Raw content of Bio::Factory::SequenceStreamI
<![CDATA[# $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 <jason@bioperl.org>
#
# 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.
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://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
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;
]]>