalysisParserI implementing object.
	Args	: B<input>  - object/file where analysis results are coming from,
		  B<params> - parameter to use when parsing/running analysis
		  B<method> - method of analysis

perl v5.14.2							    2012-03-02			      Bio::Factory::SeqAnalysisParserFactoryI(3pm)

Bio::AnalysisParserI(3pm)				User Contributed Perl Documentation				 Bio::AnalysisParserI(3pm)

NAME

       Bio::AnalysisParserI - Generic analysis output parser interface

SYNOPSIS

	   # get a AnalysisParserI somehow.
	   # Eventually, there may be an Bio::Factory::AnalysisParserFactory.
	   # For now a SearchIO object, an implementation of AnalysisParserI, can be created
	   # directly, as in the following:
	   my $parser = Bio::SearchIO->new(
					   '-file'   => 'inputfile',
					   '-format' => 'blast');

	   while( my $result = $parser->next_result() ) {
	       print "Result:  ", $result->analysis_method,
		     ", Query:	", $result->query_name, "
";

		 while( my $feature = $result->next_feature() ) {
		     print "Feature from ", $feature->start, " to ",
			   $feature->end, "
";
		 }
	   }

DESCRIPTION

       AnalysisParserI is a interface for describing generic analysis result parsers. This module makes no assumption about the nature of analysis
       being parsed, only that zero or more result sets can be obtained from the input source.

       This module was derived from Bio::SeqAnalysisParserI, the differences being

       1. next_feature() was replaced with next_result().
	   Instead of flattening a stream containing potentially multiple analysis results into a single set of features, AnalysisParserI segments
	   the stream in terms of analysis result sets (Bio::AnalysisResultI objects). Each AnalysisResultI can then be queried for its features
	   (if any) as well as other information about the result

       2. AnalysisParserI is a pure interface.
	   It does not inherit from Bio::Root::RootI and does not provide a new() method. Implementations are free to choose how to implement it.

   Rationale (copied from Bio::SeqAnalysisParserI)
       The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used e.g. in high-throughput
       automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers without the
       necessity for modifying the core of the annotation pipeline. In this concept the annotation pipeline has to rely on only a list of methods
       for which to process the results, and a factory from which it can obtain the corresponding parser implementing this interface.

   TODO
       Create Bio::Factory::AnalysisParserFactoryI and Bio::Factory::AnalysisParserFactory for interface and an implementation.  Note that this
       factory could return Bio::SearchIO-derived 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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
       Email sac@bioperl.org

       Authors of Bio::SeqAnalysisParserI on which this module is based: Email jason@bioperl.org Email hlapp@gmx.net

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 _

   next_result
	Title	: next_result
	Usage	: $result = $obj->next_result();
	Function: Returns the next result available from the input, or
		  undef if there are no more results.
	Example :
	Returns : A Bio::Search::Result::ResultI implementing object,
		  or undef if there are no more results.
	Args	: none

perl v5.14.2							    2012-03-02						 Bio::AnalysisParserI(3pm)