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::setParameters(){
  15         try {
  16                 CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paxes);
  17                 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
  18                 CommandParameter pmaxdim("maxdim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmaxdim);
  19                 CommandParameter pmindim("mindim", "Number", "", "2", "", "", "",false,false); parameters.push_back(pmindim);
  20                 CommandParameter piters("iters", "Number", "", "10", "", "", "",false,false); parameters.push_back(piters);
  21                 CommandParameter pmaxiters("maxiters", "Number", "", "500", "", "", "",false,false); parameters.push_back(pmaxiters);
  22                 CommandParameter pepsilon("epsilon", "Number", "", "0.000000000001", "", "", "",false,false); parameters.push_back(pepsilon);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "NMDSCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string NMDSCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "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.\n";
  40                 helpString += "The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon.\n";
  41                 helpString += "The phylip parameter allows you to enter your distance file.\n";
  42                 helpString += "The axes parameter allows you to enter a file containing a starting configuration.\n";
  43                 helpString += "The maxdim parameter allows you to select the maximum dimensions to use. Default=2\n";
  44                 helpString += "The mindim parameter allows you to select the minimum dimensions to use. Default=2\n";
  45                 helpString += "The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500\n";
  46                 helpString += "The iters parameter allows you to select the number of random configuration to try. Default=10\n";
  47                 helpString += "The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12.\n";
  48                 helpString += "Example nmds(phylip=yourDistanceFile).\n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "NMDSCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 NMDSCommand::NMDSCommand(){
  59         try {
  60                 abort = true; calledHelp = true;
  61                 setParameters();
  62                 vector<string> tempOutNames;
  63                 outputTypes["nmds"] = tempOutNames;
  64                 outputTypes["stress"] = tempOutNames;
  65                 outputTypes["iters"] = tempOutNames;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73
  74 NMDSCommand::NMDSCommand(string option)  {
  75         try {
  76                 abort = false; calledHelp = false;
  77
  78                 //allow user to run help
  79                 if(option == "help") { help(); abort = true; calledHelp = true; }
  80
  81                 else {
  82                         vector<string> myArray = setParameters();
  83
  84                         OptionParser parser(option);
  85                         map<string, string> parameters = parser. getParameters();
  86
  87                         ValidParameters validParameter;
  88                         map<string, string>::iterator it;
  89
  90                         //check to make sure all parameters are valid for command
  91                         for (it = parameters.begin(); it != parameters.end(); it++) {
  92                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  93                         }
  94                         //if the user changes the input directory command factory will send this info to us in the output parameter
  95                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  96                         if (inputDir == "not found"){   inputDir = "";          }
  97                         else {
  98                                 string path;
  99                                 it = parameters.find("phylip");
 100                                 //user has given a template file
 101                                 if(it != parameters.end()){
 102                                         path = m->hasPath(it->second);
 103                                         //if the user has not given a path then, add inputdir. else leave path alone.
 104                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 105                                 }
 106
 107                                 it = parameters.find("axes");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["axes"] = inputDir + it->second;             }
 113                                 }
 114                         }
 115
 116                         //initialize outputTypes
 117                         vector<string> tempOutNames;
 118                         outputTypes["nmds"] = tempOutNames;
 119                         outputTypes["iters"] = tempOutNames;
 120                         outputTypes["stress"] = tempOutNames;
 121
 122                         //required parameters
 123                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 124                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 125                         else if (phylipfile == "not found") {
 126                                 //if there is a current phylip file, use it
 127                                 phylipfile = m->getPhylipFile();
 128                                 if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 129                                 else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
 130                         }
 131
 132                         axesfile = validParameter.validFile(parameters, "axes", true);
 133                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 134                         else if (axesfile == "not found") { axesfile = "";  }
 135
 136                         //if the user changes the output directory command factory will send this info to us in the output parameter
 137                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 138                                 outputDir = "";
 139                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 140                         }
 141
 142                         string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
 143                         convert(temp, mindim);
 144
 145                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 146                         convert(temp, maxIters);
 147
 148                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 149                         convert(temp, iters);
 150
 151                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 152                         convert(temp, maxdim);
 153
 154                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 155                         convert(temp, epsilon);
 156
 157                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 158                         if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
 159                 }
 160
 161         }
 162         catch(exception& e) {
 163                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 164                 exit(1);
 165         }
 166 }
 167 //**********************************************************************************************************************
 168 int NMDSCommand::execute(){
 169         try {
 170
 171                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 172
 173                 cout.setf(ios::fixed, ios::floatfield);
 174                 cout.setf(ios::showpoint);
 175
 176                 vector<string> names;
 177                 vector< vector< double> > matrix;
 178
 179                 //read in phylip file
 180                 ReadPhylipVector readFile(phylipfile);
 181                 names = readFile.read(matrix);
 182                 if (m->control_pressed) { return 0; }
 183
 184                 //read axes
 185                 vector< vector<double> > axes;
 186                 if (axesfile != "") {  axes = readAxes(names);          }
 187
 188                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
 189                 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
