nmdscommand.cpp

   1 /*
   2  *  nmdscommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 1/11/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "nmdscommand.h"
  11 #include "readphylipvector.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> NMDSCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"phylip","axes","mindim","maxdim","iters","maxiters","trace","epsilon","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "NMDSCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 NMDSCommand::NMDSCommand(){
  27         try {
  28                 abort = true;
  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","mindim","maxdim","iters","maxiters","trace","epsilon","outputdir", "inputdir"};
  74                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  75
  76                         OptionParser parser(option);
  77                         map<string, string> parameters = parser. getParameters();
  78
  79                         ValidParameters validParameter;
  80                         map<string, string>::iterator it;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86                         //if the user changes the input directory command factory will send this info to us in the output parameter
  87                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  88                         if (inputDir == "not found"){   inputDir = "";          }
  89                         else {
  90                                 string path;
  91                                 it = parameters.find("phylip");
  92                                 //user has given a template file
  93                                 if(it != parameters.end()){
  94                                         path = m->hasPath(it->second);
  95                                         //if the user has not given a path then, add inputdir. else leave path alone.
  96                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  97                                 }
  98
  99                                 it = parameters.find("axes");
 100                                 //user has given a template file
 101                                 if(it != parameters.end()){
 102                                         path = m->hasPath(it->second);
 103                                         //if the user has not given a path then, add inputdir. else leave path alone.
 104                                         if (path == "") {       parameters["axes"] = inputDir + it->second;             }
 105                                 }
 106                         }
 107
 108                         //initialize outputTypes
 109                         vector<string> tempOutNames;
 110                         outputTypes["nmds"] = tempOutNames;
 111                         outputTypes["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, "mindim", false);    if (temp == "not found") {      temp = "1";     }
 129                         convert(temp, mindim);
 130
 131                         temp = validParameter.validFile(parameters, "maxiters", false); if (temp == "not found") {      temp = "500";   }
 132                         convert(temp, maxIters);
 133
 134                         temp = validParameter.validFile(parameters, "iters", false);    if (temp == "not found") {      temp = "10";    }
 135                         convert(temp, iters);
 136
 137                         temp = validParameter.validFile(parameters, "maxdim", false);   if (temp == "not found") {      temp = "2";     }
 138                         convert(temp, maxdim);
 139
 140                         temp = validParameter.validFile(parameters, "epsilon", false);  if (temp == "not found") {      temp = "0.000000000001";        }
 141                         convert(temp, epsilon);
 142
 143                         temp = validParameter.validFile(parameters, "trace", false);    if (temp == "not found") {      temp = "F";     }
 144                         trace = m->isTrue(temp);
 145
 146                         if (mindim < 1) { m->mothurOut("mindim must be at least 1."); m->mothurOutEndLine(); abort = true; }
 147                         if (maxdim < mindim) { m->mothurOut("maxdim must be greater than mindim."); m->mothurOutEndLine(); abort = true; }
 148                 }
 149
 150         }
 151         catch(exception& e) {
 152                 m->errorOut(e, "NMDSCommand", "NMDSCommand");
 153                 exit(1);
 154         }
 155 }
 156 //**********************************************************************************************************************
 157 void NMDSCommand::help(){
 158         try {
 159                 m->mothurOut("The nmds command is modelled after the nmds code written in R by Sarah Goslee, using Non-metric multidimensional scaling function using the majorization algorithm from Borg & Groenen 1997, Modern Multidimensional Scaling."); m->mothurOutEndLine();
