--- /dev/null
+/*
+ * nmdscommand.cpp
+ * mothur
+ *
+ * Created by westcott on 1/11/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "nmdscommand.h"
+#include "readphylipvector.h"
+
+//**********************************************************************************************************************
+vector<string> NMDSCommand::getValidParameters(){
+ try {
+ string Array[] = {"phylip","axes","dimension","maxiters","step","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+NMDSCommand::NMDSCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["nmds"] = tempOutNames;
+ outputTypes["stress"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "NMDSCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> NMDSCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"phylip"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> NMDSCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+NMDSCommand::NMDSCommand(string option) {
+ try {
+ abort = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; }
+
+ else {
+ //valid paramters for this command
+ string Array[] = {"phylip","axes","dimension","maxiters","step","outputdir", "inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser. getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("axes");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["axes"] = inputDir + it->second; }
+ }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["nmds"] = tempOutNames;
+ outputTypes["stress"] = tempOutNames;
+
+ //required parameters
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }
+ else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("You must provide a distance file before running the nmds command."); m->mothurOutEndLine(); abort = true; }
+
+ axesfile = validParameter.validFile(parameters, "axes", true);
+ if (axesfile == "not open") { axesfile = ""; abort = true; }
+ else if (axesfile == "not found") { axesfile = ""; }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "dimension", false); if (temp == "not found") { temp = "2"; }
+ convert(temp, dimension);
+
+ temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, maxIters);
+
+ temp = validParameter.validFile(parameters, "step", false); if (temp == "not found") { temp = "0.2"; }
+ convert(temp, step);
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "2"; }
+ convert(temp, cutoff);
+ cutoff /= 100.0;
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "NMDSCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+void NMDSCommand::help(){
+ try {
+
+ m->mothurOut("The nmds command parameters are phylip, axes, dimension, maxiters, cutoff and step."); m->mothurOutEndLine();
+ m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
+ m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
+ m->mothurOut("The dimension parameter allows you to select how many dimensions to use. Default=2"); m->mothurOutEndLine();
+ m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try. Default=1000"); m->mothurOutEndLine();
+ m->mothurOut("The cutoff parameter allows you to select set an acceptable percentage of magnitude. Default=2, meaning when magnitude of g reaches 2% of it's starting value the process will stop."); m->mothurOutEndLine();
+ m->mothurOut("The step parameter allows you to set a starting step. Default=0.2"); m->mothurOutEndLine();
+ m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "help");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+NMDSCommand::~NMDSCommand(){}
+//**********************************************************************************************************************
+int NMDSCommand::execute(){
+ try {
+
+ if (abort == true) { return 0; }
+
+ cout.setf(ios::fixed, ios::floatfield);
+ cout.setf(ios::showpoint);
+ cerr.setf(ios::fixed, ios::floatfield);
+ cerr.setf(ios::showpoint);
+
+ vector<string> names;
+ vector<seqDist> matrix; //seqDist = int, int, float - index of seq1 in names, index of seq2 in names, their distance
+
+ //read in phylip file
+ ReadPhylipVector readFile(phylipfile);
+ names = readFile.read(matrix);
+ if (m->control_pressed) { return 0; }
+
+ //randomly generate the starting configuration - step 2
+ vector< vector<double> > axes;
+ if (axesfile == "") { axes = generateStartingConfiguration(names.size()); }
+ else { axes = readAxes(names); }
+ if (m->control_pressed) { return 0; }
+
