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,true); parameters.push_back(paxes);
  17                 CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","nmds-stress",false,true,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 string NMDSCommand::getOutputPattern(string type) {
  59     try {
  60         string pattern = "";
  61
  62         if (type == "nmds") {  pattern = "[filename],nmds.axes"; }
  63         else if (type == "stress") {  pattern = "[filename],nmds.stress"; }
  64         else if (type == "iters") {  pattern = "[filename],nmds.iters"; }
  65         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  66
  67         return pattern;
  68     }
  69     catch(exception& e) {
  70         m->errorOut(e, "NMDSCommand", "getOutputPattern");
  71         exit(1);
  72     }
  73 }
  74
  75 //**********************************************************************************************************************
  76 NMDSCommand::NMDSCommand(){
  77         try {
  78                 abort = true; calledHelp = true;
  79                 setParameters();
  80                 vector<string> tempOutNames;
  81                 outputTypes["nmds"] = tempOutNames;
  82                 outputTypes["stress"] = tempOutNames;
  83                 outputTypes["iters"] = tempOutNames;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91
  92 NMDSCommand::NMDSCommand(string option)  {
  93         try {
  94                 abort = false; calledHelp = false;
  95
  96                 //allow user to run help
  97                 if(option == "help") { help(); abort = true; calledHelp = true; }
  98                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  99
 100                 else {
 101                         vector<string> myArray = setParameters();
 102
 103                         OptionParser parser(option);
 104                         map<string, string> parameters = parser. getParameters();
 105
 106                         ValidParameters validParameter;
 107                         map<string, string>::iterator it;
 108
 109                         //check to make sure all parameters are valid for command
 110                         for (it = parameters.begin(); it != parameters.end(); it++) {
 111                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 112                         }
 113                         //if the user changes the input directory command factory will send this info to us in the output parameter
 114                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 115                         if (inputDir == "not found"){   inputDir = "";          }
 116                         else {
 117                                 string path;
 118                                 it = parameters.find("phylip");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 124                                 }
 125
 126                                 it = parameters.find("axes");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["axes"] = inputDir + it->second;             }
 132                                 }
 133                         }
 134
 135                         //initialize outputTypes
 136                         vector<string> tempOutNames;
 137                         outputTypes["nmds"] = tempOutNames;
 138                         outputTypes["iters"] = tempOutNames;
 139                         outputTypes["stress"] = tempOutNames;
 140
 141                         //required parameters
 142                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 143                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 144                         else if (phylipfile == "not found") {
 145                                 //if there is a current phylip file, use it
 146                                 phylipfile = m->getPhylipFile();
 147                                 if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 148                                 else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
 149                         }else { m->setPhylipFile(phylipfile); }
 150
 151                         axesfile = validParameter.validFile(parameters, "axes", true);
 152                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 153                         else if (axesfile == "not found") { axesfile = "";  }
 154
 155                         //if the user changes the output directory command factory will send this info to us in the output parameter
 156                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 157                                 outputDir = "";
 158                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 159                         }
 160
 161                         string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
 162                         m->mothurConvert(temp, mindim);
 163
 164                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 165                         m->mothurConvert(temp, maxIters);
 166
 167                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 168                         m->mothurConvert(temp, iters);
 169
 170                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 171                         m->mothurConvert(temp, maxdim);
 172
 173                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 174                         m->mothurConvert(temp, epsilon);
 175
 176                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 177                         if (maxdim < mindim) { maxdim = mindim; }
 178                 }
 179
 180         }
 181         catch(exception& e) {
 182                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 183                 exit(1);
 184         }
 185 }
 186 //**********************************************************************************************************************
 187 int NMDSCommand::execute(){
 188         try {
 189
 190                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 191
 192                 cout.setf(ios::fixed, ios::floatfield);
 193                 cout.setf(ios::showpoint);
 194
 195                 vector<string> names;
 196                 vector< vector< double> > matrix;
 197
 198                 //read in phylip file
 199                 ReadPhylipVector readFile(phylipfile);
 200                 names = readFile.read(matrix);
 201                 if (m->control_pressed) { return 0; }
 202
 203                 //read axes
 204                 vector< vector<double> > axes;
 205                 if (axesfile != "") {  axes = readAxes(names);          }
 206
 207         map<string, string> variables;
 208         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile));
 209                 string outputFileName = getOutputFileName("iters",variables);
 210                 string stressFileName = getOutputFileName("stress",variables);
 211                 outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 212                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 213
 214                 ofstream out, out2;
 215                 m->openOutputFile(outputFileName, out);
 216                 m->openOutputFile(stressFileName, out2);
 217
 218                 out2.setf(ios::fixed, ios::floatfield);
 219                 out2.setf(ios::showpoint);
 220                 out.setf(ios::fixed, ios::floatfield);
 221                 out.setf(ios::showpoint);
 222
 223                 out2 << "Dimension\tIter\tStress\tRsq" << endl;
 224
 225                 double bestStress = 10000000;
 226                 double bestR2 = 10000000;
 227                 vector< vector<double> > bestConfig;
 228                 int bestDim = 0;
 229
 230                 for (int i = mindim; i <= maxdim; i++) {
 231                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 232
 233                         for (int j = 0; j < iters; j++) {