 160                 m->mothurOut("The nmds command parameters are phylip, axes, mindim, maxdim, maxiters, iters, epsilon and trace."); m->mothurOutEndLine();
 161                 m->mothurOut("The phylip parameter allows you to enter your distance file."); m->mothurOutEndLine();
 162                 m->mothurOut("The axes parameter allows you to enter a file containing a starting configuration."); m->mothurOutEndLine();
 163                 m->mothurOut("The maxdim parameter allows you to select how maximum dimensions to use. Default=2"); m->mothurOutEndLine();
 164                 m->mothurOut("The mindim parameter allows you to select how minimum dimensions to use. Default=1"); m->mothurOutEndLine();
 165                 m->mothurOut("The maxiters parameter allows you to select the maximum number of iters to try with each random configuration. Default=500"); m->mothurOutEndLine();
 166                 m->mothurOut("The iters parameter allows you to select the number of random configuration to try. Default=10"); m->mothurOutEndLine();
 167                 m->mothurOut("The epsilon parameter allows you to select set an acceptable stopping point. Default=1e-12."); m->mothurOutEndLine();
 168                 m->mothurOut("The trace parameter allows you to see the output after each iter. Default=F"); m->mothurOutEndLine();
 169                 m->mothurOut("Example nmds(phylip=yourDistanceFile).\n");
 170                 m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n");
 171         }
 172         catch(exception& e) {
 173                 m->errorOut(e, "NMDSCommand", "help");
 174                 exit(1);
 175         }
 176 }
 177 //**********************************************************************************************************************
 178 NMDSCommand::~NMDSCommand(){}
 179 //**********************************************************************************************************************
 180 int NMDSCommand::execute(){
 181         try {
 182
 183                 if (abort == true) { return 0; }
 184
 185                 cout.setf(ios::fixed, ios::floatfield);
 186                 cout.setf(ios::showpoint);
 187
 188                 vector<string> names;
 189                 vector< vector< double> > matrix;
 190
 191                 //read in phylip file
 192                 ReadPhylipVector readFile(phylipfile);
 193                 names = readFile.read(matrix);
 194                 if (m->control_pressed) { return 0; }
 195
 196                 //read axes
 197                 vector< vector<double> > axes;
 198                 if (axesfile != "") {  axes = readAxes(names);          }
 199
 200                 for (int i = mindim; i <= maxdim; i++) {
 201                         m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
 202
 203                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "dim" + toString(i) + ".nmds";
 204                         string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "dim" + toString(i) + ".stress.nmds";
 205                         outputNames.push_back(outputFileName); outputTypes["nmds"].push_back(outputFileName);
 206                         outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
 207
 208                         ofstream out, out2;
 209                         m->openOutputFile(outputFileName, out);
 210                         m->openOutputFile(stressFileName, out2);
 211
 212                         out2.setf(ios::fixed, ios::floatfield);
 213                         out2.setf(ios::showpoint);
 214                         out.setf(ios::fixed, ios::floatfield);
 215                         out.setf(ios::showpoint);
 216
 217                         out2 << "Iter\tStress\tCorr" << endl;
 218
 219                         for (int j = 0; j < iters; j++) {
 220                                 if (trace) { m->mothurOut(toString(j+1)); m->mothurOutEndLine(); }
 221
 222                                 //get configuration - either randomly generate or resize to this dimension
 223                                 vector< vector<double> > thisConfig;
 224                                 if (axesfile == "") {   thisConfig = generateStartingConfiguration(names.size(), i);            }
 225                                 else                            {       thisConfig = getConfiguration(axes, i);                                                         }
 226                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 227
 228                                 //calc nmds for this dimension
 229                                 double stress;
 230                                 vector< vector<double> > endConfig = nmdsCalc(matrix, thisConfig, stress);
