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 string NMDSCommand::getOutputFileNameTag(string type, string inputName=""){
  59         try {
  60         string outputFileName = "";
  61                 map<string, vector<string> >::iterator it;
  62
  63         //is this a type this command creates
  64         it = outputTypes.find(type);
  65         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  66         else {
  67             if (type == "nmds") {  outputFileName =  "nmds.axes"; }
  68             else if (type == "stress") {  outputFileName =  "nmds.stress"; }
  69             else if (type == "iters") {  outputFileName =  "nmds.iters"; }
  70             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  71         }
  72         return outputFileName;
  73         }
  74         catch(exception& e) {
  75                 m->errorOut(e, "NMDSCommand", "getOutputFileNameTag");
  76                 exit(1);
  77         }
  78 }
  79 //**********************************************************************************************************************
  80 NMDSCommand::NMDSCommand(){
  81         try {
  82                 abort = true; calledHelp = true;
  83                 setParameters();
  84                 vector<string> tempOutNames;
  85                 outputTypes["nmds"] = tempOutNames;
  86                 outputTypes["stress"] = tempOutNames;
  87                 outputTypes["iters"] = tempOutNames;
  88         }
  89         catch(exception& e) {
  90                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
  91                 exit(1);
  92         }
  93 }
  94 //**********************************************************************************************************************
  95
  96 NMDSCommand::NMDSCommand(string option)  {
  97         try {
  98                 abort = false; calledHelp = false;
  99
 100                 //allow user to run help
 101                 if(option == "help") { help(); abort = true; calledHelp = true; }
 102                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 103
 104                 else {
 105                         vector<string> myArray = setParameters();
 106
 107                         OptionParser parser(option);
 108                         map<string, string> parameters = parser. getParameters();
 109
 110                         ValidParameters validParameter;
 111                         map<string, string>::iterator it;
 112
 113                         //check to make sure all parameters are valid for command
 114                         for (it = parameters.begin(); it != parameters.end(); it++) {
 115                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 116                         }
 117                         //if the user changes the input directory command factory will send this info to us in the output parameter
 118                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 119                         if (inputDir == "not found"){   inputDir = "";          }
 120                         else {
 121                                 string path;
 122                                 it = parameters.find("phylip");
 123                                 //user has given a template file
 124                                 if(it != parameters.end()){
 125                                         path = m->hasPath(it->second);
 126                                         //if the user has not given a path then, add inputdir. else leave path alone.
 127                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
 128                                 }
 129
 130                                 it = parameters.find("axes");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["axes"] = inputDir + it->second;             }
 136                                 }
 137                         }
 138
 139                         //initialize outputTypes
 140                         vector<string> tempOutNames;
 141                         outputTypes["nmds"] = tempOutNames;
 142                         outputTypes["iters"] = tempOutNames;
 143                         outputTypes["stress"] = tempOutNames;
 144
 145                         //required parameters
 146                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 147                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 148                         else if (phylipfile == "not found") {
 149                                 //if there is a current phylip file, use it
 150                                 phylipfile = m->getPhylipFile();
 151                                 if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
 152                                 else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
 153                         }else { m->setPhylipFile(phylipfile); }
 154
 155                         axesfile = validParameter.validFile(parameters, "axes", true);
 156                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 157                         else if (axesfile == "not found") { axesfile = "";  }
 158
 159                         //if the user changes the output directory command factory will send this info to us in the output parameter
 160                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 161                                 outputDir = "";
 162                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 163                         }
 164
 165                         string temp = validParameter.validFile(parameters, "mindim", false);    if (temp == "not found") {      temp = "2";     }
 166                         m->mothurConvert(temp, mindim);
 167
 168                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 169                         m->mothurConvert(temp, maxIters);
 170
 171                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 172                         m->mothurConvert(temp, iters);
 173
 174                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 175                         m->mothurConvert(temp, maxdim);
 176
