Bio::Seq
BaseSeqProcessor
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Summary
Bio::Seq::BaseSeqProcessor - Base implementation for a SequenceProcessor
Package variables
No package variables defined.
Inherit
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
Methods description
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 |
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) |
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 |
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 |
Title : sequence_factory
Usage : $seqio->sequence_factory($seqfactory)
Function: Get the Bio::Factory::SequenceFactoryI
Returns : Bio::Factory::SequenceFactoryI
Args : none |
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) |
Title : close
Usage :
Function: Closes the stream. We override this here in order to cascade
to the source stream.
Example :
Returns :
Args : none |
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
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;} | 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'};} | sub next_seq
{ my $self = shift;
my $seq;
if(@{$self->{'_queue'}} == 0) {
my @seqs = ();
while($seq = $self->source_stream->next_seq()) {
@seqs = $self->process_seq($seq);
last if @seqs;
}
push(@{$self->{'_queue'}}, @seqs) if @seqs;
}
$seq = shift(@{$self->{'_queue'}});
return $seq;} | sub write_seq
{ my ($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;} | sub sequence_factory
{ my $self = shift;
return $self->{'sequence_factory'} = shift if @_;
return $self->{'sequence_factory'};} | sub object_factory
{ return shift->sequence_factory(@_); } | sub close
{ my $self = shift;
return $self->source_stream() ? $self->source_stream->close(@_) : 1;} | sub process_seq
{ my ($self,$seq) = @_;
return ($seq);
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
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bioperl-l@bioperl.org - General discussion
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Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and
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with code and data examples if at all possible.
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/
Email hlapp at gmx.net
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| To be overridden by a derived class | Top |