Bio::SeqEvolution::EvoUseroContributed Perl DoBio::SeqEvolution::EvolutionI(3)NAMEBio::SeqEvolution::EvolutionI - the interface for evolving sequences
SYNOPSIS
# not an instantiable class
DESCRIPTION
This is the interface that all classes that mutate sequence objects in
constant fashion must implement. A good example is
Bio::SeqEvolution::DNAPoint.
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
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.
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:
http://bugzilla.open-bio.org/
AUTHOR
Heikki Lehvaslaiho E<lt>heikki at bioperl dot orgE<gt>
CONTRIBUTORS
Additional contributor's names and emails here
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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 Bio::AnnotationCollectionI
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.
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 : -
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().
perl v5.14.1 2011-07-22 Bio::SeqEvolution::EvolutionI(3)
