Bio::SeqEvolution::EvolutionI.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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:
   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().