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; calledHelp = true;
  29                 vector<string> tempOutNames;
  30                 outputTypes["nmds"] = tempOutNames;
  31                 outputTypes["stress"] = tempOutNames;
  32                 outputTypes["iters"] = tempOutNames;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 vector<string> NMDSCommand::getRequiredParameters(){
  41         try {
  42                 string Array[] =  {"phylip"};
  43                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "NMDSCommand", "getRequiredParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 vector<string> NMDSCommand::getRequiredFiles(){
  53         try {
  54                 vector<string> myArray;
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "NMDSCommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63
  64 NMDSCommand::NMDSCommand(string option)  {
  65         try {
  66                 abort = false; calledHelp = false;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; calledHelp = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"phylip","axes","mindim","maxdim","iters","maxiters","epsilon","outputdir", "inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string, string> parameters = parser. getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86                         //if the user changes the input directory command factory will send this info to us in the output parameter
  87                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  88                         if (inputDir == "not found"){   inputDir = "";          }
  89                         else {
  90                                 string path;
  91                                 it = parameters.find("phylip");
  92                                 //user has given a template file
  93                                 if(it != parameters.end()){
  94                                         path = m->hasPath(it->second);
  95                                         //if the user has not given a path then, add inputdir. else leave path alone.
  96                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  97                                 }
  98
  99                                 it = parameters.find("axes");
 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["axes"] = inputDir + it->second;             }
 105                                 }
 106                         }
 107
 108                         //initialize outputTypes
 109                         vector<string> tempOutNames;
 110                         outputTypes["nmds"] = tempOutNames;
 111                         outputTypes["iters"] = tempOutNames;
 112                         outputTypes["stress"] = tempOutNames;
 113
 114                         //required parameters
 115                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 116                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 117                         else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("You must provide a distance file before running the nmds command."); m->mothurOutEndLine(); abort = true; }
 118
 119                         axesfile = validParameter.validFile(parameters, "axes", true);
 120                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 121                         else if (axesfile == "not found") { axesfile = "";  }
 122
 123                         //if the user changes the output directory command factory will send this info to us in the output parameter
 124                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 125                                 outputDir = "";
 126                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 127                         }
 128
 129                         string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
 130                         convert(temp, mindim);
 131
 132                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 133                         convert(temp, maxIters);
 134
 135                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 136                         convert(temp, iters);
 137
 138                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 139                         convert(temp, maxdim);
 140
 141                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 142                         convert(temp, epsilon);
 143
 144                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 145                         if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
 146                 }
 147
 148         }
 149         catch(exception& e) {
 150                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 151                 exit(1);
 152         }
 153 }
 154 //**********************************************************************************************************************
 155 void NMDSCommand::help(){
 156         try {
 157                 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();
 158                 m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters and epsilon."); m->mothurOutEndLine();
 159                 m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
 160                 m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
 161                 m->mothurOut("The maxdim parameter allows you to select the maximum dimensions to use. Default=2"); m->mothurOutEndLine();
 162                 m->mothurOut("The mindim parameter allows you to select the minimum dimensions to use. Default=2"); m->mothurOutEndLine();
 163                 m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
 164                 m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
 165                 m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();
 166                 m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
 167                 m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
 168         }
 169         catch(exception& e) {
 170                 m->errorOut(e, "NMDSCommand", "help");
 171                 exit(1);
 172         }
 173 }
 174 //**********************************************************************************************************************
 175 NMDSCommand::~NMDSCommand(){}
 176 //**********************************************************************************************************************
 177 int NMDSCommand::execute(){
 178         try {
 179
 180                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 181
 182                 cout.setf(ios::fixed, ios::floatfield);
 183                 cout.setf(ios::showpoint);
 184
 185                 vector<string> names;
 186                 vector< vector< double> > matrix;
 187
 188                 //read in phylip file
 189                 ReadPhylipVector readFile(phylipfile);
 190                 names = readFile.read(matrix);
 191                 if (m->control_pressed) { return 0; }
 192
 193                 //read axes
 194                 vector< vector<double> > axes;
 195                 if (axesfile != "") {  axes = readAxes(names);          }
 196
 197                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
 198                 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.stress";
 199                 outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 200                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 201
 202                 ofstream out, out2;
 203                 m->openOutputFile(outputFileName, out);
 204                 m->openOutputFile(stressFileName, out2);
 205
 206                 out2.setf(ios::fixed, ios::floatfield);
 207                 out2.setf(ios::showpoint);
 208                 out.setf(ios::fixed, ios::floatfield);
 209                 out.setf(ios::showpoint);
 210
 211                 out2 << "Dimension\tIter\tStress\tRsq" << endl;
 212
 213                 double bestStress = 10000000;
