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


    # you need to derive your own processor from this one


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().


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


 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


 Title   : source_stream
 Usage   : $obj->source_stream($newval)
 Function: Get/set the source sequence stream for this sequence

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

Bio::Factory::SequenceStreamI methods


 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


 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


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


 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)


 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


 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.