Reference

Bio::SeqEvolution::EvolutionI(3pm)

the interface for evolving sequences

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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().

History