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","dimension","maxiters","step","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;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["nmds"] = tempOutNames;
  32                 outputTypes["stress"] = 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;
  67
  68                 //allow user to run help
  69                 if(option == "help") { help(); abort = true; }
  70
  71                 else {
  72                         //valid paramters for this command
  73                         string Array[] =  {"phylip","axes","dimension","maxiters","step","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["stress"] = tempOutNames;
 112
 113                         //required parameters
 114                         phylipfile = validParameter.validFile(parameters, "phylip", true);
 115                         if (phylipfile == "not open") { phylipfile = ""; abort = true; }
 116                         else if (phylipfile == "not found") { phylipfile = ""; m->mothurOut("You must provide a distance file before running the nmds command."); m->mothurOutEndLine(); abort = true; }
 117
 118                         axesfile = validParameter.validFile(parameters, "axes", true);
 119                         if (axesfile == "not open") { axesfile = ""; abort = true; }
 120                         else if (axesfile == "not found") { axesfile = "";  }
 121
 122                         //if the user changes the output directory command factory will send this info to us in the output parameter
 123                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 124                                 outputDir = "";
 125                                 outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it
 126                         }
 127
 128                         string temp = validParameter.validFile(parameters, "dimension", false); if (temp == "not found") {      temp = "2";     }
 129                         convert(temp, dimension);
 130
 131                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "1000";  }
 132                         convert(temp, maxIters);
 133
 134                         temp = validParameter.validFile(parameters, "step", false);     if (temp == "not found") {      temp = "0.2";   }
 135                         convert(temp, step);
 136
 137                         temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found") {      temp = "2";     }
 138                         convert(temp, cutoff);
 139                         cutoff /= 100.0;
 140                 }
 141
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 145                 exit(1);
 146         }
 147 }
 148 //**********************************************************************************************************************
 149 void NMDSCommand::help(){
 150         try {
 151
 152                 m->mothurOut("The nmds command parameters are phylip, axes, dimension, maxiters, cutoff and step."); m->mothurOutEndLine();
 153                 m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
 154                 m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
 155                 m->mothurOut("The dimension parameter allows you to select how many dimensions to use. Default=2"); m->mothurOutEndLine();
 156                 m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try. Default=1000"); m->mothurOutEndLine();
 157                 m->mothurOut("The cutoff parameter allows you to select set an acceptable percentage of magnitude. Default=2, meaning when magnitude of g reaches 2% of it's starting value the process will stop."); m->mothurOutEndLine();
 158                 m->mothurOut("The step parameter allows you to set a starting step. Default=0.2"); m->mothurOutEndLine();
 159                 m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
 160                 m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
 161         }
 162         catch(exception& e) {
 163                 m->errorOut(e, "NMDSCommand", "help");
 164                 exit(1);
 165         }
 166 }
 167 //**********************************************************************************************************************
 168 NMDSCommand::~NMDSCommand(){}
 169 //**********************************************************************************************************************
 170 int NMDSCommand::execute(){
 171         try {
 172
 173                 if (abort == true) { return 0; }
 174
 175                 cout.setf(ios::fixed, ios::floatfield);
 176                 cout.setf(ios::showpoint);
 177                 cerr.setf(ios::fixed, ios::floatfield);
 178                 cerr.setf(ios::showpoint);
 179
 180                 vector<string> names;
 181                 vector<seqDist> matrix; //seqDist = int, int, float - index of seq1 in names, index of seq2 in names, their distance
 182
 183                 //read in phylip file
 184                 ReadPhylipVector readFile(phylipfile);
 185                 names = readFile.read(matrix);
 186                 if (m->control_pressed) { return 0; }
 187
 188                 //randomly generate the starting configuration - step 2
 189                 vector< vector<double> > axes;
 190                 if (axesfile == "") {   axes = generateStartingConfiguration(names.size());             }
