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";
  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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  81
  82                 else {
  83                         vector<string> myArray = setParameters();
  84
  85                         OptionParser parser(option);
  86                         map<string, string> parameters = parser. getParameters();
  87
  88                         ValidParameters validParameter;
  89                         map<string, string>::iterator it;
  90
  91                         //check to make sure all parameters are valid for command
  92                         for (it = parameters.begin(); it != parameters.end(); it++) {
  93                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  94                         }
  95                         //if the user changes the input directory command factory will send this info to us in the output parameter
  96                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  97                         if (inputDir == "not found"){   inputDir = "";          }
  98                         else {
  99                                 string path;
 100                                 it = parameters.find("phylip");
 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["phylip"] = inputDir + it->second;           }
 106                                 }
 107
 108                                 it = parameters.find("axes");
 109                                 //user has given a template file
 110                                 if(it != parameters.end()){
 111                                         path = m->hasPath(it->second);
 112                                         //if the user has not given a path then, add inputdir. else leave path alone.
 113                                         if (path == "") {       parameters["axes"] = inputDir + it->second;             }
 114                                 }
 115                         }
 116
 117                         //initialize outputTypes
 118                         vector<string> tempOutNames;
 119                         outputTypes["nmds"] = tempOutNames;
 120                         outputTypes["iters"] = tempOutNames;
 121                         outputTypes["stress"] = tempOutNames;
 122
 123                         //required parameters
 124                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 125                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 126                         else if (phylipfile == "not found") {
 127                                 //if there is a current phylip file, use it
 128                                 phylipfile = m->getPhylipFile();
 129                                 if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 130                                 else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
 131                         }else { m->setPhylipFile(phylipfile); }
 132
 133                         axesfile = validParameter.validFile(parameters, "axes", true);
 134                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 135                         else if (axesfile == "not found") { axesfile = "";  }
 136
 137                         //if the user changes the output directory command factory will send this info to us in the output parameter
 138                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 139                                 outputDir = "";
 140                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 141                         }
 142
 143                         string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
 144                         m->mothurConvert(temp, mindim);
 145
 146                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 147                         m->mothurConvert(temp, maxIters);
 148
 149                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 150                         m->mothurConvert(temp, iters);
 151
 152                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 153                         m->mothurConvert(temp, maxdim);
 154
 155                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 156                         m->mothurConvert(temp, epsilon);
 157
 158                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 159                         if (maxdim < mindim) { maxdim = mindim; }
 160                 }
 161
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 165                 exit(1);
 166         }
 167 }
 168 //**********************************************************************************************************************
 169 int NMDSCommand::execute(){
 170         try {
 171
 172                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 173
 174                 cout.setf(ios::fixed, ios::floatfield);
 175                 cout.setf(ios::showpoint);
 176
 177                 vector<string> names;
 178                 vector< vector< double> > matrix;
 179
 180                 //read in phylip file
 181                 ReadPhylipVector readFile(phylipfile);
 182                 names = readFile.read(matrix);
 183                 if (m->control_pressed) { return 0; }
 184
 185                 //read axes
 186                 vector< vector<double> > axes;
 187                 if (axesfile != "") {  axes = readAxes(names);          }
 188
 189                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
 190                 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
 191                 outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 192                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 193
 194                 ofstream out, out2;
 195                 m->openOutputFile(outputFileName, out);
 196                 m->openOutputFile(stressFileName, out2);
 197
 198                 out2.setf(ios::fixed, ios::floatfield);
 199                 out2.setf(ios::showpoint);
 200                 out.setf(ios::fixed, ios::floatfield);
 201                 out.setf(ios::showpoint);
 202
 203                 out2 << "Dimension\tIter\tStress\tRsq" << endl;
 204
 205                 double bestStress = 10000000;
 206                 double bestR2 = 10000000;
 207                 vector< vector<double> > bestConfig;
 208                 int bestDim = 0;
 209
 210                 for (int i = mindim; i <= maxdim; i++) {
 211                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 212
 213                         for (int j = 0; j < iters; j++) {
 214                                 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
 215
 216                                 //get configuration - either randomly generate or resize to this dimension
 217                                 vector< vector<double> > thisConfig;
 218                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 219                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 220                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 221
 222                                 //calc nmds for this dimension
 223                                 double stress;
 224                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 225                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 226
 227                                 //calc euclid distances for new config
