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
Returns : A Bio::Factory::SequenceStreamI compliant object
Args : on set, new value (a Bio::Factory::SequenceStreamI compliant
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
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.
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
Function: Closes the stream. We override this here in order to cascade
to the source stream.
Args : none
Title : process_seq
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.
Returns : An array of zero or more Bio::PrimarySeqI (or derived
interface) compliant object as the result of processing the
Args : A Bio::PrimarySeqI (or derived interface) compliant object
to be processed.
To install BioPerl, copy and paste the appropriate command in to your terminal.
perl -MCPAN -e shell
For more information on module installation, please visit the detailed CPAN module installation guide.