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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Factory/SequenceStreamI.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,134 @@
+# $Id: SequenceStreamI.pm,v 1.3 2002/10/22 07:45:14 lapp Exp $
+#
+# BioPerl module for Bio::Factory::SequenceStreamI
+#
+# Cared for by Jason Stajich <[e-mail]>
+#
+# Copyright Jason Stajich
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Factory::SequenceStreamI - Interface describing the basics of a Sequence Stream.
+
+=head1 SYNOPSIS
+
+  # get a SequenceStreamI object somehow like with SeqIO
+  use Bio::SeqIO;
+  my $in = new Bio::SeqIO(-file => '< fastafile');
+  while( my $seq = $in->next_seq ) {
+  }
+
+=head1 DESCRIPTION
+
+This interface is for describing objects which produces
+Bio::PrimarySeqI objects or processes Bio::PrimarySeqI objects to a
+data stream.
+
+=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://bugzilla.bioperl.org/
+
+=head1 AUTHOR - Jason Stajich
+
+Email [e-mail]
+
+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::SequenceStreamI;
+use vars qw(@ISA);
+use strict;
+use Bio::Root::RootI;
+
+@ISA= qw(Bio::Root::RootI);
+
+=head2 next_seq
+
+ Title   : next_seq
+ Usage   : $seq = stream->next_seq
+ Function: Reads the next sequence object from the stream and returns it.
+
+           Certain driver modules may encounter entries in the stream that
+           are either misformatted or that use syntax not yet understood
+           by the driver. If such an incident is recoverable, e.g., by
+           dismissing a feature of a feature table or some other non-mandatory
+           part of an entry, the driver will issue a warning. 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
+
+sub next_seq {
+    shift->throw_not_implemented();
+}
+
+=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
+
+sub write_seq {
+    shift->throw_not_implemented();
+}
+
+=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{
+    shift->throw_not_implemented();
+}
+
+1;