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# BioPerl module for Bio::SeqEvolution::EvolutionI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki at bioperl dot org>
#
# Copyright Heikki Lehvaslaiho
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SeqEvolution::EvolutionI - the interface for evolving sequences
=head1 SYNOPSIS
# not an instantiable class
=head1 DESCRIPTION
This is the interface that all classes that mutate sequence objects in
constant fashion must implement. A good example is
Bio::SeqEvolution::DNAPoint.
=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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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 the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR
Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
=head1 CONTRIBUTORS
Additional contributor's 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::SeqEvolution::EvolutionI;
use strict;
use base qw(Bio::Root::RootI);
=head2 annotation
Title : annotation
Usage : $obj->annotation($newval)
Function: Get the annotation collection for this annotatable object.
Example :
Returns : a Bio::AnnotationCollectionI implementing object, or undef
Args : on set, new value (a Bio::AnnotationCollectionI
implementing object, optional) (an implementation may not
support changing the annotation collection)
See L<Bio::AnnotationCollectionI>
=cut
=head2 seq
Title : seq
Usage : $obj->seq($newval)
Function: Set the sequence object for the original sequence
Returns : The sequence object
Args : newvalue (optional)
Setting this will reset mutation and generated mutation counters.
=cut
sub seq { shift->throw_not_implemented(); }
=head2 next_seq
Title : next_seq
Usage : $obj->next_seq
Function: Evolve the reference sequence to desired level
Returns : A new sequence object mutated from the reference sequence
Args : -
=cut
sub next_seq{ shift->throw_not_implemented(); }
=head2 mutate
Title : mutate
Usage : $obj->mutate
Function: mutate the sequence at the given location according to the model
Returns : true
Args : integer, start location of the mutation, required argument
Called from next_seq().
=cut
sub mutate { shift->throw_not_implemented(); }
1;
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