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
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)
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
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
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.