 177                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 178                         m->mothurConvert(temp, epsilon);
 179
 180                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 181                         if (maxdim < mindim) { maxdim = mindim; }
 182                 }
 183
 184         }
 185         catch(exception& e) {
 186                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 187                 exit(1);
 188         }
 189 }
 190 //**********************************************************************************************************************
 191 int NMDSCommand::execute(){
 192         try {
 193
 194                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 195
 196                 cout.setf(ios::fixed, ios::floatfield);
 197                 cout.setf(ios::showpoint);
 198
 199                 vector<string> names;
 200                 vector< vector< double> > matrix;
 201
 202                 //read in phylip file
 203                 ReadPhylipVector readFile(phylipfile);
 204                 names = readFile.read(matrix);
 205                 if (m->control_pressed) { return 0; }
 206
 207                 //read axes
 208                 vector< vector<double> > axes;
 209                 if (axesfile != "") {  axes = readAxes(names);          }
 210
 211                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("iters");
 212                 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("stress");
 213                 outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
 214                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 215
 216                 ofstream out, out2;
 217                 m->openOutputFile(outputFileName, out);
 218                 m->openOutputFile(stressFileName, out2);
 219
 220                 out2.setf(ios::fixed, ios::floatfield);
 221                 out2.setf(ios::showpoint);
 222                 out.setf(ios::fixed, ios::floatfield);
 223                 out.setf(ios::showpoint);
 224
 225                 out2 << "Dimension\tIter\tStress\tRsq" << endl;
 226
 227                 double bestStress = 10000000;
 228                 double bestR2 = 10000000;
 229                 vector< vector<double> > bestConfig;
 230                 int bestDim = 0;
 231
 232                 for (int i = mindim; i <= maxdim; i++) {
 233                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 234
 235                         for (int j = 0; j < iters; j++) {
 236                                 m->mothurOut(toString(j+1)); m->mothurOutEndLine();
 237
 238                                 //get configuration - either randomly generate or resize to this dimension
 239                                 vector< vector<double> > thisConfig;
 240                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 241                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 242                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 243
 244                                 //calc nmds for this dimension
 245                                 double stress;
 246                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 247                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 248
 249                                 //calc euclid distances for new config
 250                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 251                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 252
 253                                 //calc correlation between original distances and euclidean distances from this config
 254                                 double rsquared = linearCalc.calcPearson(newEuclid, matrix);
 255                                 rsquared *= rsquared;
 256                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 257
 258                                 //output results
 259                                 out << "Config" << (j+1) << '\t';
 260                                 for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
 261                                 out << endl;
 262                                 out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << rsquared << endl;
 263
 264                                 output(endConfig, names, out);
 265
 266                                 //save best
 267                                 if (stress < bestStress) {
 268                                         bestDim = i;
 269                                         bestStress = stress;
 270                                         bestR2 = rsquared;
 271                                         bestConfig = endConfig;
 272                                 }
 273
 274                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     m->mothurRemove(outputNames[k]);        } return 0; }
 275                         }
 276                 }
 277
 278                 out.close(); out2.close();
 279
 280                 //output best config
 281                 string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + getOutputFileNameTag("nmds");
 282                 outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
 283
 284                 m->mothurOut("\nNumber of dimensions:\t" + toString(bestDim) + "\n");
 285                 m->mothurOut("Lowest stress :\t" + toString(bestStress) + "\n");
 286                 m->mothurOut("R-squared for configuration:\t" + toString(bestR2) + "\n");
 287
 288                 ofstream outBest;
 289                 m->openOutputFile(BestFileName, outBest);
 290                 outBest.setf(ios::fixed, ios::floatfield);
 291                 outBest.setf(ios::showpoint);
 292
 293                 outBest << '\t';
 294                 for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
 295                 outBest << endl;
 296
 297                 output(bestConfig, names, outBest);
 298
 299                 outBest.close();
 300
 301                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
 302
 303                 m->mothurOutEndLine();
