Inserter Class Reference

The Inserter class provides basic functionality for classes that perform insertion mutations. More...

#include <Mutator.h>

Inheritance diagram for Inserter:

[legend]Collaboration diagram for Inserter:

[legend]List of all members.

Public Member Functions
	Inserter (mems::gnAlignedSequences &donor_seqs)
void	mutate (node_id_t nodeI, const PhyloTree< TreeNode > &tree, Alignment &evolved_alignment)
	Perform a mutation on a sequence alignment.
Protected Member Functions
virtual void	getLocation (gnSeqI &source_start, gnSeqI &source_len, gnSeqI &dest, gnSeqI dest_len)=0
void	recursiveInsert (node_id_t cur_node, node_id_t insert_node, const PhyloTree< TreeNode > &t, Alignment &evolved_alignment, gnSeqI point, gnSeqI source_left, gnSeqI source_length)

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Detailed Description

The Inserter class provides basic functionality for classes that perform insertion mutations.

Definition at line 62 of file Mutator.h.

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Constructor & Destructor Documentation

Inserter::Inserter (  mems::gnAlignedSequences &  donor_seqs  )  [inline]

Definition at line 73 of file Mutator.h.

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Member Function Documentation

virtual void Inserter::getLocation (  gnSeqI &  source_start, gnSeqI &  source_len, gnSeqI &  dest, gnSeqI  dest_len )  [protected, pure virtual]

Implemented in IndelInserter, SmallHTInserter, and LargeHTInserter. Referenced by mutate().

void Inserter::mutate (  node_id_t  nodeI, const PhyloTree< TreeNode > &  tree, Alignment &  evolved_alignment )  [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. Implements Mutator. Definition at line 120 of file Mutator.cpp. References Alignment::checkLengths(), debugChecks(), Alignment::getColumnIndex(), getLocation(), recursiveInsert(), and Alignment::sequenceLength().

void Inserter::recursiveInsert (  node_id_t  cur_node, node_id_t  insert_node, const PhyloTree< TreeNode > &  t, Alignment &  evolved_alignment, gnSeqI  point, gnSeqI  source_left, gnSeqI  source_length )  [protected]

Definition at line 133 of file Mutator.cpp. References Alignment::applyGapInsertion(), and Alignment::applyInsertion(). Referenced by mutate().

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

• src/Mutator.h
• src/Mutator.cpp

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