Raw content of Bio::Factory::SequenceProcessorI # $Id: SequenceProcessorI.pm,v 1.1 2002/10/24 18:35:46 lapp Exp $ # # BioPerl module for Bio::Factory::SequenceProcessorI # # 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::Factory::SequenceProcessorI - Interface for chained sequence processing algorithms =head1 SYNOPSIS use Bio::SeqIO; use MySeqProcessor; # is-a Bio::Factory::SequenceProcessorI # obtain your source stream, e.g., an EMBL file my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => 'embl'); # create your processor (it must implement this interface) my $seqalgo = MySeqProcessor->new(); # chain together $seqalgo->source_stream($seqin); # you could create more processors and chain them one after another # ... # finally, the last link in the chain is your SeqIO stream my $seqpipe = $seqalgo; # once you've established the pipeline, proceed as if you had a # single SeqIO stream while(my $seq = $seqpipe->next_seq()) { # ... do something ... } =head1 DESCRIPTION This defines an interface that allows seamless chaining of sequence processing algorithms encapsulated in modules while retaining the overall Bio::SeqIO interface at the end of the pipeline. This is especially useful if you want an easily configurable processing pipeline of re-usable algorithms as building blocks instead of (hard-)coding the whole algorithm in a single script. There are literally no restrictions as to what an individual module can do with a sequence object it obtains from the source stream before it makes it available through its own next_seq() method. It can manipulate the sequence object, but otherwise keep it intact, but it can also create any number of new sequence objects from it, or it can discard some, or any combination thereof. The only requirement is that its next_seq() method return Bio::PrimarySeqI compliant objects. In order to play nice, if a processor creates new objects it should try to use the same sequence factory that the source stream uses, but this is not strongly mandated. =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::Factory::SequenceProcessorI; use vars qw(@ISA); use strict; use Carp; use Bio::Root::RootI; use Bio::Factory::SequenceStreamI; @ISA = qw( Bio::Factory::SequenceStreamI ); =head2 source_stream Title : source_stream Usage : $obj->source_stream($newval) Function: Get/set the source sequence stream for this sequence processor. An implementation is not required to allow set, but will usually do so. Example : Returns : A Bio::Factory::SequenceStreamI compliant object Args : on set, new value (a Bio::Factory::SequenceStreamI compliant object) =cut sub source_stream{ shift->throw_not_implemented(); } =head1 Bio::Factory::SequenceStreamI methods The requirement to implement these methods is inherited from L<Bio::Factory::SequenceStreamI>. An implementation may not necessarily have to implement all methods in a meaningful way. Which methods will be necessary very much depends on the context in which an implementation of this interface is used. E.g., if it is only used for post-processing sequences read from a SeqIO stream, write_seq() will not be used and hence does not need to be implemented in a meaningful way (it may in fact even throw an exception). Also, since an implementor will already receive built objects from a sequence stream, sequence_factory() may or may not be relevant, depending on whether the processing method does or does not involve creating new objects. =cut =head2 next_seq Title : next_seq Usage : $seq = stream->next_seq Function: Reads the next sequence object from the stream and returns it. In the case of a non-recoverable situation an exception will be thrown. Do not assume that you can resume parsing the same stream after catching the exception. Note that you can always turn recoverable errors into exceptions by calling $stream->verbose(2). Returns : a Bio::Seq sequence object Args : none See L<Bio::Root::RootI> =cut =head2 write_seq Title : write_seq Usage : $stream->write_seq($seq) Function: writes the $seq object into the stream Returns : 1 for success and 0 for error Args : Bio::Seq object =cut =head2 sequence_factory Title : sequence_factory Usage : $seqio->sequence_factory($seqfactory) Function: Get the Bio::Factory::SequenceFactoryI Returns : Bio::Factory::SequenceFactoryI Args : none =cut 1;