Upgma and Newick

[JohnHickey]

Hi,

I realize that for experienced C++ programmers this is a ridiculous question, but as a fortran programmer who has only just begun C++ I submit it in the hope of finding some help.

I am trying to write a program that uses Numerical Recipes UPGMA and Newick routines to make a hierarchical clustering of some data and write the output in Newick format.

I am not sure how I get the program to call these routines. The code I have written here is supposed to read in a distance matrix (Dmat). The last two lines then attempt to call Phylo_upgma and newick. This is where I am having problems

Any help would be greatly appreciated.

Regards,

John.

#include "nr3.h"
#include "phylo.h"
#include <iostream> // for input/output
#include <fstream> // for opening data streams: read/write to files
#include <cstring> // to manipulate classic C strings
#include <string> // to manipulate C++ strings types - not exactly portable across compilers, try to avoid
#include <cstdlib> // to recast from one type to another e.g. character to integer
#include <math.h>


using namespace std;


void runread(char *file);

int main()
{
char out='N';

cout << "\n\nProgram reading in the data file ";
cout << "\n\n ";

char *datafile="HapCommonality1.txt";
runread(datafile);

return 0;
}


void runread(char *file)
{
string line;
ifstream in;
in.open(file,ios::in);

int counter = 0;
int nHap=410;
char **HapNames;

HapNames=(char**) malloc(nHap * sizeof(char));
for(int i = 0; i < nHap; i ++)
HapNames[i] = (char*) malloc(sizeof(char) * 200);

MatDoub Dmat(nHap,nHap);
for(int i = 0; i < nHap; i ++)
{
counter++;
getline(in,line);
int size=line.length();
char *datline = new char[size];
line.copy(datline,line.length());
char *tabdata=strtok(datline,",");
strcpy(HapNames[i],tabdata);
int HapCounter=1;
for (int j = 0; j < nHap; j ++)
{
Dmat[i][j]=atof(strtok(NULL,","));
}
}
in.close();
printf ("\n");
for (int i = 0; i < 10; i++)
{
cout << i;
printf ("\n");
for (int j = 0; j < 10; j++) {
cout << j << "\t";
}
for (int j = 0; j < 10; j++) {
cout << Dmat[i][j] << "\t";
}

printf ("\n");
}
Phylo_upgma p(Dmat);

newick(Phylo_upgma p(Dmat) , Dmat, "Output.txt");

}

[JohnHickey]

Problem solved. Code below. How about cutting the tree (cutree in R)?

Regards,

John







#include "nr3.h"
#include "phylo.h"
#include <iostream> // for input/output
#include <fstream> // for opening data streams: read/write to files
#include <cstring> // to manipulate classic C strings
#include <string> // to manipulate C++ strings types - not exactly portable across compilers, try to avoid
#include <cstdlib> // to recast from one type to another e.g. character to integer
#include <math.h>


using namespace std;


void runread(char *file);

int main()
{
char out='N';

cout << "\n\nProgram reading in the data file ";
cout << "\n\n ";

char *datafile="HapCommonality1.txt";
runread(datafile);

return 0;
}


void runread(char *file)
{
string line;
ifstream in;
in.open(file,ios::in);

int counter = 0;
int nHap=410;

MatChar HapNames(nHap,200);

MatDoub Dmat(nHap,nHap);
for(int i = 0; i < nHap; i ++)
{
counter++;
getline(in,line);
int size=line.length();
char *datline = new char[size];
line.copy(datline,line.length());
char *tabdata=strtok(datline,",");
int HapCounter=1;
for (int j = 0; j < nHap; j ++)
{
Dmat[i][j]=atof(strtok(NULL,","));
}
}
in.close();
printf ("\n");
for (int i = 0; i < 10; i++)
{
cout << i;
printf ("\n");
for (int j = 0; j < 10; j++) {
cout << j << "\t";
}
for (int j = 0; j < 10; j++) {
cout << Dmat[i][j] << "\t";
}

printf ("\n");
}
Phylo_upgma p(Dmat);
newick(p,HapNames,"NewickOutput.txt");
}