NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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().