Bio::SeqEvolution EvolutionI
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Summary
Bio::SeqEvolution::EvolutionI - the interface for evolving sequences
Package variables
No package variables defined.
Inherit
Bio::Root::RootI
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.
Methods
seqDescriptionCode
next_seqDescriptionCode
mutateDescriptionCode
Methods description
seqcode    nextTop
 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_seqcodeprevnextTop
  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 : -
mutatecodeprevnextTop
  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().
Methods code
seqdescriptionprevnextTop
sub seq {
 shift->throw_not_implemented();
}
next_seqdescriptionprevnextTop
sub next_seq {
shift->throw_not_implemented();
}
mutatedescriptionprevnextTop
sub mutate {
 shift->throw_not_implemented();
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHORTop
  Heikki Lehvaslaiho <heikki at bioperl dot org>
CONTRIBUTORSTop
Additional contributor's names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
annotationTop
 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