 304                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 305                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 306                 m->mothurOutEndLine();
 307
 308                 return 0;
 309         }
 310         catch(exception& e) {
 311                 m->errorOut(e, "NMDSCommand", "execute");
 312                 exit(1);
 313         }
 314 }
 315 //**********************************************************************************************************************
 316 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 317         try {
 318
 319                 vector< vector<double> > newConfig = config;
 320
 321                 //calc euclid distances
 322                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 323                 if (m->control_pressed) { return newConfig; }
 324
 325                 double stress2 = calculateStress(matrix, euclid);
 326                 stress1 = stress2 + 1.0 + epsilon;
 327
 328                 int count = 0;
 329                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 330                         count++;
 331
 332                         stress1 = stress2;
 333
 334                         if (m->control_pressed) { return newConfig; }
 335
 336                         vector< vector<double> > b; b.resize(euclid.size());
 337                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 338
 339                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 340                         for (int i = 0; i < euclid.size(); i++) {
 341                                 for (int j = 0; j < euclid[i].size(); j++) {
 342                                         //eliminate divide by zero error
 343                                         if (euclid[i][j] != 0) {
 344                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 345                                                 columnSums[j] += b[i][j];
 346                                                 b[i][j] *= -1.0;
 347                                         }
 348                                 }
 349                         }
 350
 351                         //put in diagonal sums
 352                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 353
 354                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 355                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 356
 357                         //matrix mult
 358                         newConfig = linearCalc.matrix_mult(newConfig, b);
 359                         for (int i = 0; i < newConfig.size(); i++) {
 360                                 for (int j = 0; j < newConfig[i].size(); j++) {
 361                                         newConfig[i][j] *= (1.0 / n);
 362                                 }
 363                         }
 364
 365                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 366
 367                         stress2 = calculateStress(matrix, euclid);
 368                 }
 369
 370                 return newConfig;
 371         }
 372         catch(exception& e) {
 373                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 374                 exit(1);
 375         }
 376 }
 377
 378 //**********************************************************************************************************************
 379 //generate random config
 380 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 381         try {
 382                 vector< vector<double> > axes;  axes.resize(dimension);
 383                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 384
 385                 //generate random number between -1 and 1, precision 6
 386                 for (int i = 0; i < axes.size(); i++) {
 387                         for (int j = 0; j < axes[i].size(); j++) {
 388
 389                                 if (m->control_pressed) { return axes; }
 390
 391                                 //generate random int between 0 and 99999
 392                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 393
 394                                 //generate random sign
 395                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 396
 397                                 //if mysign is even then sign = positive, else sign = negative
 398                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 399                                 else { mysign = -1.0; }
 400
 401                                 axes[i][j] = mysign * myrand / (float) 100000;
 402                         }
 403                 }
 404
 405                 return axes;
 406         }
 407         catch(exception& e) {
 408                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 409                 exit(1);
 410         }
 411 }
 412 //**********************************************************************************************************************
 413 //normalize configuration
 414 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 415         try {
 416                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 417
 418                 //find average
 419                 for (int i = 0; i < axes.size(); i++) {
 420                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 421
 422                         averageAxes[i] /= (float) numNames;
 423                 }
 424
 425                 //normalize axes
 426                 double sumDenom = 0.0;
 427                 for (int i = 0; i < axes.size(); i++) {
 428                         for (int j = 0; j < axes[i].size(); j++) {
 429                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 430                         }
 431                 }
 432
 433                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 434
 435                 for (int i = 0; i < axes.size(); i++) {
 436                         for (int j = 0; j < axes[i].size(); j++) {
 437                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 438                         }
 439                 }
 440
 441                 return 0;
 442         }
 443         catch(exception& e) {
 444                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 445                 exit(1);
 446         }