 231                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 232
 233                                 //calc euclid distances for new config
 234                                 vector< vector<double> > newEuclid = linearCalc.calculateEuclidianDistance(endConfig);
 235                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 236
 237                                 //calc correlation between original distances and euclidean distances from this config
 238                                 double corr = linearCalc.calcPearson(matrix, newEuclid);
 239                                 corr *= corr;
 240                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 241
 242                                 //output results
 243                                 out << "Config" << (j+1) << '\t';
 244                                 for (int k = 0; k < i; k++) { out << "X" << (k+1) << '\t'; }
 245                                 out << endl;
 246                                 out2 << (j+1) << '\t' << stress << '\t' << corr << endl;
 247
 248                                 output(endConfig, names, out);
 249
 250                                 if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
 251
 252                         }
 253
 254                         out.close(); out2.close();
 255                 }
 256
 257                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
 258
 259                 m->mothurOutEndLine();
 260                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 261                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 262                 m->mothurOutEndLine();
 263
 264                 return 0;
 265         }
 266         catch(exception& e) {
 267                 m->errorOut(e, "NMDSCommand", "execute");
 268                 exit(1);
 269         }
 270 }
 271 //**********************************************************************************************************************
 272 vector< vector<double> > NMDSCommand::nmdsCalc(vector< vector<double> >& matrix, vector< vector<double> >& config, double& stress1) {
 273         try {
 274
 275                 vector< vector<double> > newConfig = config;
 276
 277                 //calc euclid distances
 278                 vector< vector<double> > euclid = linearCalc.calculateEuclidianDistance(newConfig);
 279                 if (m->control_pressed) { return newConfig; }
 280
 281                 double stress2 = calculateStress(matrix, euclid);
 282                 stress1 = stress2 + 1.0 + epsilon;
 283
 284                 if (trace) { m->mothurOutEndLine(); m->mothurOut("Iter\tStress"); m->mothurOutEndLine(); }
 285
 286                 int count = 0;
 287                 while ((count < maxIters) && (abs(stress1 - stress2) > epsilon)) {
 288                         count++;
 289
 290                         stress1 = stress2;
 291
 292                         if (m->control_pressed) { return newConfig; }
 293
 294                         vector< vector<double> > b; b.resize(euclid.size());
 295                         for (int i = 0; i < b.size(); i++) { b[i].resize(euclid[i].size(), 0.0); }
 296
 297                         vector<double> columnSums; columnSums.resize(euclid.size(), 0.0);
 298                         for (int i = 0; i < euclid.size(); i++) {
 299                                 for (int j = 0; j < euclid[i].size(); j++) {
 300                                         //eliminate divide by zero error
 301                                         if (euclid[i][j] != 0) {
 302                                                 b[i][j] = matrix[i][j] / euclid[i][j];
 303                                                 columnSums[j] += b[i][j];
 304                                                 b[i][j] *= -1.0;
 305                                         }
 306                                 }
 307                         }
 308
 309                         //put in diagonal sums
 310                         for (int i = 0; i < euclid.size(); i++) {  b[i][i] = columnSums[i]; }
 311
 312                         int numInLowerTriangle = matrix.size() * (matrix.size()-1) / 2.0;
 313                         double n = (1.0 + sqrt(1.0 + 8.0 * numInLowerTriangle)) / 2.0;
 314
 315                         //matrix mult
 316                         newConfig = linearCalc.matrix_mult(newConfig, b);
 317                         for (int i = 0; i < newConfig.size(); i++) {
 318                                 for (int j = 0; j < newConfig[i].size(); j++) {
 319                                         newConfig[i][j] *= (1.0 / n);
 320                                 }
 321                         }
 322
 323                         euclid = linearCalc.calculateEuclidianDistance(newConfig);
 324
 325                         stress2 = calculateStress(matrix, euclid);
