Raw content of Bio::SeqAnalysisParserI
<![CDATA[# $Id: SeqAnalysisParserI.pm,v 1.12 2002/12/01 00:05:19 jason Exp $
#
# BioPerl module for Bio::SeqAnalysisParserI
#
# Cared for by Jason Stajich <jason@bioperl.org>,
# and Hilmar Lapp <hlapp@gmx.net>
#
# Copyright Jason Stajich, Hilmar Lapp
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqAnalysisParserI - Sequence analysis output parser interface
=head1 SYNOPSIS
# get a SeqAnalysisParserI somehow, e.g. by
my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
'-input' => 'inputfile', '-method' => 'genscan');
while( my $feature = $parser->next_feature() ) {
print "Feature from ", $feature->start, " to ", $feature->end, "\n";
}
=head1 DESCRIPTION
SeqAnalysisParserI is a generic interface for describing sequence analysis
result parsers. Sequence analysis in this sense is a search for similarities
or the identification of features on the sequence, like a databank search or a
a gene prediction result.
The concept behind this interface is to have a generic interface in sequence
annotation pipelines (as used e.g. in high-throughput automated
sequence annotation). This interface enables plug-and-play for new analysis
methods and their corresponding parsers without the necessity for modifying
the core of the annotation pipeline. In this concept the annotation pipeline
has to rely on only a list of methods for which to process the results, and a
factory from which it can obtain the corresponding parser implementing this
interface.
See Bio::Factory::SeqAnalysisParserFactoryI and
Bio::Factory::SeqAnalysisParserFactory for interface and an implementation
of the corresponding factory.
=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 one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Hilmar Lapp, Jason Stajich
Email Hilmar Lapp E<lt>hlapp@gmx.netE<gt>, Jason Stajich E<lt>jason@bioperl.orgE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::SeqAnalysisParserI;
use strict;
use vars qw(@ISA);
use Bio::Root::RootI;
use Carp;
@ISA = qw(Bio::Root::RootI);
=head2 next_feature
Title : next_feature
Usage : $seqfeature = $obj->next_feature();
Function: Returns the next feature available in the analysis result, or
undef if there are no more features.
Example :
Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
more features.
Args : none
=cut
sub next_feature {
my ($self) = shift;
$self->throw_not_implemented();
}
1;
]]>