+ //sort matrix from smallest distance to largest - step 5
+ sort(matrix.begin(), matrix.end(), compareSequenceDistance);
+
+ bool stable = false;
+ int count = 0;
+ vector<double> previousStresses;
+ vector< vector<double> > previousGradient = axes;
+ double initialMagnitude;
+ m->mothurOutEndLine(); m->mothurOut("Iter\tStress\tMagnitude"); m->mothurOutEndLine();
+ while ((count != maxIters) && (!stable)) {
+ count++;
+
+ //normalize axes - step 3
+ normalizeConfiguration(axes, names.size());
+ if (m->control_pressed) { return 0; }
+
+ //calculate Euclidean distances - step 4
+ vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(axes);
+ if (m->control_pressed) { return 0; }
+
+ //order euclid elements in same order as matrix - step 6
+ //if there are ties in the matrix we want to arrange the euclid distances in the best way so we do not to add unnecessary stress
+ vector<seqDist> eDists;
+ vector<seqDist> ties;
+ for (int i = 0; i < matrix.size(); i++) {
+
+ seqDist temp(matrix[i].seq1, matrix[i].seq2, euclid[matrix[i].seq1][matrix[i].seq2]);
+ ties.push_back(temp);
+
+ if (i != matrix.size()-1) { // you are not the last so you can look ahead
+ if (matrix[i].dist != matrix[i+1].dist) { // you are done with ties, sort and save them, then continue
+ sort(ties.begin(), ties.end(), compareSequenceDistance);
+ for (int k = 0; k < ties.size(); k++) { eDists.push_back(ties[k]); }
+ ties.clear();
+ }
+ }else { // you are the last one
+ sort(ties.begin(), ties.end(), compareSequenceDistance);
+ for (int k = 0; k < ties.size(); k++) { eDists.push_back(ties[k]); }
+ }
+ }
+
+ for (int i = 0; i < euclid.size(); i++) { euclid[i].clear(); } euclid.clear();
+ if (m->control_pressed) { return 0; }
+
+ //find D - from step 7
+ vector<seqDist> D = satisfyMonotonicity(eDists);
+ if (m->control_pressed) { return 0; }
+
+ //calculate the raw stress and normalize it - steps 8 and 9
+ double rawStress;
+ double stress = calculateStress(eDists, D, rawStress);
+ previousStresses.push_back(stress);
+ if (stress == 0) { m->mothurOut("Stress reached zero after " + toString(count) + " iters, stopping."); m->mothurOutEndLine(); break; }
+ if (m->control_pressed) { return 0; }
+
+ //calculate stress gradient - step 10
+ vector< vector<double> > stressGradient = calculateStressGradientVector(eDists, D, rawStress, stress, axes);
+ if (m->control_pressed) { return 0; }
+
+ //calculate magnitude
+ double magnitude = calculateMagnitude(stressGradient);
+ if (count == 1) { initialMagnitude = magnitude; }
+ if (m->control_pressed) { return 0; }
+
+ //save gradient before adjusting config.
+ previousGradient = stressGradient;
+
+ if ((count % 100) == 0) { m->mothurOut(toString(count) + "\t" + toString(previousStresses[previousStresses.size()-1]) + "\t" + toString(magnitude)); m->mothurOutEndLine(); }
+
+ //are we done - we are done if percentage of magnitude compared to initial magnitude is less than cutoff
+ double percentage = magnitude / initialMagnitude;
+ if (percentage < cutoff) { stable = true; }
+ else {
+
+ //calculate new step size
+ step = calculateStep(previousGradient, stressGradient, previousStresses);
+ cout << "count = " << count << '\t' << step << endl;
+ if (m->control_pressed) { return 0; }
+
+ //find new config.
+ axes = calculateNewConfiguration(magnitude, axes, stressGradient);
+ if (m->control_pressed) { return 0; }
+ }
+ }
+
+ if (m->control_pressed) { return 0; }
+
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds";
+ string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "stress.nmds";
+ outputNames.push_back(outputFileName); outputTypes["nmds"].push_back(outputFileName);
+ outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
+
+ output(outputFileName, stressFileName, previousGradient, previousStresses, names);
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//generate random config
+vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames) {
+ try {
+ vector< vector<double> > axes; axes.resize(dimension);
+ for (int i = 0; i < axes.size(); i++) { axes[i].resize(numNames); }
+
+ //generate random number between -1 and 1, precision 6
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) {
+
+ if (m->control_pressed) { return axes; }
+
+ //generate random int between 0 and 99999
+ int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
+
+ //generate random sign
