libMems/PhyloTree.h File Reference

#include <vector>
#include <string>
#include <iostream>
#include <sstream>
#include <stack>

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Namespaces
namespace	std
Classes
class	PhyloTree
class	TreeNode
Typedefs
typedef size_t	node_id_t
Functions
template<class TreeType> void	getDescendants (TreeType &alignment_tree, node_id_t node, std::vector< node_id_t > &descendants)
	determine which nodes are descendants of a given node
template<class TreeType> void	getLeaves (TreeType &tree, node_id_t node, std::vector< node_id_t > &leaves)
	determine which nodes are leaf nodes below a given node

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Typedef Documentation

typedef size_t node_id_t

Definition at line 15 of file PhyloTree.h. Referenced by mems::ProgressiveAligner::alignPP(), mems::chooseNextAlignmentPair(), mems::ProgressiveAligner::computeAvgAncestralMatchScores(), mems::ProgressiveAligner::computeInternalNodeDistances(), mems::ProgressiveAligner::constructLcbTrackingMatches(), mems::ProgressiveAligner::ConstructSuperIntervalFromMSA(), mems::containsNode(), mems::countUnrefined(), mems::ProgressiveAligner::doGappedAlignment(), mems::extendRootBranches(), mems::ProgressiveAligner::extractAlignment(), mems::ProgressiveAligner::FixLeftEnds(), mems::ProgressiveAligner::getAlignedChildren(), mems::ProgressiveAligner::getAlignment(), mems::ProgressiveAligner::getAncestralMatches(), getDescendants(), getLeaves(), mems::ProgressiveAligner::getPath(), mems::ProgressiveAligner::linkSuperIntervals(), mems::makeAlignmentTree(), mems::markAsRefined(), mems::ProgressiveAligner::pairwiseScoreTrackingMatches(), mems::ProgressiveAligner::propagateDescendantBreakpoints(), mems::propagateInvert(), PhyloTree< T >::readTree(), mems::ProgressiveAligner::recursiveApplyAncestralBreakpoints(), mems::ProgressiveAligner::refineAlignment(), mems::rerootTree(), mems::ProgressiveAligner::translateGappedCoordinates(), and PhyloTree< T >::writeTree().

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Function Documentation

template<class TreeType> void getDescendants (  TreeType &  alignment_tree, node_id_t  node, std::vector< node_id_t > &  descendants )

determine which nodes are descendants of a given node Definition at line 331 of file PhyloTree.h. References node_id_t. Referenced by mems::ProgressiveAligner::alignProfileToProfile().

template<class TreeType> void getLeaves (  TreeType &  tree, node_id_t  node, std::vector< node_id_t > &  leaves )

determine which nodes are leaf nodes below a given node Definition at line 353 of file PhyloTree.h. References node_id_t.

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