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91 lines
3.1 KiB
C++
91 lines
3.1 KiB
C++
// $Id: nj.h 962 2006-11-07 15:13:34Z privmane $
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// version 1.00
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// last modified 3 Nov 2002
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#ifndef ___NJ
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#define ___NJ
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#include "definitions.h"
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#include "tree.h"
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#include "sequenceContainer.h"
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#include "njConstrain.h"
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#include "distances2Tree.h"
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using namespace std;
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class NJalg : public distances2Tree {
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public:
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virtual NJalg* clone() const {return new NJalg(*this);}
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// changed from computeNJtree to computeTree for competability to "distances2Tree"
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virtual tree computeTree(VVdouble distances, const vector<string>& names, const tree * const constriantTree = NULL);
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tree startingTree(const vector<string>& names);
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tree startingTree(const tree& inTree);
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void NJiterate(tree& et,vector<tree::nodeP>& currentNodes,
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VVdouble& distanceTable);
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void NJiterate(tree& et,vector<tree::nodeP>& currentNodes,
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VVdouble& distanceTable, njConstraint& njc);
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void calc_M_matrix(vector<tree::nodeP>& currentNodes,
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const VVdouble& distanceTable,
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const Vdouble & r_values,
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int& minRaw,int& minCol);
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void calc_M_matrix(vector<tree::nodeP>& currentNodes,
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const VVdouble& distanceTable,
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const Vdouble & r_values,
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int& minRaw,int& minCol, const njConstraint& njc);
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Vdouble calc_r_values(vector<tree::nodeP>& currentNodes,const VVdouble& distanceTable);
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tree::nodeP SeparateNodes(tree& et,tree::nodeP node1,tree::nodeP node2);
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void update3taxaLevel(VVdouble& distanceTable,Vdouble & r_values,vector<tree::nodeP>& currentNodes);
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void updateBranchDistance(const VVdouble& disT,
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const Vdouble& rValues,
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tree::nodeP nodeNew,
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tree::nodeP nodeI,
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tree::nodeP nodeJ,
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int Iplace, int Jplace);
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void UpdateDistanceTableAndCurrentNodes(vector<tree::nodeP>& currentNodes,
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VVdouble& distanceTable,
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tree::nodeP nodeI,
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tree::nodeP nodeJ,
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tree::nodeP theNewNode,
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int Iplace, int Jplace);
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};
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/*
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//explicit NJalg(const tree& inTree, const computeDistance* cd);
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explicit NJalg();
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tree getNJtree() const {return *_myET;}// return a copy...
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void computeTree(const sequenceContainer& sd,const computeDistance* cd,const vector<MDOUBLE> * weights = NULL);
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VVdouble getDistanceTable(vector<string>& names) {
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names.erase(names.begin(),names.end());
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names = _nodeNames;
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return _startingDistanceTable;}
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VVdouble getLTable(vector<string>& names) {
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names.erase(names.begin(),names.end());
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names = _nodeNames;
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return LTable;}
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private:
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//void starTreeFromInputTree(const tree& inTree);
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void starTreeFromInputsequenceContainer(const sequenceContainer& sd);
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void GetDisTable(const sequenceContainer& sd,const vector<MDOUBLE> * weights);
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MDOUBLE dis(const int i, const int j) const{
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return (i<j) ? distanceTable[i][j] : distanceTable[j][i];
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}
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void findMinM(int& minRaw,int& minCol);
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tree* _myET;
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VVdouble distanceTable;
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VVdouble Mmatrix;
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Vdouble r_values;
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vector<tree::nodeP> currentNodes;
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const computeDistance* _cd;
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VVdouble _startingDistanceTable; // for printing etc... not used by the algorithm.
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vector<string> _nodeNames; // for printing etc... not used by the algorithm.
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VVdouble LTable;// for printing etc... not used by the algorithm.
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*/
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#endif
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