Reference

Bio::Seq::BaseSeqProcessor(3pm)

Base implementation for a SequenceProcessor

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

  https://github.com/bioperl/bioperl-live/issues

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.

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