 191                 else                            {       axes = readAxes(names);                                                                 }
 192                 if (m->control_pressed) { return 0; }
 193
 194                 //sort matrix from smallest distance to largest - step 5
 195                 sort(matrix.begin(), matrix.end(), compareSequenceDistance);
 196
 197                 bool stable = false;
 198                 int count = 0;
 199                 vector<double> previousStresses;
 200                 vector< vector<double> > previousGradient = axes;
 201                 double initialMagnitude;
 202                 m->mothurOutEndLine(); m->mothurOut("Iter\tStress\tMagnitude"); m->mothurOutEndLine();
 203                 while ((count != maxIters) && (!stable)) {
 204                         count++;
 205
 206                         //normalize axes - step 3
 207                         normalizeConfiguration(axes, names.size());
 208                         if (m->control_pressed) { return 0; }
 209
 210                         //calculate Euclidean distances - step 4
 211                         vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(axes);
 212                         if (m->control_pressed) { return 0; }
 213
 214                         //order euclid elements in same order as matrix - step 6
 215                         //if there are ties in the matrix we want to arrange the euclid distances in the best way so we do not to add unnecessary stress
 216                         vector<seqDist> eDists;
 217                         vector<seqDist> ties;
 218                         for (int i = 0; i < matrix.size(); i++) {
 219
 220                                 seqDist temp(matrix[i].seq1, matrix[i].seq2, euclid[matrix[i].seq1][matrix[i].seq2]);
 221                                 ties.push_back(temp);
 222
 223                                 if (i != matrix.size()-1) { // you are not the last so you can look ahead
 224                                         if (matrix[i].dist != matrix[i+1].dist) { // you are done with ties, sort and save them, then continue
 225                                                 sort(ties.begin(), ties.end(), compareSequenceDistance);
 226                                                 for (int k = 0; k < ties.size(); k++) { eDists.push_back(ties[k]);      }
 227                                                 ties.clear();
 228                                         }
 229                                 }else { // you are the last one
 230                                         sort(ties.begin(), ties.end(), compareSequenceDistance);
 231                                         for (int k = 0; k < ties.size(); k++) { eDists.push_back(ties[k]);      }
 232                                 }
 233                         }
 234
 235                         for (int i = 0; i < euclid.size(); i++) {  euclid[i].clear(); } euclid.clear();
 236                         if (m->control_pressed) { return 0; }
 237
 238                         //find D - from step 7
 239                         vector<seqDist> D = satisfyMonotonicity(eDists);
 240                         if (m->control_pressed) { return 0; }
 241
 242                         //calculate the raw stress and normalize it - steps 8 and 9
 243                         double rawStress;
 244                         double stress = calculateStress(eDists, D, rawStress);
 245                         previousStresses.push_back(stress);
 246                         if (stress == 0) { m->mothurOut("Stress reached zero after " + toString(count) + " iters, stopping."); m->mothurOutEndLine(); break; }
 247                         if (m->control_pressed) { return 0; }
 248
 249                         //calculate stress gradient - step 10
 250                         vector< vector<double> > stressGradient = calculateStressGradientVector(eDists, D, rawStress, stress, axes);
 251                         if (m->control_pressed) { return 0; }
 252
 253                         //calculate magnitude
 254                         double magnitude = calculateMagnitude(stressGradient);
 255                         if (count == 1) { initialMagnitude = magnitude; }
 256                         if (m->control_pressed) { return 0; }
 257
 258                         //save gradient before adjusting config.
 259                         previousGradient = stressGradient;
 260
 261                         if ((count % 100) == 0) { m->mothurOut(toString(count) + "\t" + toString(previousStresses[previousStresses.size()-1]) + "\t" + toString(magnitude)); m->mothurOutEndLine(); }
 262
 263                         //are we done - we are done if percentage of magnitude compared to initial magnitude is less than cutoff
 264                         double percentage = magnitude / initialMagnitude;
 265                         if (percentage < cutoff) { stable = true; }
 266                         else {
 267
 268                                 //calculate new step size
 269                                 step = calculateStep(previousGradient, stressGradient, previousStresses);
 270                                 cout << "count = " << count << '\t' << step << endl;
 271                                 if (m->control_pressed) { return 0; }
 272
 273                                 //find new config.