 234                                 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
 235
 236                                 //get configuration - either randomly generate or resize to this dimension
 237                                 vector< vector<double> > thisConfig;
 238                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 239                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 240                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 241
 242                                 //calc nmds for this dimension
 243                                 double stress;
 244                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 245                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 246
 247                                 //calc euclid distances for new config
 248                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 249                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 250
 251                                 //calc correlation between original distances and euclidean distances from this config
 252                                 double rsquared = linearCalc.calcPearson(newEuclid, matrix);
 253                                 rsquared *= rsquared;
 254                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 255
 256                                 //output results
 257                                 out << "Config" << (j+1) << '\t';
 258                                 for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
 259                                 out << endl;
 260                                 out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
 261
 262                                 output(endConfig, names, out);
 263
 264                                 //save best
 265                                 if (stress < bestStress) {
 266                                         bestDim = i;
 267                                         bestStress = stress;
 268                                         bestR2 = rsquared;
 269                                         bestConfig = endConfig;
 270                                 }
 271
 272                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 273                         }
 274                 }
 275
 276                 out.close(); out2.close();
 277
 278                 //output best config
 279                 string BestFileName = getOutputFileName("nmds",variables);
 280                 outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 281
 282                 m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
 283                 m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
 284                 m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
 285
 286                 ofstream outBest;
 287                 m->openOutputFile(BestFileName, outBest);
 288                 outBest.setf(ios::fixed, ios::floatfield);
 289                 outBest.setf(ios::showpoint);
 290
 291                 outBest << "group" << '\t';
 292                 for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
 293                 outBest << endl;
 294
 295                 output(bestConfig, names, outBest);
 296
 297                 outBest.close();
 298
 299                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 300
 301                 m->mothurOutEndLine();
 302                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 303                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 304                 m->mothurOutEndLine();
 305
 306                 return 0;
 307         }
 308         catch(exception& e) {
 309                 m->errorOut(e, "NMDSCommand", "execute");
 310                 exit(1);
 311         }
 312 }
 313 //**********************************************************************************************************************
 314 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 315         try {
 316
 317                 vector< vector<double> > newConfig = config;
 318
 319                 //calc euclid distances
 320                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 321                 if (m->control_pressed) { return newConfig; }
 322
 323                 double stress2 = calculateStress(matrix, euclid);
 324                 stress1 = stress2 + 1.0 + epsilon;
 325
 326                 int count = 0;
 327                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 328                         count++;
 329
 330                         stress1 = stress2;
 331
 332                         if (m->control_pressed) { return newConfig; }
 333
 334                         vector< vector<double> > b; b.resize(euclid.size());
 335                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 336
 337                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 338                         for (int i = 0; i < euclid.size(); i++) {
 339                                 for (int j = 0; j < euclid[i].size(); j++) {
 340                                         //eliminate divide by zero error
 341                                         if (euclid[i][j] != 0) {
 342                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 343                                                 columnSums[j] += b[i][j];
 344                                                 b[i][j] *= -1.0;
 345                                         }
 346                                 }
 347                         }
 348
 349                         //put in diagonal sums
 350                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 351
 352                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 353                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 354
 355                         //matrix mult
 356                         newConfig = linearCalc.matrix_mult(newConfig, b);
 357                         for (int i = 0; i < newConfig.size(); i++) {
 358                                 for (int j = 0; j < newConfig[i].size(); j++) {
 359                                         newConfig[i][j] *= (1.0 / n);
 360                                 }
 361                         }
 362
 363                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 364
 365                         stress2 = calculateStress(matrix, euclid);
 366                 }
 367
 368                 return newConfig;
 369         }
 370         catch(exception& e) {
 371                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 372                 exit(1);
 373         }
 374 }
 375
 376 //**********************************************************************************************************************
 377 //generate random config
 378 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 379         try {
 380                 vector< vector<double> > axes;  axes.resize(dimension);
 381                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 382
 383                 //generate random number between -1 and 1, precision 6
 384                 for (int i = 0; i < axes.size(); i++) {
 385                         for (int j = 0; j < axes[i].size(); j++) {
 386
 387                                 if (m->control_pressed) { return axes; }
 388
 389                                 //generate random int between 0 and 99999
 390                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 391
 392                                 //generate random sign
 393                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 394
 395                                 //if mysign is even then sign = positive, else sign = negative
 396                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 397                                 else { mysign = -1.0; }
 398
