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:

[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 ()

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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.

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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]

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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.

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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().

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The documentation for this class was generated from the following file:

• src/Mutator.h

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