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://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 _

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