 228                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 229                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 230
 231                                 //calc correlation between original distances and euclidean distances from this config
 232                                 double rsquared = linearCalc.calcPearson(newEuclid, matrix);
 233                                 rsquared *= rsquared;
 234                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 235
 236                                 //output results
 237                                 out << "Config" << (j+1) << '\t';
 238                                 for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
 239                                 out << endl;
 240                                 out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
 241
 242                                 output(endConfig, names, out);
 243
 244                                 //save best
 245                                 if (stress < bestStress) {
 246                                         bestDim = i;
 247                                         bestStress = stress;
 248                                         bestR2 = rsquared;
 249                                         bestConfig = endConfig;
 250                                 }
 251
 252                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 253                         }
 254                 }
 255
 256                 out.close(); out2.close();
 257
 258                 //output best config
 259                 string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
 260                 outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 261
 262                 m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
 263                 m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
 264                 m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
 265
 266                 ofstream outBest;
 267                 m->openOutputFile(BestFileName, outBest);
 268                 outBest.setf(ios::fixed, ios::floatfield);
 269                 outBest.setf(ios::showpoint);
 270
 271                 outBest << '\t';
 272                 for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
 273                 outBest << endl;
 274
 275                 output(bestConfig, names, outBest);
 276
 277                 outBest.close();
 278
 279                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 280
 281                 m->mothurOutEndLine();
 282                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 283                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 284                 m->mothurOutEndLine();
 285
 286                 return 0;
 287         }
 288         catch(exception& e) {
 289                 m->errorOut(e, "NMDSCommand", "execute");
 290                 exit(1);
 291         }
 292 }
 293 //**********************************************************************************************************************
 294 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 295         try {
 296
 297                 vector< vector<double> > newConfig = config;
 298
 299                 //calc euclid distances
 300                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 301                 if (m->control_pressed) { return newConfig; }
 302
 303                 double stress2 = calculateStress(matrix, euclid);
 304                 stress1 = stress2 + 1.0 + epsilon;
 305
 306                 int count = 0;
 307                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 308                         count++;
 309
 310                         stress1 = stress2;
 311
 312                         if (m->control_pressed) { return newConfig; }
 313
 314                         vector< vector<double> > b; b.resize(euclid.size());
 315                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 316
 317                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 318                         for (int i = 0; i < euclid.size(); i++) {
 319                                 for (int j = 0; j < euclid[i].size(); j++) {
 320                                         //eliminate divide by zero error
 321                                         if (euclid[i][j] != 0) {
 322                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 323                                                 columnSums[j] += b[i][j];
 324                                                 b[i][j] *= -1.0;
 325                                         }
 326                                 }
 327                         }
 328
 329                         //put in diagonal sums
 330                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 331
 332                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 333                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 334
 335                         //matrix mult
 336                         newConfig = linearCalc.matrix_mult(newConfig, b);
 337                         for (int i = 0; i < newConfig.size(); i++) {
 338                                 for (int j = 0; j < newConfig[i].size(); j++) {
 339                                         newConfig[i][j] *= (1.0 / n);
 340                                 }
 341                         }
 342
 343                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 344
 345                         stress2 = calculateStress(matrix, euclid);
 346                 }
 347
 348                 return newConfig;
 349         }
 350         catch(exception& e) {
 351                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 352                 exit(1);
 353         }
 354 }
 355
 356 //**********************************************************************************************************************
 357 //generate random config
 358 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 359         try {
 360                 vector< vector<double> > axes;  axes.resize(dimension);
 361                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 362
 363                 //generate random number between -1 and 1, precision 6
 364                 for (int i = 0; i < axes.size(); i++) {
 365                         for (int j = 0; j < axes[i].size(); j++) {
 366
 367                                 if (m->control_pressed) { return axes; }
 368
 369                                 //generate random int between 0 and 99999
 370                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 371
 372                                 //generate random sign
 373                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 374
 375                                 //if mysign is even then sign = positive, else sign = negative
 376                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 377                                 else { mysign = -1.0; }
 378
 379                                 axes[i][j] = mysign * myrand / (float) 100000;
 380                         }
 381                 }
 382
 383                 return axes;
 384         }
 385         catch(exception& e) {
 386                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 387                 exit(1);
 388         }
 389 }
 390 //**********************************************************************************************************************
