Search Toolkit Book for NJ_TreeAlgorithm

#include <algo/structure/cd_utils/cuSeqTreeNj.hpp>

Inheritance diagram for NJ_TreeAlgorithm:

Collaboration diagram for NJ_TreeAlgorithm:

Public Member Functions
	NJ_TreeAlgorithm ()

	NJ_TreeAlgorithm (DistanceMatrix *dm)

virtual	~NJ_TreeAlgorithm ()

virtual long	GetNumLoopsForTreeCalc ()

virtual void	ComputeTree (SeqTree *tree, pProgressFunction pFunc)

virtual string	toString ()

virtual void	SetDistMat (DistanceMatrix *dm)

Public Member Functions inherited from TreeAlgorithm
	TreeAlgorithm (Rootedness rooted=DEF_ROOTED, ETreeMethod tmethod=eNoTreeMethod)

const SeqTree *	GetTree () const

string	GetName ()

ETreeMethod	GetTreeMethod ()

void	SetRootedness (Rootedness rooted)

Rootedness	GetRootedness ()

bool	isRooted ()

void	SetMidpointRooting (bool rooting)

bool	useMidpointRooting ()

virtual	~TreeAlgorithm ()

const DistanceMatrix *	GetDistMat () const

Private Member Functions
void	initializeNodes ()

bool	isHub (const TSeqIt &sit)

bool	isInternal (const TSeqIt &sit)

int	numChildren (const TSeqIt &sit)

void	Join (int inode1, int inode2, double len1, double len2)

Private Attributes
int	m_nseqs

int	m_nextNode

vector< SeqItem * >	m_items

TTreeIt	m_seqiters

Static Private Attributes
static const double	REPLACE_NEG_DIST = 0.001

static const Rootedness	MY_ROOTEDNESS = TreeAlgorithm::eUnrooted

static const ETreeMethod	MY_TREE_METHOD = eNJ

static const DistanceMatrix::TMatType	INIT_MINIMA = kMax_Double

static const int	USED_ROW = -1

static const int	BAD_INDEX = -1

Additional Inherited Members
Public Types inherited from TreeAlgorithm
enum	Rootedness { eUnrooted =0 , eRooted =1 , eMidpointRooted =2 }

typedef SeqTree::iterator	TSeqIt

typedef SeqTree::sibling_iterator	TChildIt

typedef vector< TSeqIt >	TTreeIt

Protected Member Functions inherited from TreeAlgorithm
void	midpointRootIfNeeded ()

Protected Attributes inherited from TreeAlgorithm
SeqTree *	m_tree

DistanceMatrix *	m_dm

Rootedness	m_rootedness

ETreeMethod	m_tmethod

Detailed Description

Definition at line 47 of file cuSeqTreeNj.hpp.

Constructor & Destructor Documentation

◆ NJ_TreeAlgorithm() [1/2]

NJ_TreeAlgorithm::NJ_TreeAlgorithm ( )

Definition at line 52 of file cuSeqTreeNj.cpp.

References initializeNodes(), TreeAlgorithm::m_dm, and NULL.

◆ NJ_TreeAlgorithm() [2/2]

NJ_TreeAlgorithm::NJ_TreeAlgorithm ( DistanceMatrix * dm )

Definition at line 59 of file cuSeqTreeNj.cpp.

References initializeNodes(), and TreeAlgorithm::m_dm.

◆ ~NJ_TreeAlgorithm()

NJ_TreeAlgorithm::~NJ_TreeAlgorithm ( )

virtual

Definition at line 143 of file cuSeqTreeNj.cpp.

References i, m_items, m_nseqs, and m_seqiters.

Member Function Documentation

◆ ComputeTree()

void NJ_TreeAlgorithm::ComputeTree	(	SeqTree *	tree,
		pProgressFunction	pFunc
	)

virtual

◆ GetNumLoopsForTreeCalc()

long NJ_TreeAlgorithm::GetNumLoopsForTreeCalc ( )

virtual

Implements TreeAlgorithm.

Definition at line 202 of file cuSeqTreeNj.cpp.

References count, i, m_nseqs, and USED_ROW.

Referenced by ComputeTree().

◆ initializeNodes()

void NJ_TreeAlgorithm::initializeNodes ( )

private

Definition at line 98 of file cuSeqTreeNj.cpp.

References AMatrix_base::GetNumCols(), AMatrix_base::GetNumRows(), i, NStr::IntToString(), TreeAlgorithm::m_dm, m_items, m_nextNode, m_nseqs, m_seqiters, SeqItem::name, and NULL.

Referenced by NJ_TreeAlgorithm(), and SetDistMat().

◆ isHub()

bool NJ_TreeAlgorithm::isHub ( const TSeqIt & sit )

inlineprivate

Definition at line 94 of file cuSeqTreeNj.hpp.

References m_seqiters.