 190                 outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 191                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 192
 193                 ofstream out, out2;
 194                 m->openOutputFile(outputFileName, out);
 195                 m->openOutputFile(stressFileName, out2);
 196
 197                 out2.setf(ios::fixed, ios::floatfield);
 198                 out2.setf(ios::showpoint);
 199                 out.setf(ios::fixed, ios::floatfield);
 200                 out.setf(ios::showpoint);
 201
 202                 out2 << "Dimension\tIter\tStress\tRsq" << endl;
 203
 204                 double bestStress = 10000000;
 205                 double bestR2 = 10000000;
 206                 vector< vector<double> > bestConfig;
 207                 int bestDim = 0;
 208
 209                 for (int i = mindim; i <= maxdim; i++) {
 210                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 211
 212                         for (int j = 0; j < iters; j++) {
 213                                 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
 214
 215                                 //get configuration - either randomly generate or resize to this dimension
 216                                 vector< vector<double> > thisConfig;
 217                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 218                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 219                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 220
 221                                 //calc nmds for this dimension
 222                                 double stress;
 223                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 224                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 225
 226                                 //calc euclid distances for new config
 227                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 228                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 229
 230                                 //calc correlation between original distances and euclidean distances from this config
 231                                 double rsquared = linearCalc.calcPearson(newEuclid, matrix);
 232                                 rsquared *= rsquared;
 233                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 234
 235                                 //output results
 236                                 out << "Config" << (j+1) << '\t';
 237                                 for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
 238                                 out << endl;
 239                                 out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
 240
 241                                 output(endConfig, names, out);
 242
 243                                 //save best
 244                                 if (stress < bestStress) {
 245                                         bestDim = i;
 246                                         bestStress = stress;
 247                                         bestR2 = rsquared;
 248                                         bestConfig = endConfig;
 249                                 }
 250
 251                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 252                         }
 253                 }
 254
 255                 out.close(); out2.close();
 256
 257                 //output best config
 258                 string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
 259                 outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 260
 261                 m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
 262                 m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
 263                 m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
 264
 265                 ofstream outBest;
 266                 m->openOutputFile(BestFileName, outBest);
 267                 outBest.setf(ios::fixed, ios::floatfield);
 268                 outBest.setf(ios::showpoint);
 269
 270                 outBest << '\t';
 271                 for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
 272                 outBest << endl;
 273
 274                 output(bestConfig, names, outBest);
 275
 276                 outBest.close();
 277
 278                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 279
 280                 m->mothurOutEndLine();
 281                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 282                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 283                 m->mothurOutEndLine();
 284
 285                 return 0;
 286         }
 287         catch(exception& e) {
 288                 m->errorOut(e, "NMDSCommand", "execute");
 289                 exit(1);
 290         }
 291 }
 292 //**********************************************************************************************************************
 293 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 294         try {
 295
 296                 vector< vector<double> > newConfig = config;
 297
 298                 //calc euclid distances
 299                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 300                 if (m->control_pressed) { return newConfig; }
 301
 302                 double stress2 = calculateStress(matrix, euclid);
 303                 stress1 = stress2 + 1.0 + epsilon;
 304
 305                 int count = 0;
 306                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 307                         count++;
 308
 309                         stress1 = stress2;
 310
 311                         if (m->control_pressed) { return newConfig; }
 312
 313                         vector< vector<double> > b; b.resize(euclid.size());
 314                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 315
 316                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 317                         for (int i = 0; i < euclid.size(); i++) {
 318                                 for (int j = 0; j < euclid[i].size(); j++) {
 319                                         //eliminate divide by zero error
 320                                         if (euclid[i][j] != 0) {
 321                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 322                                                 columnSums[j] += b[i][j];
 323                                                 b[i][j] *= -1.0;
 324                                         }
 325                                 }
 326                         }
 327
 328                         //put in diagonal sums
 329                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 330
 331                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 332                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 333
 334                         //matrix mult
 335                         newConfig = linearCalc.matrix_mult(newConfig, b);
 336                         for (int i = 0; i < newConfig.size(); i++) {
 337                                 for (int j = 0; j < newConfig[i].size(); j++) {
 338                                         newConfig[i][j] *= (1.0 / n);
 339                                 }
 340                         }
 341
 342                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 343
 344                         stress2 = calculateStress(matrix, euclid);
 345                 }
 346
 347                 return newConfig;
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 351                 exit(1);
 352         }
 353 }
 354
 355 //**********************************************************************************************************************
 356 //generate random config
 357 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 358         try {
 359                 vector< vector<double> > axes;  axes.resize(dimension);
 360                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 361
 362                 //generate random number between -1 and 1, precision 6
 363                 for (int i = 0; i < axes.size(); i++) {
 364                         for (int j = 0; j < axes[i].size(); j++) {
 365
 366                                 if (m->control_pressed) { return axes; }
 367
 368                                 //generate random int between 0 and 99999
