diff variant_effect_predictor/Bio/Factory/SequenceProcessorI.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/Factory/SequenceProcessorI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $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.
+
+  [e-mail]              - 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:
+
+  [e-mail]
+  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;