+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
+ string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "stress.nmds";
+ outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
+ outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
+
+ ofstream out, out2;
+ m->openOutputFile(outputFileName, out);
+ m->openOutputFile(stressFileName, out2);
+
+ out2.setf(ios::fixed, ios::floatfield);
+ out2.setf(ios::showpoint);
+ out.setf(ios::fixed, ios::floatfield);
+ out.setf(ios::showpoint);
+
+ out2 << "Dimension\tIter\tStress\tCorr" << endl;
+
+ double bestStress = 10000000;
+ vector< vector<double> > bestConfig;
+