/usr/include/libphylo/nj.h is in rate4site 3.0.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 | // $Id: nj.h 962 2006-11-07 15:13:34Z privmane $
// version 1.00
// last modified 3 Nov 2002
#ifndef ___NJ
#define ___NJ
#include "definitions.h"
#include "tree.h"
#include "sequenceContainer.h"
#include "njConstrain.h"
#include "distances2Tree.h"
using namespace std;
class NJalg : public distances2Tree {
public:
virtual NJalg* clone() const {return new NJalg(*this);}
// changed from computeNJtree to computeTree for competability to "distances2Tree"
virtual tree computeTree(VVdouble distances, const vector<string>& names, const tree * const constriantTree = NULL);
tree startingTree(const vector<string>& names);
tree startingTree(const tree& inTree);
void NJiterate(tree& et,vector<tree::nodeP>& currentNodes,
VVdouble& distanceTable);
void NJiterate(tree& et,vector<tree::nodeP>& currentNodes,
VVdouble& distanceTable, njConstraint& njc);
void calc_M_matrix(vector<tree::nodeP>& currentNodes,
const VVdouble& distanceTable,
const Vdouble & r_values,
int& minRaw,int& minCol);
void calc_M_matrix(vector<tree::nodeP>& currentNodes,
const VVdouble& distanceTable,
const Vdouble & r_values,
int& minRaw,int& minCol, const njConstraint& njc);
Vdouble calc_r_values(vector<tree::nodeP>& currentNodes,const VVdouble& distanceTable);
tree::nodeP SeparateNodes(tree& et,tree::nodeP node1,tree::nodeP node2);
void update3taxaLevel(VVdouble& distanceTable,Vdouble & r_values,vector<tree::nodeP>& currentNodes);
void updateBranchDistance(const VVdouble& disT,
const Vdouble& rValues,
tree::nodeP nodeNew,
tree::nodeP nodeI,
tree::nodeP nodeJ,
int Iplace, int Jplace);
void UpdateDistanceTableAndCurrentNodes(vector<tree::nodeP>& currentNodes,
VVdouble& distanceTable,
tree::nodeP nodeI,
tree::nodeP nodeJ,
tree::nodeP theNewNode,
int Iplace, int Jplace);
};
/*
//explicit NJalg(const tree& inTree, const computeDistance* cd);
explicit NJalg();
tree getNJtree() const {return *_myET;}// return a copy...
void computeTree(const sequenceContainer& sd,const computeDistance* cd,const vector<MDOUBLE> * weights = NULL);
VVdouble getDistanceTable(vector<string>& names) {
names.erase(names.begin(),names.end());
names = _nodeNames;
return _startingDistanceTable;}
VVdouble getLTable(vector<string>& names) {
names.erase(names.begin(),names.end());
names = _nodeNames;
return LTable;}
private:
//void starTreeFromInputTree(const tree& inTree);
void starTreeFromInputsequenceContainer(const sequenceContainer& sd);
void GetDisTable(const sequenceContainer& sd,const vector<MDOUBLE> * weights);
MDOUBLE dis(const int i, const int j) const{
return (i<j) ? distanceTable[i][j] : distanceTable[j][i];
}
void findMinM(int& minRaw,int& minCol);
tree* _myET;
VVdouble distanceTable;
VVdouble Mmatrix;
Vdouble r_values;
vector<tree::nodeP> currentNodes;
const computeDistance* _cd;
VVdouble _startingDistanceTable; // for printing etc... not used by the algorithm.
vector<string> _nodeNames; // for printing etc... not used by the algorithm.
VVdouble LTable;// for printing etc... not used by the algorithm.
*/
#endif
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