nmdscommand.cpp

   1 /*
   2  *  nmdscommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 1/11/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "nmdscommand.h"
  11 #include "readphylipvector.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> NMDSCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "NMDSCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 NMDSCommand::NMDSCommand(){
  27         try {
  28                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["nmds"] = tempOutNames;
  32                 outputTypes["stress"] = tempOutNames;
  33                 outputTypes["iters"] = tempOutNames;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 vector<string> NMDSCommand::getRequiredParameters(){
  42         try {
  43                 string Array[] =  {"phylip"};
  44                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "NMDSCommand", "getRequiredParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 vector<string> NMDSCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "NMDSCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //**********************************************************************************************************************
  64
  65 NMDSCommand::NMDSCommand(string option)  {
  66         try {
  67                 abort = false;
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string Array[] =  {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir", "inputdir"};
  75                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser. getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87                         //if the user changes the input directory command factory will send this info to us in the output parameter
  88                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  89                         if (inputDir == "not found"){   inputDir = "";          }
  90                         else {
  91                                 string path;
  92                                 it = parameters.find("phylip");
  93                                 //user has given a template file
  94                                 if(it != parameters.end()){
  95                                         path = m->hasPath(it->second);
  96                                         //if the user has not given a path then, add inputdir. else leave path alone.
  97                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  98                                 }
  99
 100                                 it = parameters.find("axes");
 101                                 //user has given a template file
 102                                 if(it != parameters.end()){
 103                                         path = m->hasPath(it->second);
 104                                         //if the user has not given a path then, add inputdir. else leave path alone.
 105                                         if (path == "") {       parameters["axes"] = inputDir + it->second;             }
 106                                 }
 107                         }
 108
 109                         //initialize outputTypes
 110                         vector<string> tempOutNames;
 111                         outputTypes["nmds"] = tempOutNames;
 112                         outputTypes["iters"] = tempOutNames;
 113                         outputTypes["stress"] = tempOutNames;
 114
 115                         //required parameters
 116                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 117                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 118                         else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("You must provide a distance file before running the nmds command."); m->mothurOutEndLine(); abort = true; }
 119
 120                         axesfile = validParameter.validFile(parameters, "axes", true);
 121                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 122                         else if (axesfile == "not found") { axesfile = "";  }
 123
 124                         //if the user changes the output directory command factory will send this info to us in the output parameter
 125                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 126                                 outputDir = "";
 127                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 128                         }
 129
 130                         string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
 131                         convert(temp, mindim);
 132
 133                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 134                         convert(temp, maxIters);
 135
 136                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 137                         convert(temp, iters);
 138
 139                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 140                         convert(temp, maxdim);
 141
 142                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 143                         convert(temp, epsilon);
 144
 145                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 146                         if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
 147                 }
 148
 149         }
 150         catch(exception& e) {
 151                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 152                 exit(1);
 153         }
 154 }
 155 //**********************************************************************************************************************
 156 void NMDSCommand::help(){
 157         try {
 158                 m->mothurOut("The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling."); m->mothurOutEndLine();
 159                 m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon."); m->mothurOutEndLine();
 160                 m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
 161                 m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
 162                 m->mothurOut("The maxdim parameter allows you to select how maximum dimensions to use. Default=2"); m->mothurOutEndLine();
 163                 m->mothurOut("The mindim parameter allows you to select how minimum dimensions to use. Default=2"); m->mothurOutEndLine();
 164                 m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
 165                 m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
 166                 m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();
 167                 m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
 168                 m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "NMDSCommand", "help");
 172                 exit(1);
 173         }
 174 }
 175 //**********************************************************************************************************************
 176 NMDSCommand::~NMDSCommand(){}
 177 //**********************************************************************************************************************
 178 int NMDSCommand::execute(){
 179         try {
 180
 181                 if (abort == true) { return 0; }
 182
 183                 cout.setf(ios::fixed, ios::floatfield);
 184                 cout.setf(ios::showpoint);
 185
 186                 vector<string> names;
 187                 vector< vector< double> > matrix;
 188
 189                 //read in phylip file
 190                 ReadPhylipVector readFile(phylipfile);
 191                 names = readFile.read(matrix);
 192                 if (m->control_pressed) { return 0; }
 193
 194                 //read axes
 195                 vector< vector<double> > axes;
 196                 if (axesfile != "") {  axes = readAxes(names);          }
 197
 198                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
 199                 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "stress.nmds";
 200                 outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 201                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 202
 203                 ofstream out, out2;