 326
 327                         if (trace) { m->mothurOut(count + "\t" + toString(stress1)); m->mothurOutEndLine(); }
 328
 329                 }
 330
 331                 return newConfig;
 332         }
 333         catch(exception& e) {
 334                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 335                 exit(1);
 336         }
 337 }
 338
 339 //**********************************************************************************************************************
 340 //generate random config
 341 vector< vector<double> > NMDSCommand::generateStartingConfiguration(int numNames, int dimension) {
 342         try {
 343                 vector< vector<double> > axes;  axes.resize(dimension);
 344                 for (int i = 0; i < axes.size(); i++) {  axes[i].resize(numNames); }
 345
 346                 //generate random number between -1 and 1, precision 6
 347                 for (int i = 0; i < axes.size(); i++) {
 348                         for (int j = 0; j < axes[i].size(); j++) {
 349
 350                                 if (m->control_pressed) { return axes; }
 351
 352                                 //generate random int between 0 and 99999
 353                                 int myrand = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 354
 355                                 //generate random sign
 356                                 int mysign = (int)((float)(rand()) / ((RAND_MAX / 99998) + 1));
 357
 358                                 //if mysign is even then sign = positive, else sign = negative
 359                                 if ((mysign % 2) == 0) { mysign = 1.0; }
 360                                 else { mysign = -1.0; }
 361
 362                                 axes[i][j] = mysign * myrand / (float) 100000;
 363                         }
 364                 }
 365
 366                 return axes;
 367         }
 368         catch(exception& e) {
 369                 m->errorOut(e, "NMDSCommand", "generateStartingConfiguration");
 370                 exit(1);
 371         }
 372 }
 373 //**********************************************************************************************************************
 374 //normalize configuration
 375 int NMDSCommand::normalizeConfiguration(vector< vector<double> >& axes, int numNames, int dimension) {
 376         try {
 377                 vector<double> averageAxes; averageAxes.resize(dimension, 0.0);
 378
 379                 //find average
 380                 for (int i = 0; i < axes.size(); i++) {
 381                         for (int j = 0; j < axes[i].size(); j++) {      averageAxes[i] += axes[i][j];   }
 382
 383                         averageAxes[i] /= (float) numNames;
 384                 }
 385
 386                 //normalize axes
 387                 double sumDenom = 0.0;
 388                 for (int i = 0; i < axes.size(); i++) {
 389                         for (int j = 0; j < axes[i].size(); j++) {
 390                                 sumDenom += ((axes[i][j] - averageAxes[i]) * (axes[i][j] - averageAxes[i]));
 391                         }
 392                 }
 393
 394                 double denom = sqrt((sumDenom / (float) (axes.size() * numNames)));
 395
 396                 for (int i = 0; i < axes.size(); i++) {
 397                         for (int j = 0; j < axes[i].size(); j++) {
 398                                 axes[i][j] = (axes[i][j] - averageAxes[i]) / denom;
 399                         }
 400                 }
 401
 402                 return 0;
 403         }
 404         catch(exception& e) {
 405                 m->errorOut(e, "NMDSCommand", "normalizeConfiguration");
 406                 exit(1);
 407         }
 408 }
 409 //**********************************************************************************************************************
 410 //get configuration
 411 vector< vector<double> > NMDSCommand::getConfiguration(vector< vector<double> >& axes, int dimension) {
 412         try {
 413                 vector< vector<double> > newAxes; newAxes.resize(dimension);
 414
 415                 for (int i = 0; i < dimension; i++) {
 416                         newAxes[i] = axes[i];
 417                 }
 418
 419                 return newAxes;
 420         }
 421         catch(exception& e) {
 422                 m->errorOut(e, "NMDSCommand", "getConfiguration");
 423                 exit(1);
 424         }
 425 }
 426 //**********************************************************************************************************************
 427 //find raw stress, and normalize using
 428 double NMDSCommand::calculateStress(vector< vector<double> >& matrix, vector< vector<double> >& config) {
 429         try {
 430                 double normStress = 0.0;
 431                 double denom = 0.0;