 274                                 axes = calculateNewConfiguration(magnitude, axes, stressGradient);
 275                                 if (m->control_pressed) { return 0; }
 276                         }
 277                 }
 278
 279                 if (m->control_pressed) { return 0; }
 280
 281                 string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds";
 282                 string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "stress.nmds";
 283                 outputNames.push_back(outputFileName); outputTypes["nmds"].push_back(outputFileName);
 284                 outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 285
 286                 output(outputFileName, stressFileName, previousGradient, previousStresses, names);
 287
 288                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 289
 290                 m->mothurOutEndLine();
 291                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 292                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 293                 m->mothurOutEndLine();
 294
 295                 return 0;
 296         }
 297         catch(exception& e) {
 298                 m->errorOut(e, "NMDSCommand", "execute");
 299                 exit(1);
 300         }
 301 }
 302 //**********************************************************************************************************************
 303 //generate random config
 304 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames) {
 305         try {
 306                 vector< vector<double> > axes;  axes.resize(dimension);
 307                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 308
 309                 //generate random number between -1 and 1, precision 6
 310                 for (int i = 0; i < axes.size(); i++) {
 311                         for (int j = 0; j < axes[i].size(); j++) {
 312
 313                                 if (m->control_pressed) { return axes; }
 314
 315                                 //generate random int between 0 and 99999
 316                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 317
 318                                 //generate random sign
 319                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 320
 321                                 //if mysign is even then sign = positive, else sign = negative
 322                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 323                                 else { mysign = -1.0; }
 324
 325                                 axes[i][j] = mysign * myrand / (float) 100000;
 326                         }
 327                 }
 328
 329                 return axes;
 330         }
 331         catch(exception& e) {
 332                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 333                 exit(1);
 334         }
 335 }
 336 //**********************************************************************************************************************
 337 //normalize configuration
 338 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames) {
 339         try {
 340                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 341
 342                 //find average
 343                 for (int i = 0; i < axes.size(); i++) {
 344                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 345
 346                         averageAxes[i] /= (float) numNames;
 347                 }
 348
 349                 //normalize axes
 350                 double sumDenom = 0.0;
 351                 for (int i = 0; i < axes.size(); i++) {
 352                         for (int j = 0; j < axes[i].size(); j++) {
 353                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 354                         }
 355                 }
 356
 357                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 358
 359                 for (int i = 0; i < axes.size(); i++) {
 360                         for (int j = 0; j < axes[i].size(); j++) {
 361                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 362                         }
 363                 }
 364
 365                 return 0;
 366         }
 367         catch(exception& e) {
 368                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 369                 exit(1);
 370         }
 371 }
 372 //**********************************************************************************************************************
 373 //adjust eDists so that it creates monotonically increasing series of succesive values that increase or stay the same, but never decrease
 374 vector<seqDist> NMDSCommand::satisfyMonotonicity(vector<seqDist> eDists) {
 375         try {
 376
 377                 vector<seqDist> D = eDists;
 378
 379                 for (int i = 0; i < (D.size()-1); i++) {
 380
 381                         if (m->control_pressed) { return D; }
 382
 383                         //is the distance in i+1 smaller than i, if yes then adjust
 384                         if (D[i+1].dist < D[i].dist) {  D[i+1].dist = D[i].dist;  }
 385                 }
 386
 387                 return D;
 388         }
 389         catch(exception& e) {
 390                 m->errorOut(e, "NMDSCommand", "satisfyMonotonicity");
 391                 exit(1);
 392         }
 393 }
 394 //**********************************************************************************************************************
 395 //find raw stress, and normalize using
 396 double NMDSCommand::calculateStress(vector<seqDist>& eDists, vector<seqDist>& D, double& rawStress) {
 397         try {
 398                 double normStress = 0.0;
 399                 double denom = 0.0;
