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NCBI C++ ToolKit: SLC_TreeAlgorithm Class Reference

Search Toolkit Book for SLC_TreeAlgorithm

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

Definition at line 49 of file cuSeqTreeSlc.hpp.

◆ SLC_TreeAlgorithm() [1/2] SLC_TreeAlgorithm::SLC_TreeAlgorithm ( ) ◆ SLC_TreeAlgorithm() [2/2] ◆ ~SLC_TreeAlgorithm() SLC_TreeAlgorithm::~SLC_TreeAlgorithm ( ) virtual ◆ ComputeTree()

Implements TreeAlgorithm.

Definition at line 243 of file cuSeqTreeSlc.cpp.

References assert, tree< T, tree_node_allocator >::begin(), tree< T, tree_node_allocator >::clear(), count, DistanceMatrix::EnforceSymmetry(), AMatrix_base::FastGet(), GetNumLoopsForTreeCalc(), i, INIT_MINIMA, tree< T, tree_node_allocator >::insert(), Join(), TreeAlgorithm::m_dm, m_items, m_nextNode, m_nseqs, m_seqiters, TreeAlgorithm::m_tree, TreeAlgorithm::midpointRootIfNeeded(), myMin(), NULL, REPLACE_NEG_DIST, and USED_ROW.

◆ GetNumLoopsForTreeCalc() long SLC_TreeAlgorithm::GetNumLoopsForTreeCalc ( ) virtual ◆ initializeNodes() void SLC_TreeAlgorithm::initializeNodes ( ) private

Definition at line 98 of file cuSeqTreeSlc.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 SetDistMat(), and SLC_TreeAlgorithm().

◆ isHub() ◆ isInternal() ◆ Join() void SLC_TreeAlgorithm::Join ( int  inode1, int  inode2, double  len1, double  len2  ) private

Definition at line 151 of file cuSeqTreeSlc.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() ◆ SetDistMat() ◆ toString() string SLC_TreeAlgorithm::toString ( ) virtual ◆ BAD_INDEX ◆ INIT_MINIMA ◆ m_items vector< SeqItem* > SLC_TreeAlgorithm::m_items private ◆ m_nextNode int SLC_TreeAlgorithm::m_nextNode private ◆ m_nseqs int SLC_TreeAlgorithm::m_nseqs private ◆ m_seqiters TTreeIt SLC_TreeAlgorithm::m_seqiters private ◆ MY_ROOTEDNESS ◆ MY_TREE_METHOD ◆ REPLACE_NEG_DIST const double SLC_TreeAlgorithm::REPLACE_NEG_DIST = 0.001 staticprivate ◆ USED_ROW const int SLC_TreeAlgorithm::USED_ROW = -1 staticprivate

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

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