Bio::SeqEvolution
EvolutionI
Summary
Bio::SeqEvolution::EvolutionI - the interface for evolving sequences
Package variables
No package variables defined.
Inherit
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
Methods description
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. |
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 : - |
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
sub seq
{ shift->throw_not_implemented(); } | sub next_seq
{shift->throw_not_implemented(); } | sub mutate
{ shift->throw_not_implemented(); } | General documentation
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
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