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NCBI C++ ToolKit: include/algo/structure/cd_utils/cuSeqTreeAlg.hpp Source File

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1 #ifndef CU_TREEALG__HPP 2 #define CU_TREEALG__HPP 48  "Single Linkage Clustering"

,

102

: m_tree(

NULL

), m_rootedness(rooted), m_tmethod(tmethod) {

126

m_rootedness = rooted;

132  bool r

= (m_rootedness == eUnrooted) ?

false

:

true

;

138

m_rootedness = eMidpointRooted;

139

}

else if

(m_rootedness == eMidpointRooted) {

140

m_rootedness = DEF_ROOTED;

144  return

(m_rootedness == eMidpointRooted);

173  void

midpointRootIfNeeded();

const SeqTree * GetTree() const

static const Rootedness DEF_ROOTED

ETreeMethod GetTreeMethod()

bool useMidpointRooting()

virtual void ComputeTree(SeqTree *tree, pProgressFunction pFunc)=0

void SetRootedness(Rootedness rooted)

virtual void SetDistMat(DistanceMatrix *dm)

void SetMidpointRooting(bool rooting)

virtual string toString()

TreeAlgorithm(Rootedness rooted=DEF_ROOTED, ETreeMethod tmethod=eNoTreeMethod)

virtual long GetNumLoopsForTreeCalc()=0

const DistanceMatrix * GetDistMat() const

SeqTree::sibling_iterator TChildIt

Rootedness GetRootedness()

static const string NO_NAME

void(* pProgressFunction)(int Num, int Total)

const ETreeMethod GLOBAL_DEFAULT_ALGORITHM

string GetTreeAlgorithmName(ETreeMethod algorithm)

const int NUMBER_OF_TREE_ALGORITHMS

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

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

const string TREE_ALGORITHM_NAMES[]

const double RESET_WITH_TINY_DISTANCE

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

#define NCBI_CDUTILS_EXPORT

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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