 447 }
 448 //**********************************************************************************************************************
 449 //get configuration
 450 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 451         try {
 452                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 453
 454                 for (int i = 0; i < dimension; i++) {
 455                         newAxes[i] = axes[i];
 456                 }
 457
 458                 return newAxes;
 459         }
 460         catch(exception& e) {
 461                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 462                 exit(1);
 463         }
 464 }
 465 //**********************************************************************************************************************
 466 //find raw stress, and normalize using
 467 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 468         try {
 469                 double normStress = 0.0;
 470                 double denom = 0.0;
 471                 double rawStress = 0.0;
 472
 473                 //find raw stress
 474                 for (int i = 0; i < matrix.size(); i++) {
 475                         for (int j = 0; j < matrix[i].size(); j++) {
 476                                 if (m->control_pressed) { return normStress; }
 477
 478                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 479                                 denom += (config[i][j] * config[i][j]);
 480                         }
 481                 }
 482
 483                 //normalize stress
 484                 if ((rawStress != 0.0) && (denom != 0.0)) {
 485                         normStress = sqrt((rawStress / denom));
 486                 }
 487
 488                 return normStress;
 489         }
 490         catch(exception& e) {
 491                 m->errorOut(e, "NMDSCommand", "calculateStress");
 492                 exit(1);
 493         }
 494 }
 495
 496 //**********************************************************************************************************************
 497 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 498         try {
 499
 500                 for (int i = 0; i < names.size(); i++) {
 501
 502                         out << names[i] << '\t';
 503
 504                         for (int j = 0; j < config.size(); j++) {
 505                                 out << config[j][i] << '\t';
 506                         }
 507
 508                         out << endl;
 509                 }
 510
 511                 out << endl << endl;
 512
 513                 return 0;
 514         }
 515         catch(exception& e) {
 516                 m->errorOut(e, "NMDSCommand", "output");
 517                 exit(1);
 518         }
 519 }
 520 /*****************************************************************/
 521 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 522         try {
 523                 ifstream in;
 524                 m->openInputFile(axesfile, in);
 525
 526                 string headerLine = m->getline(in); m->gobble(in);
 527
 528                 //count the number of axis you are reading
 529                 bool done = false;
 530                 int count = 0;
 531                 while (!done) {
 532                         int pos = headerLine.find("axis");
 533                         if (pos != string::npos) {
 534                                 count++;
 535                                 headerLine = headerLine.substr(pos+4);
 536                         }else { done = true; }
 537                 }
 538
 539                 if (maxdim > count) {
 540                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 541                         maxdim = count;
 542                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 543                 }
 544
 545                 vector< vector<double> > axes;  axes.resize(maxdim);
 546                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 547
 548                 map <string, vector<double> > orderedAxes;
 549                 map     <string, vector<double> >::iterator it;
 550
 551                 while (!in.eof()) {
 552
 553                         if (m->control_pressed) { in.close(); return axes; }
 554
 555                         string group = "";
 556                         in >> group; m->gobble(in);
 557
 558                         bool ignore = false;
 559                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 560
 561                         vector<double> thisGroupsAxes;
 562                         for (int i = 0; i < count; i++) {
 563                                 float temp = 0.0;
 564                                 in >> temp;
 565
 566                                 //only save the axis we want
 567                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 568                         }
 569
 570                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 571
 572                         m->gobble(in);
 573                 }
 574                 in.close();
 575
 576                 //sanity check
 577                 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; }
 578
 579                 //put axes info in same order as distance file, just in case
 580                 for (int i = 0; i < names.size(); i++) {
 581                         it = orderedAxes.find(names[i]);
 582
 583                         if (it != orderedAxes.end()) {
 584                                 vector<double> thisGroupsAxes = it->second;
 585
 586                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 587                                         axes[j][i] = thisGroupsAxes[j];
 588                                 }
 589
 590                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 591                 }
 592
 593                 return axes;
 594         }
 595         catch(exception& e) {
 596                 m->errorOut(e, "NMDSCommand", "readAxes");
 597                 exit(1);
 598         }
 599 }
 600 /**********************************************************************************************************************/
 601
 602
 603