Bio::Seq::BaseSeqProcessor(3pm) 			User Contributed Perl Documentation			   Bio::Seq::BaseSeqProcessor(3pm)

NAME

       Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor

SYNOPSIS

	   # you need to derive your own processor from this one

DESCRIPTION

       This provides just a basic framework for implementations of Bio::Factory::SequenceProcessorI.

       Essentially what it does is support a parameter to new() to set sequence factory and source stream, and a next_seq() implementation that
       will use a queue to be filled by a class overriding process_seq().

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 the
       Bioperl mailing list.  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 of the bugs and their resolution. Bug reports can be submitted via the
       web:

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

AUTHOR - Hilmar Lapp
       Email hlapp at gmx.net

APPENDIX

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

   new
	Title	: new
	Usage	: my $obj = Bio::Seq::BaseSeqProcessor->new();
	Function: Builds a new Bio::Seq::BaseSeqProcessor object
	Returns : an instance of Bio::Seq::BaseSeqProcessor
	Args	: Named parameters. Currently supported are
		    -seqfactory  the Bio::Factory::SequenceFactoryI object to use
		    -source_stream the Bio::Factory::SequenceStreamI object to
				 which we are chained

Bio::Factory::SequenceProcessorI methods
   source_stream
	Title	: source_stream
	Usage	: $obj->source_stream($newval)
	Function: Get/set the source sequence stream for this sequence
		  processor.

	Example :
	Returns : A Bio::Factory::SequenceStreamI compliant object
	Args	: on set, new value (a Bio::Factory::SequenceStreamI compliant
		  object)

Bio::Factory::SequenceStreamI methods
   next_seq
	Title	: next_seq
	Usage	: $seq = stream->next_seq
	Function: Reads the next sequence object from the stream and returns it.

		  This implementation will obtain objects from the source
		  stream as necessary and pass them to process_seq() for
		  processing. This method will return the objects one at a
		  time that process_seq() returns.

	Returns : a Bio::Seq sequence object
	Args	: none

       See Bio::Factory::SequenceStreamI::next_seq

   write_seq
	Title	: write_seq
	Usage	: $stream->write_seq($seq)
	Function: Writes the result(s) of processing the sequence object into
		  the stream.

		  You need to override this method in order not to alter
		  (process) sequence objects before output.

	Returns : 1 for success and 0 for error. The method stops attempting
		  to write objects after the first error returned from the
		  source stream. Otherwise the return value is the value
		  returned from the source stream from writing the last
		  object resulting from processing the last sequence object
		  given as argument.

	Args	: Bio::SeqI object, or an array of such objects

   sequence_factory
	Title	: sequence_factory
	Usage	: $seqio->sequence_factory($seqfactory)
	Function: Get the Bio::Factory::SequenceFactoryI
	Returns : Bio::Factory::SequenceFactoryI
	Args	: none

   object_factory
	Title	: object_factory
	Usage	: $obj->object_factory($newval)
	Function: This is an alias to sequence_factory with a more generic name.
	Example :
	Returns : a L<Bio::Factory::ObjectFactoryI> compliant object
	Args	: on set, new value (a L<Bio::Factory::ObjectFactoryI>
		  compliant object or undef, optional)

   close
	Title	: close
	Usage	:
	Function: Closes the stream. We override this here in order to cascade
		  to the source stream.
	Example :
	Returns :
	Args	: none

To be overridden by a derived class
   process_seq
	Title	: process_seq
	Usage	:
	Function: This is the method that is supposed to do the actual
		  processing. It needs to be overridden to do what you want
		  it to do.

		  Generally, you do not have to override or implement any other
		  method to derive your own sequence processor.

		  The implementation provided here just returns the unaltered
		  input sequence and hence is not very useful other than
		  serving as a neutral default processor.

	Example :
	Returns : An array of zero or more Bio::PrimarySeqI (or derived
		  interface) compliant object as the result of processing the
		  input sequence.
	Args	: A Bio::PrimarySeqI (or derived interface) compliant object
		  to be processed.

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