Referenced by isInternal().

◆ isInternal()

bool NJ_TreeAlgorithm::isInternal ( const TSeqIt & sit )

inlineprivate

Definition at line 99 of file cuSeqTreeNj.hpp.

References tree< T, tree_node_allocator >::iterator_base::is_valid(), and isHub().

◆ Join()

void NJ_TreeAlgorithm::Join	(	int	inode1,
		int	inode2,
		double	len1,
		double	len2
	)

private

Definition at line 153 of file cuSeqTreeNj.cpp.

References tree< T, tree_node_allocator >::append_child(), tree< T, tree_node_allocator >::iterator_base::is_valid(), m_items, m_nextNode, m_nseqs, m_seqiters, TreeAlgorithm::m_tree, tree< T, tree_node_allocator >::parent(), tree< T, tree_node_allocator >::reparent(), and USED_ROW.

Referenced by ComputeTree().

◆ numChildren()

int NJ_TreeAlgorithm::numChildren ( const TSeqIt & sit )

private

Definition at line 471 of file cuSeqTreeNj.cpp.

References tree< T, tree_node_allocator >::iterator_base::is_valid(), TreeAlgorithm::m_tree, n, and tree< T, tree_node_allocator >::number_of_children().

◆ SetDistMat()

void NJ_TreeAlgorithm::SetDistMat ( DistanceMatrix * dm )

virtual

Reimplemented from TreeAlgorithm.

Definition at line 67 of file cuSeqTreeNj.cpp.

References initializeNodes(), and TreeAlgorithm::m_dm.

◆ toString()

string NJ_TreeAlgorithm::toString ( )

virtual

Reimplemented from TreeAlgorithm.

Definition at line 481 of file cuSeqTreeNj.cpp.

References TreeAlgorithm::m_tree, and CdTreeStream::toNestedString().

Member Data Documentation

◆ BAD_INDEX

const int NJ_TreeAlgorithm::BAD_INDEX = -1

staticprivate

Definition at line 72 of file cuSeqTreeNj.hpp.

◆ INIT_MINIMA

const DistanceMatrix::TMatType NJ_TreeAlgorithm::INIT_MINIMA = kMax_Double

staticprivate

Definition at line 52 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree().

◆ m_items

vector< SeqItem* > NJ_TreeAlgorithm::m_items

private

Definition at line 86 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree(), initializeNodes(), Join(), and ~NJ_TreeAlgorithm().

◆ m_nextNode

int NJ_TreeAlgorithm::m_nextNode

private

Definition at line 85 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree(), initializeNodes(), and Join().

◆ m_nseqs

int NJ_TreeAlgorithm::m_nseqs

private

Definition at line 84 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree(), GetNumLoopsForTreeCalc(), initializeNodes(), Join(), and ~NJ_TreeAlgorithm().

◆ m_seqiters

TTreeIt NJ_TreeAlgorithm::m_seqiters

private

Definition at line 87 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree(), initializeNodes(), isHub(), Join(), and ~NJ_TreeAlgorithm().

◆ MY_ROOTEDNESS

const TreeAlgorithm::Rootedness NJ_TreeAlgorithm::MY_ROOTEDNESS = TreeAlgorithm::eUnrooted

staticprivate

Definition at line 50 of file cuSeqTreeNj.hpp.

◆ MY_TREE_METHOD

const ETreeMethod NJ_TreeAlgorithm::MY_TREE_METHOD = eNJ

staticprivate

Definition at line 51 of file cuSeqTreeNj.hpp.

◆ REPLACE_NEG_DIST

const double NJ_TreeAlgorithm::REPLACE_NEG_DIST = 0.001

staticprivate

Definition at line 49 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree().

◆ USED_ROW

const int NJ_TreeAlgorithm::USED_ROW = -1

staticprivate

Definition at line 71 of file cuSeqTreeNj.hpp.

Referenced by ComputeTree(), GetNumLoopsForTreeCalc(), and Join().

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

include/algo/structure/cd_utils/cuSeqTreeNj.hpp
src/algo/structure/cd_utils/cuSeqTreeNj.cpp

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ NJ_TreeAlgorithm() [1/2]

◆ NJ_TreeAlgorithm() [2/2]

◆ ~NJ_TreeAlgorithm()

Member Function Documentation

◆ ComputeTree()

◆ GetNumLoopsForTreeCalc()

◆ initializeNodes()

◆ isHub()

◆ isInternal()

◆ Join()

◆ numChildren()

◆ SetDistMat()

◆ toString()

Member Data Documentation

◆ BAD_INDEX

◆ INIT_MINIMA

◆ m_items

◆ m_nextNode

◆ m_nseqs

◆ m_seqiters

◆ MY_ROOTEDNESS

◆ MY_TREE_METHOD

◆ REPLACE_NEG_DIST

◆ USED_ROW