Mutator Class Reference

The Mutator class defines a generic interface for classes that perform mutations on a sequence alignment. More...

#include <Mutator.h>

Inheritance diagram for Mutator:

Inheritance graph
[legend]
List of all members.

Public Member Functions

virtual void mutate (node_id_t nodeI, const PhyloTree< TreeNode > &tree, Alignment &evolved_alignment)=0
 Perform a mutation on a sequence alignment.

 Mutator (mems::gnAlignedSequences &donor_seqs)
 The Mutator constructor specifies a sequence alignment from which to draw insertion sequences.

virtual ~Mutator ()

Protected Attributes

mems::gnAlignedSequences & donor
std::vector< genome::gnSequence > donor_table

Private Member Functions

 Mutator ()

Detailed Description

The Mutator class defines a generic interface for classes that perform mutations on a sequence alignment.

Definition at line 19 of file Mutator.h.


Constructor & Destructor Documentation

Mutator::Mutator mems::gnAlignedSequences &  donor_seqs  )  [inline]
 

The Mutator constructor specifies a sequence alignment from which to draw insertion sequences.

Parameters:
donor_seqs Sequence alignment for insertion sequences

Definition at line 48 of file Mutator.h.

References donor_table, and gnStringSource::GetSpec().

virtual Mutator::~Mutator  )  [inline, virtual]
 

Definition at line 26 of file Mutator.h.

Mutator::Mutator  )  [private]
 


Member Function Documentation

virtual void Mutator::mutate node_id_t  nodeI,
const PhyloTree< TreeNode > &  tree,
Alignment evolved_alignment
[pure virtual]
 

Perform a mutation on a sequence alignment.

Given a sequence alignment and a phylogenetic tree relating the sequences in the alignment, this function will perform a mutation on the sequence alignment at a particular point in the alignment's phylogenetic history.

Parameters:
nodeI The node in the phylogenetic tree to perform the mutation at
tree The phylogenetic tree corresponding to the sequence alignment
evolved_alignment An alignment of sequences corresponding to each node (including ancestral nodes) of the phylogenetic tree. If there are multiple entries in the vector, the sequence is not collinear.

Implemented in Inserter, Deleter, and Inverter.


Member Data Documentation

mems::gnAlignedSequences& Mutator::donor [protected]
 

Definition at line 41 of file Mutator.h.

std::vector< genome::gnSequence > Mutator::donor_table [protected]
 

Definition at line 42 of file Mutator.h.

Referenced by Mutator().


The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:00:54 2013 for sgEvolver by doxygen 1.3.6