 432                 double rawStress = 0.0;
 433
 434                 //find raw stress
 435                 for (int i = 0; i < matrix.size(); i++) {
 436                         for (int j = 0; j < matrix[i].size(); j++) {
 437                                 if (m->control_pressed) { return normStress; }
 438
 439                                 rawStress += ((matrix[i][j] - config[i][j]) * (matrix[i][j] - config[i][j]));
 440                                 denom += (config[i][j] * config[i][j]);
 441                         }
 442                 }
 443
 444                 //normalize stress
 445                 if ((rawStress != 0.0) && (denom != 0.0)) {
 446                         normStress = sqrt((rawStress / denom));
 447                 }
 448
 449                 return normStress;
 450         }
 451         catch(exception& e) {
 452                 m->errorOut(e, "NMDSCommand", "calculateStress");
 453                 exit(1);
 454         }
 455 }
 456
 457 //**********************************************************************************************************************
 458 int NMDSCommand::output(vector< vector<double> >& config, vector<string>& names, ofstream& out) {
 459         try {
 460
 461                 for (int i = 0; i < names.size(); i++) {
 462
 463                         out << names[i] << '\t';
 464
 465                         for (int j = 0; j < config.size(); j++) {
 466                                 out << config[j][i] << '\t';
 467                         }
 468
 469                         out << endl;
 470                 }
 471
 472                 out << endl << endl;
 473
 474                 return 0;
 475         }
 476         catch(exception& e) {
 477                 m->errorOut(e, "NMDSCommand", "output");
 478                 exit(1);
 479         }
 480 }
 481 /*****************************************************************/
 482 vector< vector<double> > NMDSCommand::readAxes(vector<string> names){
 483         try {
 484                 ifstream in;
 485                 m->openInputFile(axesfile, in);
 486
 487                 string headerLine = m->getline(in); m->gobble(in);
 488
 489                 //count the number of axis you are reading
 490                 bool done = false;
 491                 int count = 0;
 492                 while (!done) {
 493                         int pos = headerLine.find("axis");
 494                         if (pos != string::npos) {
 495                                 count++;
 496                                 headerLine = headerLine.substr(pos+4);
 497                         }else { done = true; }
 498                 }
 499
 500                 if (maxdim > count) {
 501                         m->mothurOut("You requested maxdim = " + toString(maxdim) + ", but your file only includes " + toString(count) + ". Using " + toString(count) + "."); m->mothurOutEndLine();
 502                         maxdim = count;
 503                         if (maxdim < mindim) { m->mothurOut("Also adjusting mindim to " + toString(maxdim-1) + "."); m->mothurOutEndLine(); }
 504                 }
 505
 506                 vector< vector<double> > axes;  axes.resize(maxdim);
 507                 for (int i = 0; i < axes.size(); i++) { axes[i].resize(names.size(), 0.0); }
 508
 509                 map <string, vector<double> > orderedAxes;
 510                 map     <string, vector<double> >::iterator it;
 511
 512                 while (!in.eof()) {
 513
 514                         if (m->control_pressed) { in.close(); return axes; }
 515
 516                         string group = "";
 517                         in >> group; m->gobble(in);
 518
 519                         bool ignore = false;
 520                         if (!m->inUsersGroups(group, names)) { ignore = true; m->mothurOut(group + " is in your axes file and not in your distance file, ignoring."); m->mothurOutEndLine(); }
 521
 522                         vector<double> thisGroupsAxes;
 523                         for (int i = 0; i < count; i++) {
 524                                 float temp = 0.0;
 525                                 in >> temp;
 526
 527                                 //only save the axis we want
 528                                 if (i < maxdim) {  thisGroupsAxes.push_back(temp); }
 529                         }
 530
 531                         if (!ignore) {  orderedAxes[group] = thisGroupsAxes; }
 532
 533                         m->gobble(in);
 534                 }
 535                 in.close();
 536
 537                 //sanity check
 538                 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; }
 539
 540                 //put axes info in same order as distance file, just in case
 541                 for (int i = 0; i < names.size(); i++) {
 542                         it = orderedAxes.find(names[i]);