 204                 m->openOutputFile(outputFileName, out);
 205                 m->openOutputFile(stressFileName, out2);
 206
 207                 out2.setf(ios::fixed, ios::floatfield);
 208                 out2.setf(ios::showpoint);
 209                 out.setf(ios::fixed, ios::floatfield);
 210                 out.setf(ios::showpoint);
 211
 212                 out2 << "Dimension\tIter\tStress\tCorr" << endl;
 213
 214                 double bestStress = 10000000;
 215                 vector< vector<double> > bestConfig;
 216
 217                 for (int i = mindim; i <= maxdim; i++) {
 218                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 219
 220                         for (int j = 0; j < iters; j++) {
 221                                 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
 222
 223                                 //get configuration - either randomly generate or resize to this dimension
 224                                 vector< vector<double> > thisConfig;
 225                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 226                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 227                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 228
 229                                 //calc nmds for this dimension
 230                                 double stress;
 231                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 232                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 233
 234                                 //calc euclid distances for new config
 235                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 236                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 237
 238                                 //calc correlation between original distances and euclidean distances from this config
 239                                 double corr = linearCalc.calcPearson(newEuclid, matrix);
 240                                 corr *= corr;
 241                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 242
 243                                 //output results
 244                                 out << "Config" << (j+1) << '\t';
 245                                 for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
 246                                 out << endl;
 247                                 out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << corr << endl;
 248
 249                                 output(endConfig, names, out);
 250
 251                                 //save best
 252                                 if (stress < bestStress) {
 253                                         bestStress = stress;
 254                                         bestConfig = endConfig;
 255                                 }
 256
 257                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 258                         }
 259                 }
 260
 261                 out.close(); out2.close();
 262
 263                 //output best config
 264                 string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
 265                 outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 266
 267                 ofstream outBest;
 268                 m->openOutputFile(BestFileName, outBest);
 269                 outBest.setf(ios::fixed, ios::floatfield);
 270                 outBest.setf(ios::showpoint);
 271
 272                 outBest << '\t';
 273                 for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
 274                 outBest << endl;
 275
 276                 output(bestConfig, names, outBest);
 277
 278                 outBest.close();
 279
 280                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 281
 282                 m->mothurOutEndLine();
 283                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 284                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 285                 m->mothurOutEndLine();
 286
 287                 return 0;
 288         }
 289         catch(exception& e) {
 290                 m->errorOut(e, "NMDSCommand", "execute");
 291                 exit(1);
 292         }
 293 }
 294 //**********************************************************************************************************************
 295 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 296         try {
 297
 298                 vector< vector<double> > newConfig = config;
 299
 300                 //calc euclid distances
 301                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 302                 if (m->control_pressed) { return newConfig; }
 303
 304                 double stress2 = calculateStress(matrix, euclid);
 305                 stress1 = stress2 + 1.0 + epsilon;
 306
 307                 int count = 0;
 308                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 309                         count++;
 310
 311                         stress1 = stress2;
 312
 313                         if (m->control_pressed) { return newConfig; }
 314
 315                         vector< vector<double> > b; b.resize(euclid.size());
 316                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 317
 318                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 319                         for (int i = 0; i < euclid.size(); i++) {
 320                                 for (int j = 0; j < euclid[i].size(); j++) {
 321                                         //eliminate divide by zero error
 322                                         if (euclid[i][j] != 0) {
 323                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 324                                                 columnSums[j] += b[i][j];
 325                                                 b[i][j] *= -1.0;
 326                                         }
 327                                 }
 328                         }
 329
 330                         //put in diagonal sums
 331                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 332
 333                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 334                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 335
 336                         //matrix mult
 337                         newConfig = linearCalc.matrix_mult(newConfig, b);
 338                         for (int i = 0; i < newConfig.size(); i++) {
 339                                 for (int j = 0; j < newConfig[i].size(); j++) {
 340                                         newConfig[i][j] *= (1.0 / n);
 341                                 }
 342                         }
 343
 344                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 345
 346                         stress2 = calculateStress(matrix, euclid);
 347                 }
 348
 349                 return newConfig;
 350         }
 351         catch(exception& e) {
 352                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 353                 exit(1);
 354         }
 355 }
 356
 357 //**********************************************************************************************************************
 358 //generate random config
 359 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 360         try {
 361                 vector< vector<double> > axes;  axes.resize(dimension);
 362                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 363
 364                 //generate random number between -1 and 1, precision 6
 365                 for (int i = 0; i < axes.size(); i++) {
 366                         for (int j = 0; j < axes[i].size(); j++) {
 367
 368                                 if (m->control_pressed) { return axes; }
 369
 370                                 //generate random int between 0 and 99999
 371                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 372
 373                                 //generate random sign
 374                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 375
 376                                 //if mysign is even then sign = positive, else sign = negative
