plucky (3) Bio::SeqAnalysisParserI.3pm.gz

NAME

       Bio::SeqAnalysisParserI - Sequence analysis output parser interface

SYNOPSIS

           # get a SeqAnalysisParserI somehow, e.g. by
           my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
                                   '-input' => 'inputfile', '-method' => 'genscan');
           while( my $feature = $parser->next_feature() ) {
               print "Feature from ", $feature->start, " to ", $feature->end, "\n";
           }

DESCRIPTION

       SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. Sequence
       analysis in this sense is a search for similarities or the identification of features on the sequence,
       like a databank search or a a gene prediction result.

       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.

       See Bio::Factory::SeqAnalysisParserFactoryI and Bio::Factory::SeqAnalysisParserFactory for interface and
       an implementation of the corresponding factory.

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, 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 _

   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