 214                 double bestR2 = 10000000;
 215                 vector< vector<double> > bestConfig;
 216                 int bestDim = 0;
 217
 218                 for (int i = mindim; i <= maxdim; i++) {
 219                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 220
 221                         for (int j = 0; j < iters; j++) {
 222                                 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
 223
 224                                 //get configuration - either randomly generate or resize to this dimension
 225                                 vector< vector<double> > thisConfig;
 226                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 227                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 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 nmds for this dimension
 231                                 double stress;
 232                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 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                                 //calc euclid distances for new config
 236                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 237                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 238
 239                                 //calc correlation between original distances and euclidean distances from this config
 240                                 double rsquared = linearCalc.calcPearson(newEuclid, matrix);
 241                                 rsquared *= rsquared;
 242                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 243
 244                                 //output results
 245                                 out << "Config" << (j+1) << '\t';
 246                                 for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
 247                                 out << endl;
 248                                 out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
 249
 250                                 output(endConfig, names, out);
 251
 252                                 //save best
 253                                 if (stress < bestStress) {
 254                                         bestDim = i;
 255                                         bestStress = stress;
 256                                         bestR2 = rsquared;
 257                                         bestConfig = endConfig;
 258                                 }
 259
 260                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 261                         }
 262                 }
 263
 264                 out.close(); out2.close();
 265
 266                 //output best config
 267                 string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
 268                 outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 269
 270                 m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
 271                 m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
 272                 m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
 273
 274                 ofstream outBest;
 275                 m->openOutputFile(BestFileName, outBest);
 276                 outBest.setf(ios::fixed, ios::floatfield);
 277                 outBest.setf(ios::showpoint);
 278
 279                 outBest << '\t';
 280                 for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
 281                 outBest << endl;
 282
 283                 output(bestConfig, names, outBest);
 284
 285                 outBest.close();
 286
 287                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 288
 289                 m->mothurOutEndLine();
 290                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 291                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 292                 m->mothurOutEndLine();
 293
 294                 return 0;
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "NMDSCommand", "execute");
 298                 exit(1);
 299         }
 300 }
 301 //**********************************************************************************************************************
 302 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 303         try {
 304
 305                 vector< vector<double> > newConfig = config;
 306
 307                 //calc euclid distances
 308                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 309                 if (m->control_pressed) { return newConfig; }
 310
 311                 double stress2 = calculateStress(matrix, euclid);
 312                 stress1 = stress2 + 1.0 + epsilon;
 313
 314                 int count = 0;
 315                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 316                         count++;
 317
 318                         stress1 = stress2;
 319
 320                         if (m->control_pressed) { return newConfig; }
 321
 322                         vector< vector<double> > b; b.resize(euclid.size());
 323                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 324
 325                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 326                         for (int i = 0; i < euclid.size(); i++) {
 327                                 for (int j = 0; j < euclid[i].size(); j++) {
 328                                         //eliminate divide by zero error
 329                                         if (euclid[i][j] != 0) {
 330                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 331                                                 columnSums[j] += b[i][j];
 332                                                 b[i][j] *= -1.0;
 333                                         }
 334                                 }
 335                         }
 336
 337                         //put in diagonal sums
 338                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 339
 340                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 341                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 342
 343                         //matrix mult
 344                         newConfig = linearCalc.matrix_mult(newConfig, b);
 345                         for (int i = 0; i < newConfig.size(); i++) {
 346                                 for (int j = 0; j < newConfig[i].size(); j++) {
 347                                         newConfig[i][j] *= (1.0 / n);
 348                                 }
 349                         }
 350
 351                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 352
 353                         stress2 = calculateStress(matrix, euclid);
 354                 }
 355
 356                 return newConfig;
 357         }
 358         catch(exception& e) {
 359                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 360                 exit(1);
 361         }
 362 }
 363
 364 //**********************************************************************************************************************
 365 //generate random config
 366 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 367         try {
 368                 vector< vector<double> > axes;  axes.resize(dimension);
 369                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 370
 371                 //generate random number between -1 and 1, precision 6
 372                 for (int i = 0; i < axes.size(); i++) {
 373                         for (int j = 0; j < axes[i].size(); j++) {
 374
 375                                 if (m->control_pressed) { return axes; }
 376
 377                                 //generate random int between 0 and 99999
 378                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 379
 380                                 //generate random sign
 381                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 382
 383                                 //if mysign is even then sign = positive, else sign = negative
 384                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 385                                 else { mysign = -1.0; }
