Raw content of Bio::Seq::BaseSeqProcessor
<![CDATA[# $Id: BaseSeqProcessor.pm,v 1.2 2002/11/02 21:04:19 lapp Exp $
#
# BioPerl module for Bio::Seq::BaseSeqProcessor
#
# Cared for by Hilmar Lapp <hlapp at gmx.net>
#
# Copyright Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
#
# (c) Hilmar Lapp, hlapp at gmx.net, 2002.
# (c) GNF, Genomics Institute of the Novartis Research Foundation, 2002.
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor
=head1 SYNOPSIS
# you need to derive your own processor from this one
=head1 DESCRIPTION
This provides just a basic framework for implementations of
L<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().
=head1 FEEDBACK
=head2 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/MailList.shtml - About the mailing lists
=head2 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/
=head1 AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::BaseSeqProcessor;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Factory::SequenceProcessorI;
@ISA = qw(Bio::Root::Root Bio::Factory::SequenceProcessorI);
=head2 new
Title : new
Usage : my $obj = new Bio::Seq::BaseSeqProcessor();
Function: Builds a new Bio::Seq::BaseSeqProcessor object
Returns : an instance of Bio::Seq::BaseSeqProcessor
Args : Named parameters. Currently supported are
-seqfactory the Bio::Factory::SequenceFactoryI object to use
-source_stream the Bio::Factory::SequenceStreamI object to
which we are chained
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($stream,$fact) =
$self->_rearrange([qw(SOURCE_STREAM SEQFACTORY)], @args);
$self->{'_queue'} = [];
$self->sequence_factory($fact) if $fact;
$self->source_stream($stream) if $stream;
return $self;
}
=head1 L<Bio::Factory::SequenceProcessorI> methods
=cut
=head2 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)
=cut
sub source_stream{
my $self = shift;
if(@_) {
my $stream = shift;
my $fact = $stream->sequence_factory();
$self->sequence_factory($fact)
unless $self->sequence_factory() || (! $fact);
return $self->{'source_stream'} = $stream;
}
return $self->{'source_stream'};
}
=head1 L<Bio::Factory::SequenceStreamI> methods
=cut
=head2 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 L<Bio::Factory::SequenceStreamI::next_seq>
=cut
sub next_seq{
my $self = shift;
my $seq;
# if the queue is empty, fetch next from source and process it
if(@{$self->{'_queue'}} == 0) {
my @seqs = ();
while($seq = $self->source_stream->next_seq()) {
@seqs = $self->process_seq($seq);
# we may get zero seqs returned
last if @seqs;
}
push(@{$self->{'_queue'}}, @seqs) if @seqs;
}
# take next from the queue of seqs
$seq = shift(@{$self->{'_queue'}});
return $seq;
}
=head2 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
=cut
sub write_seq{
return shift->source_stream->write_seq(@_);
}
=head2 sequence_factory
Title : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : none
=cut
sub sequence_factory{
my $self = shift;
return $self->{'sequence_factory'} = shift if @_;
return $self->{'sequence_factory'};
}
=head2 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)
=cut
sub object_factory{
return shift->sequence_factory(@_);
}
=head2 close
Title : close
Usage :
Function: Closes the stream. We override this here in order to cascade
to the source stream.
Example :
Returns :
Args : none
=cut
sub close{
my $self = shift;
return $self->source_stream() ? $self->source_stream->close(@_) : 1;
}
=head1 To be overridden by a derived class
=cut
=head2 process_seq
Title : process_seq
Usage :
Function: This is the method that is supposed to do the actual
processing. It needs to be overridden to do what you want
it to do.
Generally, you do not have to override or implement any other
method to derive your own sequence processor.
The implementation provided here just returns the unaltered
input sequence and hence is not very useful other than
serving as a neutral default processor.
Example :
Returns : An array of zero or more Bio::PrimarySeqI (or derived
interface) compliant object as the result of processing the
input sequence.
Args : A Bio::PrimarySeqI (or derived interface) compliant object
to be processed.
=cut
sub process_seq{
my ($self,$seq) = @_;
return ($seq);
}
1;
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