 391 //normalize configuration
 392 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 393         try {
 394                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 395
 396                 //find average
 397                 for (int i = 0; i < axes.size(); i++) {
 398                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 399
 400                         averageAxes[i] /= (float) numNames;
 401                 }
 402
 403                 //normalize axes
 404                 double sumDenom = 0.0;
 405                 for (int i = 0; i < axes.size(); i++) {
 406                         for (int j = 0; j < axes[i].size(); j++) {
 407                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 408                         }
 409                 }
 410
 411                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 412
 413                 for (int i = 0; i < axes.size(); i++) {
 414                         for (int j = 0; j < axes[i].size(); j++) {
 415                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 416                         }
 417                 }
 418
 419                 return 0;
 420         }
 421         catch(exception& e) {
 422                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 423                 exit(1);
 424         }
 425 }
 426 //**********************************************************************************************************************
 427 //get configuration
 428 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 429         try {
 430                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 431
 432                 for (int i = 0; i < dimension; i++) {
 433                         newAxes[i] = axes[i];
 434                 }
 435
 436                 return newAxes;
 437         }
 438         catch(exception& e) {
 439                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 440                 exit(1);
 441         }
 442 }
 443 //**********************************************************************************************************************
 444 //find raw stress, and normalize using
 445 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 446         try {
 447                 double normStress = 0.0;
 448                 double denom = 0.0;
 449                 double rawStress = 0.0;
 450
 451                 //find raw stress
 452                 for (int i = 0; i < matrix.size(); i++) {
 453                         for (int j = 0; j < matrix[i].size(); j++) {
 454                                 if (m->control_pressed) { return normStress; }
 455
 456                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 457                                 denom += (config[i][j] * config[i][j]);
 458                         }
 459                 }
 460
 461                 //normalize stress
 462                 if ((rawStress != 0.0) && (denom != 0.0)) {
 463                         normStress = sqrt((rawStress / denom));
 464                 }
 465
 466                 return normStress;
 467         }
 468         catch(exception& e) {
 469                 m->errorOut(e, "NMDSCommand", "calculateStress");
 470                 exit(1);
 471         }
 472 }
 473
 474 //**********************************************************************************************************************
 475 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 476         try {
 477
 478                 for (int i = 0; i < names.size(); i++) {
 479
 480                         out << names[i] << '\t';
 481
 482                         for (int j = 0; j < config.size(); j++) {
 483                                 out << config[j][i] << '\t';
 484                         }
 485
 486                         out << endl;
 487                 }
 488
 489                 out << endl << endl;
 490
 491                 return 0;
 492         }
 493         catch(exception& e) {
 494                 m->errorOut(e, "NMDSCommand", "output");
 495                 exit(1);
 496         }
 497 }
 498 /*****************************************************************/
 499 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 500         try {
 501                 ifstream in;
 502                 m->openInputFile(axesfile, in);
 503
 504                 string headerLine = m->getline(in); m->gobble(in);
 505
 506                 //count the number of axis you are reading
 507                 bool done = false;
 508                 int count = 0;
 509                 while (!done) {
 510                         int pos = headerLine.find("axis");
 511                         if (pos != string::npos) {
 512                                 count++;
 513                                 headerLine = headerLine.substr(pos+4);
 514                         }else { done = true; }
 515                 }
 516
 517                 if (maxdim > count) {
 518                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 519                         maxdim = count;
 520                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 521                 }
 522
 523                 vector< vector<double> > axes;  axes.resize(maxdim);
 524                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 525
 526                 map <string, vector<double> > orderedAxes;
 527                 map     <string, vector<double> >::iterator it;
 528
 529                 while (!in.eof()) {
 530
 531                         if (m->control_pressed) { in.close(); return axes; }
 532
 533                         string group = "";
 534                         in >> group; m->gobble(in);
 535
 536                         bool ignore = false;
 537                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 538
 539                         vector<double> thisGroupsAxes;
 540                         for (int i = 0; i < count; i++) {
 541                                 float temp = 0.0;
 542                                 in >> temp;
 543
 544                                 //only save the axis we want
 545                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 546                         }
 547
 548                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 549
 550                         m->gobble(in);
 551                 }
 552                 in.close();
 553
 554                 //sanity check
 555                 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; }
 556
 557                 //put axes info in same order as distance file, just in case
 558                 for (int i = 0; i < names.size(); i++) {
 559                         it = orderedAxes.find(names[i]);
 560
 561                         if (it != orderedAxes.end()) {
 562                                 vector<double> thisGroupsAxes = it->second;
 563
 564                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 565                                         axes[j][i] = thisGroupsAxes[j];
 566                                 }
 567
 568                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 569                 }
 570
 571                 return axes;
 572         }
 573         catch(exception& e) {
 574                 m->errorOut(e, "NMDSCommand", "readAxes");
 575                 exit(1);
 576         }
 577 }
 578 /**********************************************************************************************************************/
 579
 580
 581