matrixoutputcommand.cpp

   1 /*
   2  *  matrixoutputcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "matrixoutputcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> MatrixOutputCommand::setParameters(){
  14         try {
  15                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
  16                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  17                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  18                 CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
  19                 CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
  20                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "MatrixOutputCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string MatrixOutputCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 ValidCalculators validCalculator;
  38                 helpString += "The dist.shared command parameters are shared, groups, calc, output, processors and label.  shared is a required, unless you have a valid current file.\n";
  39                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  40                 helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n";
  41                 helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
  42                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
  43                 helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
  44                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  45                 helpString += "The default value for calc is jclass and thetayc.\n";
  46                 helpString += validCalculator.printCalc("matrix");
  47                 helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
  48                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  49                 return helpString;
  50         }
  51         catch(exception& e) {
  52                 m->errorOut(e, "MatrixOutputCommand", "getHelpString");
  53                 exit(1);
  54         }
  55 }
  56 //**********************************************************************************************************************
  57 MatrixOutputCommand::MatrixOutputCommand(){
  58         try {
  59                 abort = true; calledHelp = true;
  60                 setParameters();
  61                 vector<string> tempOutNames;
  62                 outputTypes["phylip"] = tempOutNames;
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 MatrixOutputCommand::MatrixOutputCommand(string option)  {
  72         try {
  73                 abort = false; calledHelp = false;
  74                 allLines = 1;
  75
  76                 //allow user to run help
  77                 if(option == "help") {  help(); abort = true; calledHelp = true; }
  78                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  79
  80                 else {
  81                         vector<string> myArray = setParameters();
  82
  83                         OptionParser parser(option);
  84                         map<string,string> parameters  = parser.getParameters();
  85                         map<string,string>::iterator it;
  86
  87                         ValidParameters validParameter;
  88
  89                         //check to make sure all parameters are valid for command
  90                         for (it = parameters.begin(); it != parameters.end(); it++) {
  91                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  92                         }
  93
  94                         //initialize outputTypes
  95                         vector<string> tempOutNames;
  96                         outputTypes["phylip"] = tempOutNames;
  97
  98                         //if the user changes the input directory command factory will send this info to us in the output parameter
  99                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 100                         if (inputDir == "not found"){   inputDir = "";          }
 101                         else {
 102                                 string path;
 103                                 it = parameters.find("shared");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 109                                 }
 110                         }
 111
 112                         sharedfile = validParameter.validFile(parameters, "shared", true);
 113                         if (sharedfile == "not found") {
 114                                 //if there is a current shared file, use it
 115                                 sharedfile = m->getSharedFile();
 116                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 117                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 118                         }else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 119                         else { m->setSharedFile(sharedfile); }
 120
 121                         //if the user changes the output directory command factory will send this info to us in the output parameter
 122                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 123                                 outputDir = "";
 124                                 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 125                         }
 126
 127                         //check for optional parameter and set defaults
 128                         // ...at some point should added some additional type checking...
 129                         label = validParameter.validFile(parameters, "label", false);
 130                         if (label == "not found") { label = ""; }
 131                         else {
 132                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 133                                 else { allLines = 1;  }
 134                         }
 135
 136                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
 137                         if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
 138
 139                         groups = validParameter.validFile(parameters, "groups", false);
 140                         if (groups == "not found") { groups = ""; }
 141                         else {
 142                                 m->splitAtDash(groups, Groups);
 143                                 m->setGroups(Groups);
 144                         }
 145
 146                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 147                         m->setProcessors(temp);
 148                         m->mothurConvert(temp, processors);
 149
 150                         calc = validParameter.validFile(parameters, "calc", false);
 151                         if (calc == "not found") { calc = "jclass-thetayc";  }
 152                         else {
 153                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 154                         }
 155                         m->splitAtDash(calc, Estimators);
 156                         if (m->inUsersGroups("citation", Estimators)) {
 157                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 158                                 //remove citation from list of calcs
 159                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 160                         }
 161
 162                         if (abort == false) {
 163
 164                                 ValidCalculators validCalculator;
 165
 166                                 int i;
 167                                 for (i=0; i<Estimators.size(); i++) {
 168                                         if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
 169                                                 if (Estimators[i] == "sharedsobs") {
 170                                                         matrixCalculators.push_back(new SharedSobsCS());
 171                                                 }else if (Estimators[i] == "sharedchao") {
 172                                                         matrixCalculators.push_back(new SharedChao1());
 173                                                 }else if (Estimators[i] == "sharedace") {
 174                                                         matrixCalculators.push_back(new SharedAce());
 175                                                 }else if (Estimators[i] == "jabund") {
 176                                                         matrixCalculators.push_back(new JAbund());
 177                                                 }else if (Estimators[i] == "sorabund") {
 178                                                         matrixCalculators.push_back(new SorAbund());
 179                                                 }else if (Estimators[i] == "jclass") {
 180                                                         matrixCalculators.push_back(new Jclass());
 181                                                 }else if (Estimators[i] == "sorclass") {