 400                 rawStress = 0.0;
 401
 402                 //find raw stress
 403                 for (int i = 0; i < D.size(); i++) {
 404
 405                         if (m->control_pressed) { return normStress; }
 406
 407                         rawStress += ((eDists[i].dist - D[i].dist) * (eDists[i].dist - D[i].dist));
 408                         denom += (eDists[i].dist * eDists[i].dist);
 409                 }
 410
 411                 //normalize stress
 412                 if (rawStress != 0.0) {
 413                         normStress = 100 * sqrt((rawStress / denom));
 414                 }
 415
 416                 return normStress;
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "NMDSCommand", "calculateStress");
 420                 exit(1);
 421         }
 422 }
 423 //**********************************************************************************************************************
 424 vector< vector<double> > NMDSCommand::calculateStressGradientVector(vector<seqDist>& eDists, vector<seqDist>& D, double rawStress, double stress, vector< vector<double> >& axes) {
 425         try {
 426                 vector< vector<double> > gradient; gradient.resize(dimension);
 427                 for (int i = 0; i < gradient.size(); i++) { gradient[i].resize(axes[0].size(), 0.0); }
 428
 429                 double sumDij = 0.0;
 430                 for (int i = 0; i < eDists.size(); i++) {  sumDij += (eDists[i].dist * eDists[i].dist); }
 431
 432                 for (int i = 0; i < eDists.size(); i++) {
 433
 434                         for (int j = 0; j < dimension; j++) {
 435
 436                                 if (m->control_pressed) { return gradient; }
 437
 438                                 double firstTerm1 = (stress / rawStress) * (eDists[i].dist - D[i].dist);
 439                                 double firstTerm2 = eDists[i].dist * (stress / sumDij);
 440                                 double firstTerm = firstTerm1 - firstTerm2;
 441
 442                                 double secondTerm = (axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]) / eDists[i].dist;
 443
 444                                 double results = (firstTerm * secondTerm);
 445
 446                                 gradient[j][eDists[i].seq1] += results;
 447                                 gradient[j][eDists[i].seq2] -= results;
 448                         }
 449                 }
 450
 451                 return gradient;
 452         }
 453         catch(exception& e) {
 454                 m->errorOut(e, "NMDSCommand", "calculateStressGradientVector");
 455                 exit(1);
 456         }
 457 }
 458 //**********************************************************************************************************************
 459 double NMDSCommand::calculateMagnitude(vector< vector<double> >& gradient) {
 460         try {
 461                 double magnitude = 0.0;
 462
 463                 double sum = 0.0;
 464                 for (int i = 0; i < gradient.size(); i++) {
 465                         for (int j = 0; j < gradient[i].size(); j++) {
 466                                 sum += (gradient[i][j] * gradient[i][j]);
 467                         }
 468                 }
 469
 470                 magnitude = sqrt(((1.0/(float)gradient[0].size()) * sum));
 471
 472                 return magnitude;
 473         }
 474         catch(exception& e) {
 475                 m->errorOut(e, "NMDSCommand", "calculateMagnitude");
 476                 exit(1);
 477         }
 478 }
 479 //**********************************************************************************************************************
 480 //described in Kruskal paper page 121 + 122
 481 double NMDSCommand::calculateStep(vector< vector<double> >& prevGrad, vector< vector<double> >& grad, vector<double>& prevStress) {
 482         try {
 483                 double newStep = step;
 484
 485                 //calc the cos theta
 486                 double sumNum = 0.0;
 487                 double sumDenom1 = 0.0;
 488                 double sumDenom2 = 0.0;
 489                 for (int i = 0; i < prevGrad.size(); i++) {
 490                         for (int j = 0; j < prevGrad[i].size(); j++) {
 491                                 sumDenom1 += (grad[i][j] * grad[i][j]);
 492                                 sumDenom2 += (prevGrad[i][j] * prevGrad[i][j]);
 493                                 sumNum += (grad[i][j] * prevGrad[i][j]);
 494                         }
 495                 }
 496
 497                 double cosTheta = sumNum / (sqrt(sumDenom1) * sqrt(sumDenom2));
 498                 cosTheta *= cosTheta;
 499
 500                 //calc angle factor
 501                 double angle = pow(4.0, cosTheta);
 502
 503                 //calc 5 step ratio
 504                 double currentStress = prevStress[prevStress.size()-1];
 505                 double lastStress = prevStress[0];
 506                 if (prevStress.size() > 1) {  lastStress = prevStress[prevStress.size()-2];             }
 507                 double fivePrevStress = prevStress[0];
 508                 if (prevStress.size() > 5) {  fivePrevStress = prevStress[prevStress.size()-6]; }
 509
 510                 double fiveStepRatio = min(1.0, (currentStress / fivePrevStress));
 511
 512                 //calc relaxation factor
 513                 double relaxation = 1.3 / (1.0 + pow(fiveStepRatio, 5.0));
 514
 515                 //calc good luck factor
 516                 double goodLuck = min(1.0, (currentStress / lastStress));
 517
 518                 //calc newStep