 377                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 378                                 else { mysign = -1.0; }
 379
 380                                 axes[i][j] = mysign * myrand / (float) 100000;
 381                         }
 382                 }
 383
 384                 return axes;
 385         }
 386         catch(exception& e) {
 387                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 388                 exit(1);
 389         }
 390 }
 391 //**********************************************************************************************************************
 392 //normalize configuration
 393 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 394         try {
 395                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 396
 397                 //find average
 398                 for (int i = 0; i < axes.size(); i++) {
 399                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 400
 401                         averageAxes[i] /= (float) numNames;
 402                 }
 403
 404                 //normalize axes
 405                 double sumDenom = 0.0;
 406                 for (int i = 0; i < axes.size(); i++) {
 407                         for (int j = 0; j < axes[i].size(); j++) {
 408                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 409                         }
 410                 }
 411
 412                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 413
 414                 for (int i = 0; i < axes.size(); i++) {
 415                         for (int j = 0; j < axes[i].size(); j++) {
 416                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 417                         }
 418                 }
 419
 420                 return 0;
 421         }
 422         catch(exception& e) {
 423                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 424                 exit(1);
 425         }
 426 }
 427 //**********************************************************************************************************************
 428 //get configuration
 429 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 430         try {
 431                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 432
 433                 for (int i = 0; i < dimension; i++) {
 434                         newAxes[i] = axes[i];
 435                 }
 436
 437                 return newAxes;
 438         }
 439         catch(exception& e) {
 440                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 441                 exit(1);
 442         }
 443 }
 444 //**********************************************************************************************************************
 445 //find raw stress, and normalize using
 446 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 447         try {
 448                 double normStress = 0.0;
 449                 double denom = 0.0;
 450                 double rawStress = 0.0;
 451
 452                 //find raw stress
 453                 for (int i = 0; i < matrix.size(); i++) {
 454                         for (int j = 0; j < matrix[i].size(); j++) {
 455                                 if (m->control_pressed) { return normStress; }
 456
 457                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 458                                 denom += (config[i][j] * config[i][j]);
 459                         }
 460                 }
 461
 462                 //normalize stress
 463                 if ((rawStress != 0.0) && (denom != 0.0)) {
 464                         normStress = sqrt((rawStress / denom));
 465                 }
 466
 467                 return normStress;
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "NMDSCommand", "calculateStress");
 471                 exit(1);
 472         }
 473 }
 474
 475 //**********************************************************************************************************************
 476 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 477         try {
 478
 479                 for (int i = 0; i < names.size(); i++) {
 480
 481                         out << names[i] << '\t';
 482
 483                         for (int j = 0; j < config.size(); j++) {
 484                                 out << config[j][i] << '\t';
 485                         }
 486
 487                         out << endl;
 488                 }
 489
 490                 out << endl << endl;
 491
 492                 return 0;
 493         }
 494         catch(exception& e) {
 495                 m->errorOut(e, "NMDSCommand", "output");
 496                 exit(1);
 497         }
 498 }
 499 /*****************************************************************/
 500 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 501         try {
 502                 ifstream in;
 503                 m->openInputFile(axesfile, in);
 504
 505                 string headerLine = m->getline(in); m->gobble(in);
 506
 507                 //count the number of axis you are reading
 508                 bool done = false;
 509                 int count = 0;
 510                 while (!done) {
 511                         int pos = headerLine.find("axis");
 512                         if (pos != string::npos) {
 513                                 count++;
 514                                 headerLine = headerLine.substr(pos+4);
 515                         }else { done = true; }
 516                 }
 517
 518                 if (maxdim > count) {
 519                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 520                         maxdim = count;
 521                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 522                 }
 523
 524                 vector< vector<double> > axes;  axes.resize(maxdim);
 525                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 526
 527                 map <string, vector<double> > orderedAxes;
 528                 map     <string, vector<double> >::iterator it;
 529
 530                 while (!in.eof()) {
 531
 532                         if (m->control_pressed) { in.close(); return axes; }
 533
 534                         string group = "";
 535                         in >> group; m->gobble(in);
 536
 537                         bool ignore = false;
 538                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 539
 540                         vector<double> thisGroupsAxes;
 541                         for (int i = 0; i < count; i++) {
 542                                 float temp = 0.0;
 543                                 in >> temp;
 544
 545                                 //only save the axis we want
 546                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 547                         }
 548
 549                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 550
 551                         m->gobble(in);
 552                 }
 553                 in.close();
 554
 555                 //sanity check
 556                 if (names.size() != orderedAxes.size()) { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 557
 558                 //put axes info in same order as distance file, just in case
 559                 for (int i = 0; i < names.size(); i++) {
 560                         it = orderedAxes.find(names[i]);
 561
 562                         if (it != orderedAxes.end()) {
 563                                 vector<double> thisGroupsAxes = it->second;
 564
 565                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 566                                         axes[j][i] = thisGroupsAxes[j];
 567                                 }
 568
 569                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 570                 }
 571
 572                 return axes;
 573         }
 574         catch(exception& e) {
 575                 m->errorOut(e, "NMDSCommand", "readAxes");
 576                 exit(1);
 577         }
 578 }
 579 /**********************************************************************************************************************/
 580
 581
 582