/**************************************************************************/
//This constructor reads a distance matrix file and stores the data in the matrix.
-FullMatrix::FullMatrix(ifstream& filehandle) {
+FullMatrix::FullMatrix(ifstream& filehandle, GroupMap* g, bool s) : groupmap(g), sim(s) {
try{
m = MothurOut::getInstance();
- globaldata = GlobalData::getInstance();
- groupmap = globaldata->gGroupmap;
string name, group;
for(int i=0;i<numSeqs;i++){
filehandle >> matrix[0][i];
- if (globaldata->sim) { matrix[0][i] = 1.0 - matrix[0][i]; }
+ if (sim) { matrix[0][i] = 1.0 - matrix[0][i]; }
}
break;
}
break;
}
}
- cout << "here" << endl;
+
//read rest of matrix
if (square == true) { readSquareMatrix(filehandle); }
else { readLTMatrix(filehandle); }
/**************************************************************************/
int FullMatrix::readSquareMatrix(ifstream& filehandle) {
try {
- cout << "square" << endl;
+
Progress* reading;
reading = new Progress("Reading matrix: ", numSeqs * numSeqs);
if (m->control_pressed) { delete reading; return 0; }
filehandle >> matrix[i][j];
- if (globaldata->sim) { matrix[i][j] = 1.0 - matrix[i][j]; }
+ if (sim) { matrix[i][j] = 1.0 - matrix[i][j]; }
count++;
reading->update(count);
/**************************************************************************/
int FullMatrix::readLTMatrix(ifstream& filehandle) {
try {
- cout << "lt" << endl;
+
Progress* reading;
reading = new Progress("Reading matrix: ", numSeqs * (numSeqs - 1) / 2);
if (m->control_pressed) { delete reading; return 0; }
filehandle >> distance;
- if (globaldata->sim) { distance = 1.0 - distance; }
+ if (sim) { distance = 1.0 - distance; }
matrix[i][j] = distance; matrix[j][i] = distance;