 369                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 370
 371                                 //generate random sign
 372                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 373
 374                                 //if mysign is even then sign = positive, else sign = negative
 375                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 376                                 else { mysign = -1.0; }
 377
 378                                 axes[i][j] = mysign * myrand / (float) 100000;
 379                         }
 380                 }
 381
 382                 return axes;
 383         }
 384         catch(exception& e) {
 385                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 386                 exit(1);
 387         }
 388 }
 389 //**********************************************************************************************************************
 390 //normalize configuration
 391 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 392         try {
 393                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 394
 395                 //find average
 396                 for (int i = 0; i < axes.size(); i++) {
 397                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 398
 399                         averageAxes[i] /= (float) numNames;
 400                 }
 401
 402                 //normalize axes
 403                 double sumDenom = 0.0;
 404                 for (int i = 0; i < axes.size(); i++) {
 405                         for (int j = 0; j < axes[i].size(); j++) {
 406                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 407                         }
 408                 }
 409
 410                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 411
 412                 for (int i = 0; i < axes.size(); i++) {
 413                         for (int j = 0; j < axes[i].size(); j++) {
 414                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 415                         }
 416                 }
 417
 418                 return 0;
 419         }
 420         catch(exception& e) {
 421                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 422                 exit(1);
 423         }
 424 }
 425 //**********************************************************************************************************************
 426 //get configuration
 427 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 428         try {
 429                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 430
 431                 for (int i = 0; i < dimension; i++) {
 432                         newAxes[i] = axes[i];
 433                 }
 434
 435                 return newAxes;
 436         }
 437         catch(exception& e) {
 438                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 439                 exit(1);
 440         }
 441 }
 442 //**********************************************************************************************************************
 443 //find raw stress, and normalize using
 444 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 445         try {
 446                 double normStress = 0.0;
 447                 double denom = 0.0;
 448                 double rawStress = 0.0;
 449
 450                 //find raw stress
 451                 for (int i = 0; i < matrix.size(); i++) {
 452                         for (int j = 0; j < matrix[i].size(); j++) {
 453                                 if (m->control_pressed) { return normStress; }
 454
 455                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 456                                 denom += (config[i][j] * config[i][j]);
 457                         }
 458                 }
 459
 460                 //normalize stress
 461                 if ((rawStress != 0.0) && (denom != 0.0)) {
 462                         normStress = sqrt((rawStress / denom));
 463                 }
 464
 465                 return normStress;
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "NMDSCommand", "calculateStress");
 469                 exit(1);
 470         }
 471 }
 472
 473 //**********************************************************************************************************************
 474 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 475         try {
 476
 477                 for (int i = 0; i < names.size(); i++) {
 478
 479                         out << names[i] << '\t';
 480
 481                         for (int j = 0; j < config.size(); j++) {
 482                                 out << config[j][i] << '\t';
 483                         }
 484
 485                         out << endl;
 486                 }
 487
 488                 out << endl << endl;
 489
 490                 return 0;
 491         }
 492         catch(exception& e) {
 493                 m->errorOut(e, "NMDSCommand", "output");
 494                 exit(1);
 495         }
 496 }
 497 /*****************************************************************/
 498 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 499         try {
 500                 ifstream in;
 501                 m->openInputFile(axesfile, in);
 502
 503                 string headerLine = m->getline(in); m->gobble(in);
 504
 505                 //count the number of axis you are reading
 506                 bool done = false;
 507                 int count = 0;
 508                 while (!done) {
 509                         int pos = headerLine.find("axis");
 510                         if (pos != string::npos) {
 511                                 count++;
 512                                 headerLine = headerLine.substr(pos+4);
 513                         }else { done = true; }
 514                 }
 515
 516                 if (maxdim > count) {
 517                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 518                         maxdim = count;
 519                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 520                 }
 521
 522                 vector< vector<double> > axes;  axes.resize(maxdim);
 523                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 524
 525                 map <string, vector<double> > orderedAxes;
 526                 map     <string, vector<double> >::iterator it;
 527
 528                 while (!in.eof()) {
 529
 530                         if (m->control_pressed) { in.close(); return axes; }
 531
 532                         string group = "";
 533                         in >> group; m->gobble(in);
 534
 535                         bool ignore = false;
 536                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 537
 538                         vector<double> thisGroupsAxes;
 539                         for (int i = 0; i < count; i++) {
 540                                 float temp = 0.0;
 541                                 in >> temp;
 542
 543                                 //only save the axis we want
 544                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 545                         }
 546
 547                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 548
 549                         m->gobble(in);
 550                 }
 551                 in.close();
 552
 553                 //sanity check
 554                 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; }
 555
 556                 //put axes info in same order as distance file, just in case
 557                 for (int i = 0; i < names.size(); i++) {
 558                         it = orderedAxes.find(names[i]);
 559
 560                         if (it != orderedAxes.end()) {
 561                                 vector<double> thisGroupsAxes = it->second;
 562
 563                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 564                                         axes[j][i] = thisGroupsAxes[j];
 565                                 }
 566
 567                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 568                 }
 569
 570                 return axes;
 571         }
 572         catch(exception& e) {
 573                 m->errorOut(e, "NMDSCommand", "readAxes");
 574                 exit(1);
 575         }
 576 }
 577 /**********************************************************************************************************************/
 578
 579
 580