 386
 387                                 axes[i][j] = mysign * myrand / (float) 100000;
 388                         }
 389                 }
 390
 391                 return axes;
 392         }
 393         catch(exception& e) {
 394                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 395                 exit(1);
 396         }
 397 }
 398 //**********************************************************************************************************************
 399 //normalize configuration
 400 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 401         try {
 402                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 403
 404                 //find average
 405                 for (int i = 0; i < axes.size(); i++) {
 406                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 407
 408                         averageAxes[i] /= (float) numNames;
 409                 }
 410
 411                 //normalize axes
 412                 double sumDenom = 0.0;
 413                 for (int i = 0; i < axes.size(); i++) {
 414                         for (int j = 0; j < axes[i].size(); j++) {
 415                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 416                         }
 417                 }
 418
 419                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 420
 421                 for (int i = 0; i < axes.size(); i++) {
 422                         for (int j = 0; j < axes[i].size(); j++) {
 423                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 424                         }
 425                 }
 426
 427                 return 0;
 428         }
 429         catch(exception& e) {
 430                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 431                 exit(1);
 432         }
 433 }
 434 //**********************************************************************************************************************
 435 //get configuration
 436 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 437         try {
 438                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 439
 440                 for (int i = 0; i < dimension; i++) {
 441                         newAxes[i] = axes[i];
 442                 }
 443
 444                 return newAxes;
 445         }
 446         catch(exception& e) {
 447                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 448                 exit(1);
 449         }
 450 }
 451 //**********************************************************************************************************************
 452 //find raw stress, and normalize using
 453 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 454         try {
 455                 double normStress = 0.0;
 456                 double denom = 0.0;
 457                 double rawStress = 0.0;
 458
 459                 //find raw stress
 460                 for (int i = 0; i < matrix.size(); i++) {
 461                         for (int j = 0; j < matrix[i].size(); j++) {
 462                                 if (m->control_pressed) { return normStress; }
 463
 464                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 465                                 denom += (config[i][j] * config[i][j]);
 466                         }
 467                 }
 468
 469                 //normalize stress
 470                 if ((rawStress != 0.0) && (denom != 0.0)) {
 471                         normStress = sqrt((rawStress / denom));
 472                 }
 473
 474                 return normStress;
 475         }
 476         catch(exception& e) {
 477                 m->errorOut(e, "NMDSCommand", "calculateStress");
 478                 exit(1);
 479         }
 480 }
 481
 482 //**********************************************************************************************************************
 483 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 484         try {
 485
 486                 for (int i = 0; i < names.size(); i++) {
 487
 488                         out << names[i] << '\t';
 489
 490                         for (int j = 0; j < config.size(); j++) {
 491                                 out << config[j][i] << '\t';
 492                         }
 493
 494                         out << endl;
 495                 }
 496
 497                 out << endl << endl;
 498
 499                 return 0;
 500         }
 501         catch(exception& e) {
 502                 m->errorOut(e, "NMDSCommand", "output");
 503                 exit(1);
 504         }
 505 }
 506 /*****************************************************************/
 507 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 508         try {
 509                 ifstream in;
 510                 m->openInputFile(axesfile, in);
 511
 512                 string headerLine = m->getline(in); m->gobble(in);
 513
 514                 //count the number of axis you are reading
 515                 bool done = false;
 516                 int count = 0;
 517                 while (!done) {
 518                         int pos = headerLine.find("axis");
 519                         if (pos != string::npos) {
 520                                 count++;
 521                                 headerLine = headerLine.substr(pos+4);
 522                         }else { done = true; }
 523                 }
 524
 525                 if (maxdim > count) {
 526                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 527                         maxdim = count;
 528                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 529                 }
 530
 531                 vector< vector<double> > axes;  axes.resize(maxdim);
 532                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 533
 534                 map <string, vector<double> > orderedAxes;
 535                 map     <string, vector<double> >::iterator it;
 536
 537                 while (!in.eof()) {
 538
 539                         if (m->control_pressed) { in.close(); return axes; }
 540
 541                         string group = "";
 542                         in >> group; m->gobble(in);
 543
 544                         bool ignore = false;
 545                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 546
 547                         vector<double> thisGroupsAxes;
 548                         for (int i = 0; i < count; i++) {
 549                                 float temp = 0.0;
 550                                 in >> temp;
 551
 552                                 //only save the axis we want
 553                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 554                         }
 555
 556                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 557
 558                         m->gobble(in);
 559                 }
 560                 in.close();
 561
 562                 //sanity check
 563                 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; }
 564
 565                 //put axes info in same order as distance file, just in case
 566                 for (int i = 0; i < names.size(); i++) {
 567                         it = orderedAxes.find(names[i]);
 568
 569                         if (it != orderedAxes.end()) {
 570                                 vector<double> thisGroupsAxes = it->second;
 571
 572                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 573                                         axes[j][i] = thisGroupsAxes[j];
 574                                 }
 575
 576                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 577                 }
 578
 579                 return axes;
 580         }
 581         catch(exception& e) {
 582                 m->errorOut(e, "NMDSCommand", "readAxes");
 583                 exit(1);
 584         }
 585 }
 586 /**********************************************************************************************************************/
 587
 588
 589