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

perl v5.32.1                                       2021-08-15                          Bio::AnalysisParserI(3pm)