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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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 email or the web: bioperl-bugs@bioperl.org http://bioperl.org/bioperl-bugs/ Email hlapp at gmx.net Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : my $obj = new Bio::Seq::BaseSeqProcessor(); 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

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)

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 $seq object into the stream This implementation passes the sequences to the source stream unaltered. You need to override this in order to have sequence objects altered before output. Returns : 1 for success and 0 for error Args : Bio::Seq object

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

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.