# $Id: BaseSeqProcessor.pm 16123 2009-09-17 12:57:27Z cjfields $ # # BioPerl module for Bio::Seq::BaseSeqProcessor # # Please direct questions and support issues to # # Cared for by Hilmar Lapp # # 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. 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/wiki/Mailing_lists - About the mailing lists =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =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 the web: http://bugzilla.open-bio.org/ =head1 AUTHOR - Hilmar Lapp Email hlapp at gmx.net =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 strict; # Object preamble - inherits from Bio::Root::Root use base qw(Bio::Root::Root Bio::Factory::SequenceProcessorI); =head2 new Title : new Usage : my $obj = Bio::Seq::BaseSeqProcessor->new(); Function: Builds a new Bio::Seq::BaseSeqProcessor object Returns : an instance of Bio::Seq::BaseSeqProcessor Args : Named parameters. Currently supported are -seqfactory the Bio::Factory::SequenceFactoryI object to use -source_stream the Bio::Factory::SequenceStreamI object to which we are chained =cut sub new { my($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 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 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 =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 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 =cut 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; } =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 compliant object Args : on set, new value (a L 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;