Bio::Seq BaseSeqProcessor
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Summary
Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor
Package variables
No package variables defined.
Inherit
Bio::Factory::SequenceProcessorI Bio::Root::Root
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().
Methods
newDescriptionCode
source_streamDescriptionCode
next_seqDescriptionCode
write_seqDescriptionCode
sequence_factoryDescriptionCode
object_factoryDescriptionCode
closeDescriptionCode
process_seqDescriptionCode
Methods description
newcode    nextTop
 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
source_streamcodeprevnextTop
 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)
next_seqcodeprevnextTop
 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_seqcodeprevnextTop
 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_factorycodeprevnextTop
 Title   : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : none
object_factorycodeprevnextTop
 Title   : object_factory
Usage : $obj->object_factory($newval)
Function: This is an alias to sequence_factory with a more generic name.
Example :
Returns : a Bio::Factory::ObjectFactoryI compliant object
Args : on set, new value (a Bio::Factory::ObjectFactoryI
compliant object or undef, optional)
closecodeprevnextTop
 Title   : close
Usage :
Function: Closes the stream. We override this here in order to cascade
to the source stream.
Example :
Returns :
Args : none
process_seqcodeprevnextTop
 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.
Methods code
newdescriptionprevnextTop
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;
}
source_streamdescriptionprevnextTop
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'};
}
next_seqdescriptionprevnextTop
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 $seq;
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self, @seqs) = @_;
    my $ret;
    foreach my $seq (@seqs) {
        foreach my $processed ($self->process_seq($seq)) {
            $ret = $self->source_stream->write_seq($seq);
            return unless $ret;
        }
    }
    return $ret;
}
sequence_factorydescriptionprevnextTop
sub sequence_factory {
    my $self = shift;

    return $self->{'sequence_factory'} = shift if @_;
    return $self->{'sequence_factory'};
}
object_factorydescriptionprevnextTop
sub object_factory {
    return shift->sequence_factory(@_);
}
closedescriptionprevnextTop
sub close {
    my $self = shift;
    return $self->source_stream() ? $self->source_stream->close(@_) : 1;
}
process_seqdescriptionprevnextTop
sub process_seq {
    my ($self,$seq) = @_;

    return ($seq);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar LappTop
Email hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Bio::Factory::SequenceProcessorI methodsTop
Bio::Factory::SequenceStreamI methodsTop
To be overridden by a derived classTop