mems::AlignmentTreeNode Class Reference

A class that stores alignment-related information as a node in a phylogenetic tree. More...

#include <ProgressiveAligner.h>

Inheritance diagram for mems::AlignmentTreeNode:

[legend]Collaboration diagram for mems::AlignmentTreeNode:

[legend]List of all members.

Public Member Functions
	AlignmentTreeNode ()
Public Attributes
std::vector< boolean >	children_aligned
	have children been aligned?
std::vector< SuperInterval >	ordering
	A total ordering on alignments of sequence contained by leafs below this node.
std::vector< boolean >	parents_aligned
	have parents been aligned?
bool	refined
	true if iterative refinement has been applied to the alignment at this node
genome::gnSequence *	sequence
	The sequence associated with this node, NULL for ancestral nodes.

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Detailed Description

A class that stores alignment-related information as a node in a phylogenetic tree.

Definition at line 36 of file ProgressiveAligner.h.

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Constructor & Destructor Documentation

mems::AlignmentTreeNode::AlignmentTreeNode (   )  [inline]

Definition at line 39 of file ProgressiveAligner.h. References refined.

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Member Data Documentation

std::vector< boolean > mems::AlignmentTreeNode::children_aligned

have children been aligned? Definition at line 42 of file ProgressiveAligner.h. Referenced by mems::chooseNextAlignmentPair(), and mems::createAlignmentTreeRoot().

std::vector< SuperInterval > mems::AlignmentTreeNode::ordering

A total ordering on alignments of sequence contained by leafs below this node. Definition at line 40 of file ProgressiveAligner.h. Referenced by mems::chooseNextAlignmentPair(), and mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints().

std::vector< boolean > mems::AlignmentTreeNode::parents_aligned

have parents been aligned? Definition at line 41 of file ProgressiveAligner.h. Referenced by mems::chooseNextAlignmentPair(), and mems::createAlignmentTreeRoot().

bool mems::AlignmentTreeNode::refined

true if iterative refinement has been applied to the alignment at this node Definition at line 44 of file ProgressiveAligner.h. Referenced by AlignmentTreeNode().

genome::gnSequence* mems::AlignmentTreeNode::sequence

The sequence associated with this node, NULL for ancestral nodes. Definition at line 43 of file ProgressiveAligner.h. Referenced by mems::chooseNextAlignmentPair(), and mems::createAlignmentTreeRoot().

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

• libMems/ProgressiveAligner.h

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