 399                                 axes[i][j] = mysign * myrand / (float) 100000;
 400                         }
 401                 }
 402
 403                 return axes;
 404         }
 405         catch(exception& e) {
 406                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 407                 exit(1);
 408         }
 409 }
 410 //**********************************************************************************************************************
 411 //normalize configuration
 412 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 413         try {
 414                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 415
 416                 //find average
 417                 for (int i = 0; i < axes.size(); i++) {
 418                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 419
 420                         averageAxes[i] /= (float) numNames;
 421                 }
 422
 423                 //normalize axes
 424                 double sumDenom = 0.0;
 425                 for (int i = 0; i < axes.size(); i++) {
 426                         for (int j = 0; j < axes[i].size(); j++) {
 427                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 428                         }
 429                 }
 430
 431                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 432
 433                 for (int i = 0; i < axes.size(); i++) {
 434                         for (int j = 0; j < axes[i].size(); j++) {
 435                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 436                         }
 437                 }
 438
 439                 return 0;
 440         }
 441         catch(exception& e) {
 442                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 443                 exit(1);
 444         }
 445 }
 446 //**********************************************************************************************************************
 447 //get configuration
 448 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 449         try {
 450                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 451
 452                 for (int i = 0; i < dimension; i++) {
 453                         newAxes[i] = axes[i];
 454                 }
 455
 456                 return newAxes;
 457         }
 458         catch(exception& e) {
 459                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 460                 exit(1);
 461         }
 462 }
 463 //**********************************************************************************************************************
 464 //find raw stress, and normalize using
 465 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 466         try {
 467                 double normStress = 0.0;
 468                 double denom = 0.0;
 469                 double rawStress = 0.0;
 470
 471                 //find raw stress
 472                 for (int i = 0; i < matrix.size(); i++) {
 473                         for (int j = 0; j < matrix[i].size(); j++) {
 474                                 if (m->control_pressed) { return normStress; }
 475
 476                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 477                                 denom += (config[i][j] * config[i][j]);
 478                         }
 479                 }
 480
 481                 //normalize stress
 482                 if ((rawStress != 0.0) && (denom != 0.0)) {
 483                         normStress = sqrt((rawStress / denom));
 484                 }
 485
 486                 return normStress;
 487         }
 488         catch(exception& e) {
 489                 m->errorOut(e, "NMDSCommand", "calculateStress");
 490                 exit(1);
 491         }
 492 }
 493
 494 //**********************************************************************************************************************
 495 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 496         try {
 497
 498                 for (int i = 0; i < names.size(); i++) {
 499
 500                         out << names[i] << '\t';
 501
 502                         for (int j = 0; j < config.size(); j++) {
 503                                 out << config[j][i] << '\t';
 504                         }
 505
 506                         out << endl;
 507                 }
 508
 509                 out << endl << endl;
 510
 511                 return 0;
 512         }
 513         catch(exception& e) {
 514                 m->errorOut(e, "NMDSCommand", "output");
 515                 exit(1);
 516         }
 517 }
 518 /*****************************************************************/
 519 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 520         try {
 521                 ifstream in;
 522                 m->openInputFile(axesfile, in);
 523
 524                 string headerLine = m->getline(in); m->gobble(in);
 525
 526                 //count the number of axis you are reading
 527                 bool done = false;
 528                 int count = 0;
 529                 while (!done) {
 530                         int pos = headerLine.find("axis");
 531                         if (pos != string::npos) {
 532                                 count++;
 533                                 headerLine = headerLine.substr(pos+4);
 534                         }else { done = true; }
 535                 }
 536
 537                 if (maxdim > count) {
 538                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 539                         maxdim = count;
 540                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 541                 }
 542
 543                 vector< vector<double> > axes;  axes.resize(maxdim);
 544                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 545
 546                 map <string, vector<double> > orderedAxes;
 547                 map     <string, vector<double> >::iterator it;
 548
 549                 while (!in.eof()) {
 550
 551                         if (m->control_pressed) { in.close(); return axes; }
 552
 553                         string group = "";
 554                         in >> group; m->gobble(in);
 555
 556                         bool ignore = false;
 557                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 558
 559                         vector<double> thisGroupsAxes;
 560                         for (int i = 0; i < count; i++) {
 561                                 float temp = 0.0;
 562                                 in >> temp;
 563
 564                                 //only save the axis we want
 565                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 566                         }
 567
 568                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 569
 570                         m->gobble(in);
 571                 }
 572                 in.close();
 573
 574                 //sanity check
 575                 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; }
 576
 577                 //put axes info in same order as distance file, just in case
 578                 for (int i = 0; i < names.size(); i++) {
 579                         it = orderedAxes.find(names[i]);
 580
 581                         if (it != orderedAxes.end()) {
 582                                 vector<double> thisGroupsAxes = it->second;
 583
 584                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 585                                         axes[j][i] = thisGroupsAxes[j];
 586                                 }
 587
 588                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 589                 }
 590
 591                 return axes;
 592         }
 593         catch(exception& e) {
 594                 m->errorOut(e, "NMDSCommand", "readAxes");
 595                 exit(1);
 596         }
 597 }
 598 /**********************************************************************************************************************/
 599
 600
 601