Bio::Seq::BaseSeqProceUser(Contributed Perl DocumBio::Seq::BaseSeqProcessor(3)NAMEBio::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
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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.
perl v5.14.1 2011-07-22 Bio::Seq::BaseSeqProcessor(3)