+ int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
+
+ //if mysign is even then sign = positive, else sign = negative
+ if ((mysign % 2) == 0) { mysign = 1.0; }
+ else { mysign = -1.0; }
+
+ axes[i][j] = mysign * myrand / (float) 100000;
+ }
+ }
+
+ return axes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//normalize configuration
+int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames) {
+ try {
+ vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
+
+ //find average
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) { averageAxes[i] += axes[i][j]; }
+
+ averageAxes[i] /= (float) numNames;
+ }
+
+ //normalize axes
+ double sumDenom = 0.0;
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) {
+ sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
+ }
+ }
+
+ double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
+
+ for (int i = 0; i < axes.size(); i++) {
+ for (int j = 0; j < axes[i].size(); j++) {
+ axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//adjust eDists so that it creates monotonically increasing series of succesive values that increase or stay the same, but never decrease
+vector<seqDist> NMDSCommand::satisfyMonotonicity(vector<seqDist> eDists) {
+ try {
+
+ vector<seqDist> D = eDists;
+
+ for (int i = 0; i < (D.size()-1); i++) {
+
+ if (m->control_pressed) { return D; }
+
+ //is the distance in i+1 smaller than i, if yes then adjust
+ if (D[i+1].dist < D[i].dist) { D[i+1].dist = D[i].dist; }
+ }
+
+ return D;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "satisfyMonotonicity");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//find raw stress, and normalize using
+double NMDSCommand::calculateStress(vector<seqDist>& eDists, vector<seqDist>& D, double& rawStress) {
+ try {
+ double normStress = 0.0;
+ double denom = 0.0;
+ rawStress = 0.0;
+
+ //find raw stress
+ for (int i = 0; i < D.size(); i++) {
+
+ if (m->control_pressed) { return normStress; }
+
+ rawStress += ((eDists[i].dist - D[i].dist) * (eDists[i].dist - D[i].dist));
+ denom += (eDists[i].dist * eDists[i].dist);
+ }
+
+ //normalize stress
+ if (rawStress != 0.0) {
+ normStress = 100 * sqrt((rawStress / denom));
+ }
+
+ return normStress;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "calculateStress");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<double> > NMDSCommand::calculateStressGradientVector(vector<seqDist>& eDists, vector<seqDist>& D, double rawStress, double stress, vector< vector<double> >& axes) {
+ try {
+ vector< vector<double> > gradient; gradient.resize(dimension);
+ for (int i = 0; i < gradient.size(); i++) { gradient[i].resize(axes[0].size(), 0.0); }
+
+ double sumDij = 0.0;
+ for (int i = 0; i < eDists.size(); i++) { sumDij += (eDists[i].dist * eDists[i].dist); }
+
+ for (int i = 0; i < eDists.size(); i++) {
+
+ for (int j = 0; j < dimension; j++) {
+
+ if (m->control_pressed) { return gradient; }
+
+ double firstTerm1 = (stress / rawStress) * (eDists[i].dist - D[i].dist);
+ double firstTerm2 = eDists[i].dist * (stress / sumDij);
+ double firstTerm = firstTerm1 - firstTerm2;
+
+ double secondTerm = (axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]) / eDists[i].dist;
+
+ double results = (firstTerm * secondTerm);
+
+ gradient[j][eDists[i].seq1] += results;
+ gradient[j][eDists[i].seq2] -= results;
+ }
+ }
+
+ return gradient;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "calculateStressGradientVector");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+double NMDSCommand::calculateMagnitude(vector< vector<double> >& gradient) {
+ try {
+ double magnitude = 0.0;
+
+ double sum = 0.0;
+ for (int i = 0; i < gradient.size(); i++) {
+ for (int j = 0; j < gradient[i].size(); j++) {
+ sum += (gradient[i][j] * gradient[i][j]);
+ }
+ }
+
+ magnitude = sqrt(((1.0/(float)gradient[0].size()) * sum));
+
+ return magnitude;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "calculateMagnitude");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//described in Kruskal paper page 121 + 122
+double NMDSCommand::calculateStep(vector< vector<double> >& prevGrad, vector< vector<double> >& grad, vector<double>& prevStress) {
+ try {
+ double newStep = step;
+
+ //calc the cos theta
+ double sumNum = 0.0;
+ double sumDenom1 = 0.0;
+ double sumDenom2 = 0.0;
+ for (int i = 0; i < prevGrad.size(); i++) {
