cuSeqTreeAlg.hpp File Reference

#include <algo/structure/cd_utils/cuSeqTreeStream.hpp>
#include <algo/structure/cd_utils/cuDistmat.hpp>

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Classes
class	TreeAlgorithm

Enumerations
enum	ETreeMethod { eNoTreeMethod =0 , eSLC =1 , eNJ =2 }

Functions
	USING_SCOPE (objects)
string	GetTreeAlgorithmName (ETreeMethod algorithm)
void	MidpointRootSeqTree (const SeqTree &oldTree, SeqTree &newTree)
bool	GetMaxPath (const SeqTree &atree, double &dMax, SeqTree::iterator &end1, SeqTree::iterator &end2)
bool	GetMaxPath (const SeqTree::iterator &cursor, double &dMax, double &dBranch1, SeqTree::iterator &end1, double &dBranch2, SeqTree::iterator &end2)

Variables
const int	NUMBER_OF_TREE_ALGORITHMS = 2
const string	TREE_ALGORITHM_NAMES []
const ETreeMethod	GLOBAL_DEFAULT_ALGORITHM = eNJ
const double	RESET_WITH_TINY_DISTANCE = 0.0001

Enumeration Type Documentation

ETreeMethod

enum ETreeMethod

Enumerator
eNoTreeMethod
eSLC
eNJ

Definition at line 53 of file cuSeqTreeAlg.hpp.

Function Documentation

GetMaxPath() [1/2]

bool GetMaxPath	(	const SeqTree &	atree,
		double &	dMax,
		SeqTree::iterator &	end1,
		SeqTree::iterator &	end2
	)

Definition at line 203 of file cuSeqTreeAlg.cpp.

References tree< T, tree_node_allocator >::append_child(), tree< T, tree_node_allocator >::begin(), tree< T, tree_node_allocator >::clear(), tree< T, tree_node_allocator >::end(), tree< T, tree_node_allocator >::insert(), tree< T, tree_node_allocator >::iterator_base::is_valid(), tree< T, tree_node_allocator >::next_sibling(), result, and tree< T, tree_node_allocator >::size().

Referenced by GetMaxPath(), and MidpointRootSeqTree().

GetMaxPath() [2/2]

bool GetMaxPath	(	const SeqTree::iterator &	cursor,
		double &	dMax,
		double &	dBranch1,
		SeqTree::iterator &	end1,
		double &	dBranch2,
		SeqTree::iterator &	end2
	)

Definition at line 273 of file cuSeqTreeAlg.cpp.

References assert, tree< T, tree_node_allocator >::iterator_base::begin(), tree< T, tree_node_allocator >::iterator_base::end(), GetMaxPath(), tree< T, tree_node_allocator >::iterator_base::number_of_children(), and result.

GetTreeAlgorithmName()

string GetTreeAlgorithmName

(

ETreeMethod

algorithm

)

Definition at line 47 of file cuSeqTreeNj.cpp.

References TREE_ALGORITHM_NAMES.

Referenced by SeqTreeAPI::layoutSeqTree().

MidpointRootSeqTree()

void MidpointRootSeqTree	(	const SeqTree &	oldTree,
		SeqTree &	newTree
	)

Definition at line 49 of file cuSeqTreeAlg.cpp.

References tree< T, tree_node_allocator >::append_child(), tree< T, tree_node_allocator >::iterator_base::begin(), tree< T, tree_node_allocator >::begin(), SeqItem::distance, tree< T, tree_node_allocator >::iterator_base::end(), tree< T, tree_node_allocator >::end(), GetMaxPath(), tree< T, tree_node_allocator >::iterator_base::is_valid(), newTree(), tree< T, tree_node_allocator >::next_sibling(), tree< T, tree_node_allocator >::number_of_children(), tree< T, tree_node_allocator >::number_of_siblings(), tree< T, tree_node_allocator >::parent(), tree< T, tree_node_allocator >::previous_sibling(), tree< T, tree_node_allocator >::reparent(), tree< T, tree_node_allocator >::reroot(), result, and tree< T, tree_node_allocator >::size().

Referenced by TreeAlgorithm::midpointRootIfNeeded().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

GLOBAL_DEFAULT_ALGORITHM

const ETreeMethod GLOBAL_DEFAULT_ALGORITHM = eNJ

Definition at line 59 of file cuSeqTreeAlg.hpp.

NUMBER_OF_TREE_ALGORITHMS

const int NUMBER_OF_TREE_ALGORITHMS = 2

Definition at line 45 of file cuSeqTreeAlg.hpp.

RESET_WITH_TINY_DISTANCE

const double RESET_WITH_TINY_DISTANCE = 0.0001

Definition at line 65 of file cuSeqTreeAlg.hpp.

Referenced by TreeAlgorithm::midpointRootIfNeeded().

TREE_ALGORITHM_NAMES

const string TREE_ALGORITHM_NAMES[]

Initial value:

= {
        "",
        "Single Linkage Clustering",
        "Neighbor Joining"
        
}

Definition at line 46 of file cuSeqTreeAlg.hpp.

Referenced by TreeAlgorithm::GetName(), and GetTreeAlgorithmName().