 543
 544                         if (it != orderedAxes.end()) {
 545                                 vector<double> thisGroupsAxes = it->second;
 546
 547                                 for (int j = 0; j < thisGroupsAxes.size(); j++) {
 548                                         axes[j][i] = thisGroupsAxes[j];
 549                                 }
 550
 551                         }else { m->mothurOut("[ERROR]: your axes file does not match your distance file, aborting."); m->mothurOutEndLine(); m->control_pressed = true; return axes; }
 552                 }
 553
 554                 return axes;
 555         }
 556         catch(exception& e) {
 557                 m->errorOut(e, "NMDSCommand", "readAxes");
 558                 exit(1);
 559         }
 560 }
 561 /**********************************************************************************************************************
 562  vector< vector<double> > NMDSCommand::calculateStressGradientVector(vector<seqDist>& eDists, vector<seqDist>& D, double rawStress, double stress, vector< vector<double> >& axes) {
 563  try {
 564  vector< vector<double> > gradient; gradient.resize(dimension);
 565  for (int i = 0; i < gradient.size(); i++) { gradient[i].resize(axes[0].size(), 0.0); }
 566
 567  double sumDij = 0.0;
 568  for (int i = 0; i < eDists.size(); i++) {  sumDij += (eDists[i].dist * eDists[i].dist); }
 569
 570  for (int i = 0; i < eDists.size(); i++) {
 571
 572  for (int j = 0; j < dimension; j++) {
 573
 574  if (m->control_pressed) { return gradient; }
 575
 576  double firstTerm1 = (stress / rawStress) * (eDists[i].dist - D[i].dist);
 577  double firstTerm2 = (stress / sumDij) * eDists[i].dist;
 578  double firstTerm = firstTerm1 - firstTerm2;
 579
 580  float r = (dimension-1.0);
 581  double temp = 1.0 / (pow(eDists[i].dist, r));
 582  float absTemp = abs(axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]);
 583  double secondTerm = pow(absTemp, r) * temp;
 584
 585  double sigNum = 1.0;
 586  if ((axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]) == 0) { sigNum = 0.0; }
 587  else if ((axes[j][eDists[i].seq1] - axes[j][eDists[i].seq2]) < 0) { sigNum = -1.0; }
 588
 589  double results = (firstTerm * secondTerm * sigNum);
 590  cout << i << '\t' << j << '\t' << "results = " << results << endl;
 591  gradient[j][eDists[i].seq1] += results;
 592  gradient[j][eDists[i].seq2] -= results;
 593  }
 594  }
 595
 596  return gradient;
 597  }
 598  catch(exception& e) {
 599  m->errorOut(e, "NMDSCommand", "calculateStressGradientVector");
 600  exit(1);
 601  }
 602  }
 603  //**********************************************************************************************************************
 604  double NMDSCommand::calculateMagnitude(vector< vector<double> >& gradient) {
 605  try {
 606  double magnitude = 0.0;
 607
 608  double sum = 0.0;
 609  for (int i = 0; i < gradient.size(); i++) {
 610  for (int j = 0; j < gradient[i].size(); j++) {
 611  sum += (gradient[i][j] * gradient[i][j]);
 612  }
 613  }
 614
 615  magnitude = sqrt(((1.0/(float)gradient[0].size()) * sum));
 616
 617  return magnitude;
 618  }
 619  catch(exception& e) {
 620  m->errorOut(e, "NMDSCommand", "calculateMagnitude");
 621  exit(1);
 622  }
 623  }
 624  //**********************************************************************************************************************
 625  //described in Kruskal paper page 121 + 122
 626  double NMDSCommand::calculateStep(vector< vector<double> >& prevGrad, vector< vector<double> >& grad, vector<double>& prevStress) {
 627  try {
 628  double newStep = step;
 629
 630  //calc the cos theta
 631  double sumNum = 0.0;
 632  double sumDenom1 = 0.0;
 633  double sumDenom2 = 0.0;
 634  for (int i = 0; i < prevGrad.size(); i++) {
 635  for (int j = 0; j < prevGrad[i].size(); j++) {
 636  sumDenom1 += (grad[i][j] * grad[i][j]);
 637  sumDenom2 += (prevGrad[i][j] * prevGrad[i][j]);
 638  sumNum += (grad[i][j] * prevGrad[i][j]);
 639  }
 640  }
 641
 642  double cosTheta = sumNum / (sqrt(sumDenom1) * sqrt(sumDenom2));
 643  cosTheta *= cosTheta;
 644
 645  //calc angle factor
 646  double angle = pow(4.0, cosTheta);
 647
 648  //calc 5 step ratio
 649  double currentStress = prevStress[prevStress.size()-1];
 650  double lastStress = prevStress[0];
 651  if (prevStress.size() > 1) {  lastStress = prevStress[prevStress.size()-2];            }
 652  double fivePrevStress = prevStress[0];
 653  if (prevStress.size() > 5) {  fivePrevStress = prevStress[prevStress.size()-6]; }
 654
 655  double fiveStepRatio = min(1.0, (currentStress / fivePrevStress));
 656
 657  //calc relaxation factor
 658  double relaxation = 1.3 / (1.0 + pow(fiveStepRatio, 5.0));
 659
 660  //calc good luck factor
 661  double goodLuck = min(1.0, (currentStress / lastStress));
 662
 663  //calc newStep
