Bio::Seq::BaseSeqProcessor.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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.