 519                 cout << "\ncos = " << cosTheta << " step = " << step << " angle = " << angle << " relaxation = " << relaxation << " goodluck = " << goodLuck << endl;
 520                 newStep = step * angle * relaxation * goodLuck;
 521
 522                 return newStep;
 523         }
 524         catch(exception& e) {
 525                 m->errorOut(e, "NMDSCommand", "calculateStep");
 526                 exit(1);
 527         }
 528 }
 529 //**********************************************************************************************************************
 530 vector< vector<double> > NMDSCommand::calculateNewConfiguration(double magnitude, vector< vector<double> >& axes, vector< vector<double> >& gradient) {
 531         try {
 532
 533                 vector< vector<double> > newAxes = axes;
 534
 535                 for (int i = 0; i < newAxes.size(); i++) {
 536
 537                         if (m->control_pressed) { return newAxes; }
 538
 539                         for (int j = 0; j < newAxes[i].size(); j++) {
 540                                 newAxes[i][j] = axes[i][j] + ((step / magnitude) * gradient[i][j]);
 541                         }
 542                 }
 543
 544                 return newAxes;
 545         }
 546         catch(exception& e) {
 547                 m->errorOut(e, "NMDSCommand", "calculateNewConfiguration");
 548                 exit(1);
 549         }
 550 }
 551 //**********************************************************************************************************************
 552 int NMDSCommand::output(string outputFileName, string stressFileName, vector< vector<double> >& config, vector<double>& stresses, vector<string>& names) {
 553         try {
 554
 555                 ofstream out, out2;
 556                 m->openOutputFile(outputFileName, out);
 557                 m->openOutputFile(stressFileName, out2);
 558
 559                 //output headers
 560                 out << "group\t";
 561                 for (int i = 0; i < dimension; i++) { out << "axis" << (i+1) << '\t'; }
 562                 out << endl;
 563
 564                 out2 << "Iter\tStress" << endl;
 565
 566                 //output nmds file
 567                 for (int i = 0; i < config[0].size(); i++) {
 568
 569                         if (m->control_pressed) { out.close(); out2.close(); return 0; }
 570
 571                         out << names[i] << '\t';
 572
 573                         for (int j = 0; j < config.size(); j++) {
 574                                 out << config[j][i] << '\t';
 575                         }
 576
 577                         out << endl;
 578                 }
 579                 out.close();
 580
 581                 //output stress file
 582                 for (int j = 0; j < stresses.size(); j++) {
 583                         if (m->control_pressed) { out2.close(); return 0; }
 584
 585                         out2 << (j+1) << '\t' << stresses[j] << endl;
 586                 }
 587                 out2.close();
 588
 589
 590                 return 0;
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "NMDSCommand", "output");
 594                 exit(1);
 595         }
 596 }
 597 /*****************************************************************/
 598 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 599         try {
 600                 vector< vector<double> > axes;
 601
 602                 ifstream in;
 603                 m->openInputFile(axesfile, in);
 604
 605                 string headerLine = m->getline(in); m->gobble(in);
 606
 607                 //count the number of axis you are reading
 608                 bool done = false;
 609                 int count = 0;
 610                 while (!done) {
 611                         int pos = headerLine.find("axis");
 612                         if (pos != string::npos) {
 613                                 count++;
 614                                 headerLine = headerLine.substr(pos+4);
 615                         }else { done = true; }
 616                 }
 617
 618                 if (dimension > count) { m->mothurOut("You requested " + toString(dimension) + " axes, but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine(); dimension = count; }
 619
 620                 while (!in.eof()) {
 621
 622                         if (m->control_pressed) { in.close(); return axes; }
 623
 624                         string group = "";
 625                         in >> group; m->gobble(in);
 626
 627                         bool ignore = false;
 628                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 629
 630                         vector<double> thisGroupsAxes;
 631                         for (int i = 0; i < count; i++) {
 632                                 float temp = 0.0;
 633                                 in >> temp;
 634
 635                                 //only save the axis we want
 636                                 if (i < dimension) {  thisGroupsAxes.push_back(temp); }
 637                         }
 638
 639                         if (!ignore) {  axes.push_back(thisGroupsAxes); }
 640
 641                         m->gobble(in);
 642                 }
 643                 in.close();
 644
 645                 //sanity check
 646                 if (names.size() != axes.size()) { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
 647
 648                 return axes;
 649         }
 650         catch(exception& e) {
 651                 m->errorOut(e, "NMDSCommand", "readAxes");
 652                 exit(1);
 653         }
 654 }
 655 //**********************************************************************************************************************
 656
 657