Provided by: libbio-perl-perl_1.7.2-3_all bug

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, "\n";

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

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

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