+ for (int j = 0; j < prevGrad[i].size(); j++) {
+ sumDenom1 += (grad[i][j] * grad[i][j]);
+ sumDenom2 += (prevGrad[i][j] * prevGrad[i][j]);
+ sumNum += (grad[i][j] * prevGrad[i][j]);
+ }
+ }
+
+ double cosTheta = sumNum / (sqrt(sumDenom1) * sqrt(sumDenom2));
+ cosTheta *= cosTheta;
+
+ //calc angle factor
+ double angle = pow(4.0, cosTheta);
+
+ //calc 5 step ratio
+ double currentStress = prevStress[prevStress.size()-1];
+ double lastStress = prevStress[0];
+ if (prevStress.size() > 1) { lastStress = prevStress[prevStress.size()-2]; }
+ double fivePrevStress = prevStress[0];
+ if (prevStress.size() > 5) { fivePrevStress = prevStress[prevStress.size()-6]; }
+
+ double fiveStepRatio = min(1.0, (currentStress / fivePrevStress));
+
+ //calc relaxation factor
+ double relaxation = 1.3 / (1.0 + pow(fiveStepRatio, 5.0));
+
+ //calc good luck factor
+ double goodLuck = min(1.0, (currentStress / lastStress));
+
+ //calc newStep
+ cout << "\ncos = " << cosTheta << " step = " << step << " angle = " << angle << " relaxation = " << relaxation << " goodluck = " << goodLuck << endl;
+ newStep = step * angle * relaxation * goodLuck;
+
+ return newStep;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "calculateStep");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector< vector<double> > NMDSCommand::calculateNewConfiguration(double magnitude, vector< vector<double> >& axes, vector< vector<double> >& gradient) {
+ try {
+
+ vector< vector<double> > newAxes = axes;
+
+ for (int i = 0; i < newAxes.size(); i++) {
+
+ if (m->control_pressed) { return newAxes; }
+
+ for (int j = 0; j < newAxes[i].size(); j++) {
+ newAxes[i][j] = axes[i][j] + ((step / magnitude) * gradient[i][j]);
+ }
+ }
+
+ return newAxes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "calculateNewConfiguration");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int NMDSCommand::output(string outputFileName, string stressFileName, vector< vector<double> >& config, vector<double>& stresses, vector<string>& names) {
+ try {
+
+ ofstream out, out2;
+ m->openOutputFile(outputFileName, out);
+ m->openOutputFile(stressFileName, out2);
+
+ //output headers
+ out << "group\t";
+ for (int i = 0; i < dimension; i++) { out << "axis" << (i+1) << '\t'; }
+ out << endl;
+
+ out2 << "Iter\tStress" << endl;
+
+ //output nmds file
+ for (int i = 0; i < config[0].size(); i++) {
+
+ if (m->control_pressed) { out.close(); out2.close(); return 0; }
+
+ out << names[i] << '\t';
+
+ for (int j = 0; j < config.size(); j++) {
+ out << config[j][i] << '\t';
+ }
+
+ out << endl;
+ }
+ out.close();
+
+ //output stress file
+ for (int j = 0; j < stresses.size(); j++) {
+ if (m->control_pressed) { out2.close(); return 0; }
+
+ out2 << (j+1) << '\t' << stresses[j] << endl;
+ }
+ out2.close();
+
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "output");
+ exit(1);
+ }
+}
+/*****************************************************************/
+vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
+ try {
+ vector< vector<double> > axes;
+
+ ifstream in;
+ m->openInputFile(axesfile, in);
+
+ string headerLine = m->getline(in); m->gobble(in);
+
+ //count the number of axis you are reading
+ bool done = false;
+ int count = 0;
+ while (!done) {
+ int pos = headerLine.find("axis");
+ if (pos != string::npos) {
+ count++;
+ headerLine = headerLine.substr(pos+4);
+ }else { done = true; }
+ }
+
+ if (dimension > count) { m->mothurOut("You requested " + toString(dimension) + " axes, but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine(); dimension = count; }
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { in.close(); return axes; }
+
+ string group = "";
+ in >> group; m->gobble(in);
+
+ bool ignore = false;
+ if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
+
+ vector<double> thisGroupsAxes;
+ for (int i = 0; i < count; i++) {
+ float temp = 0.0;
+ in >> temp;
+
+ //only save the axis we want
+ if (i < dimension) { thisGroupsAxes.push_back(temp); }
+ }
+
+ if (!ignore) { axes.push_back(thisGroupsAxes); }
+
+ m->gobble(in);
+ }
+ in.close();
+
+ //sanity check
+ if (names.size() != axes.size()) { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+
+ return axes;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "NMDSCommand", "readAxes");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+
projects / mothur.git / blobdiff