 664  //cout << "\ncos = " << cosTheta << " step = " << step << " angle = " << angle << " relaxation = " << relaxation << " goodluck = " << goodLuck << endl;
 665  newStep = step * angle * relaxation * goodLuck;
 666
 667  return newStep;
 668  }
 669  catch(exception& e) {
 670  m->errorOut(e, "NMDSCommand", "calculateStep");
 671  exit(1);
 672  }
 673  }
 674  //**********************************************************************************************************************
 675  vector< vector<double> > NMDSCommand::calculateNewConfiguration(double magnitude, vector< vector<double> >& axes, vector< vector<double> >& gradient) {
 676  try {
 677
 678  vector< vector<double> > newAxes = axes;
 679
 680  for (int i = 0; i < newAxes.size(); i++) {
 681
 682  if (m->control_pressed) { return newAxes; }
 683
 684  for (int j = 0; j < newAxes[i].size(); j++) {
 685  newAxes[i][j] = axes[i][j] + ((step / magnitude) * gradient[i][j]);
 686  }
 687  }
 688
 689  return newAxes;
 690  }
 691  catch(exception& e) {
 692  m->errorOut(e, "NMDSCommand", "calculateNewConfiguration");
 693  exit(1);
 694  }
 695  }*/
 696 /**********************************************************************************************************************
 697  //adjust eDists so that it creates monotonically increasing series of succesive values that increase or stay the same, but never decrease
 698  vector<seqDist> NMDSCommand::satisfyMonotonicity(vector<seqDist> eDists, vector<int> partitions) {
 699  try {
 700
 701  //find averages of each partitions
 702  vector<double> sums; sums.resize(partitions.size(), 0.0);
 703  vector<int> sizes; sizes.resize(partitions.size(), 0);
 704
 705  for (int i = 0; i < partitions.size(); i++) {
 706  //i is not the last one
 707  int start = partitions[i];
 708  int end;
 709  if (i != (partitions.size()-1)) {  end = partitions[i+1];   }
 710  else{  end = eDists.size();    }
 711
 712  for (int j = start; j < end; j++) {   sums[i] += eDists[j].dist;  }
 713
 714  sizes[i] = (end - start);
 715  }
 716
 717
 718  vector<seqDist> D = eDists;
 719
 720  //i represents the "active block"
 721  int i = 0;
 722  while (i < partitions.size()) {
 723
 724  if (m->control_pressed) { return D; }
 725
 726  bool upActive = true;
 727  bool upSatisfied = false;
 728  bool downSatisfied = false;
 729
 730  //while we are not done with this block
 731  while ((!upSatisfied) || (!downSatisfied)) {
 732
 733  if (upActive) {
 734
 735  //are we are upSatisfied? - is the average of the next block greater than mine?
 736  if (i != (partitions.size()-1))  { //if we are the last guy then we are upsatisfied
 737  if ((sums[i+1]/(float)sizes[i+1]) >= (sums[i]/(float)sizes[i])) {
 738  upSatisfied = true;
 739  upActive = false;
 740  }else {
 741  //find new weighted average
 742  double newSum = sums[i] + sums[i+1];
 743
 744  //merge blocks - putting everything in i
 745  sums[i] = newSum;
 746  sizes[i] += sizes[i+1];
 747  partitions[i] = partitions[i+1];
 748
 749  sums.erase(sums.begin()+(i+1));
 750  sizes.erase(sizes.begin()+(i+1));
 751  partitions.erase(partitions.begin()+(i+1));
 752
 753  upActive = false;
 754  }
 755  }else { upSatisfied = true; upActive = false; }
 756
 757  }else { //downActive
 758
 759  //are we are DownSatisfied? - is the average of the previous block less than mine?
 760  if (i != 0)  { //if we are the first guy then we are downSatisfied
 761  if ((sums[i-1]/(float)sizes[i-1]) <= (sums[i]/(float)sizes[i])) {
 762  downSatisfied = true;
 763  upActive = true;
 764  }else {
 765  //find new weighted average
 766  double newSum = sums[i] + sums[i-1];;
 767
 768  //merge blocks - putting everything in i-1
 769  sums[i-1] = newSum;
 770  sizes[i-1] += sizes[i];
 771
 772  sums.erase(sums.begin()+i);
 773  sizes.erase(sizes.begin()+i);
 774  partitions.erase(partitions.begin()+i);
 775  i--;
 776
 777  upActive = true;
 778  }
 779  }else { downSatisfied = true; upActive = true; }
 780  }
 781  }
 782
 783  i++; // go to next block
 784  }
 785
 786  //sanity check - for rounding errors
 787  vector<double> averages; averages.resize(sums.size(), 0.0);
 788  for (int i = 0; i < sums.size(); i++) { averages[i] = sums[i] / (float) sizes[i];      }
 789  for (int i = 0; i < averages.size(); i++) { if (averages[i+1] < averages[i]) {  averages[i+1] = averages[i]; } }
 790
 791  //fill D
 792  int placeHolder = 0;
 793  for (int i = 0; i < averages.size(); i++) {
 794  for (int j = 0; j < sizes[i]; j++) {
 795  D[placeHolder].dist = averages[i];
 796  placeHolder++;
 797  }
 798  }
 799
 800  return D;
 801  }
 802  catch(exception& e) {
 803  m->errorOut(e, "NMDSCommand", "satisfyMonotonicity");
 804  exit(1);
 805  }
 806  }*/
 807
 808 //**********************************************************************************************************************
 809
 810