 182                                                         matrixCalculators.push_back(new SorClass());
 183                                                 }else if (Estimators[i] == "jest") {
 184                                                         matrixCalculators.push_back(new Jest());
 185                                                 }else if (Estimators[i] == "sorest") {
 186                                                         matrixCalculators.push_back(new SorEst());
 187                                                 }else if (Estimators[i] == "thetayc") {
 188                                                         matrixCalculators.push_back(new ThetaYC());
 189                                                 }else if (Estimators[i] == "thetan") {
 190                                                         matrixCalculators.push_back(new ThetaN());
 191                                                 }else if (Estimators[i] == "kstest") {
 192                                                         matrixCalculators.push_back(new KSTest());
 193                                                 }else if (Estimators[i] == "sharednseqs") {
 194                                                         matrixCalculators.push_back(new SharedNSeqs());
 195                                                 }else if (Estimators[i] == "ochiai") {
 196                                                         matrixCalculators.push_back(new Ochiai());
 197                                                 }else if (Estimators[i] == "anderberg") {
 198                                                         matrixCalculators.push_back(new Anderberg());
 199                                                 }else if (Estimators[i] == "kulczynski") {
 200                                                         matrixCalculators.push_back(new Kulczynski());
 201                                                 }else if (Estimators[i] == "kulczynskicody") {
 202                                                         matrixCalculators.push_back(new KulczynskiCody());
 203                                                 }else if (Estimators[i] == "lennon") {
 204                                                         matrixCalculators.push_back(new Lennon());
 205                                                 }else if (Estimators[i] == "morisitahorn") {
 206                                                         matrixCalculators.push_back(new MorHorn());
 207                                                 }else if (Estimators[i] == "braycurtis") {
 208                                                         matrixCalculators.push_back(new BrayCurtis());
 209                                                 }else if (Estimators[i] == "whittaker") {
 210                                                         matrixCalculators.push_back(new Whittaker());
 211                                                 }else if (Estimators[i] == "odum") {
 212                                                         matrixCalculators.push_back(new Odum());
 213                                                 }else if (Estimators[i] == "canberra") {
 214                                                         matrixCalculators.push_back(new Canberra());
 215                                                 }else if (Estimators[i] == "structeuclidean") {
 216                                                         matrixCalculators.push_back(new StructEuclidean());
 217                                                 }else if (Estimators[i] == "structchord") {
 218                                                         matrixCalculators.push_back(new StructChord());
 219                                                 }else if (Estimators[i] == "hellinger") {
 220                                                         matrixCalculators.push_back(new Hellinger());
 221                                                 }else if (Estimators[i] == "manhattan") {
 222                                                         matrixCalculators.push_back(new Manhattan());
 223                                                 }else if (Estimators[i] == "structpearson") {
 224                                                         matrixCalculators.push_back(new StructPearson());
 225                                                 }else if (Estimators[i] == "soergel") {
 226                                                         matrixCalculators.push_back(new Soergel());
 227                                                 }else if (Estimators[i] == "spearman") {
 228                                                         matrixCalculators.push_back(new Spearman());
 229                                                 }else if (Estimators[i] == "structkulczynski") {
 230                                                         matrixCalculators.push_back(new StructKulczynski());
 231                                                 }else if (Estimators[i] == "speciesprofile") {
 232                                                         matrixCalculators.push_back(new SpeciesProfile());
 233                                                 }else if (Estimators[i] == "hamming") {
 234                                                         matrixCalculators.push_back(new Hamming());
 235                                                 }else if (Estimators[i] == "structchi2") {
 236                                                         matrixCalculators.push_back(new StructChi2());
 237                                                 }else if (Estimators[i] == "gower") {
 238                                                         matrixCalculators.push_back(new Gower());
 239                                                 }else if (Estimators[i] == "memchi2") {
 240                                                         matrixCalculators.push_back(new MemChi2());
 241                                                 }else if (Estimators[i] == "memchord") {
 242                                                         matrixCalculators.push_back(new MemChord());
 243                                                 }else if (Estimators[i] == "memeuclidean") {
 244                                                         matrixCalculators.push_back(new MemEuclidean());
 245                                                 }else if (Estimators[i] == "mempearson") {
 246                                                         matrixCalculators.push_back(new MemPearson());
 247                                                 }
 248                                         }
 249                                 }
 250
 251                         }
 252                 }
 253
 254         }
 255         catch(exception& e) {
 256                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 257                 exit(1);
 258         }
 259 }
 260
 261 //**********************************************************************************************************************
 262
 263 MatrixOutputCommand::~MatrixOutputCommand(){}
 264
 265 //**********************************************************************************************************************
 266
 267 int MatrixOutputCommand::execute(){
 268         try {
 269
 270                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 271
 272                 //if the users entered no valid calculators don't execute command
 273                 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }
 274
 275                 input = new InputData(sharedfile, "sharedfile");
 276                 lookup = input->getSharedRAbundVectors();
 277                 string lastLabel = lookup[0]->getLabel();
 278
 279                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 280                 set<string> processedLabels;
 281                 set<string> userLabels = labels;
 282
 283                 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0;}
 284
 285                 numGroups = lookup.size();
 286                 lines.resize(processors);
 287                 for (int i = 0; i < processors; i++) {
 288                         lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
 289                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 290                 }
 291
 292                 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0;  }
 293
 294                 //as long as you are not at the end of the file or done wih the lines you want
 295                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 296
 297                         if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 298
 299                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 300                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 301                                 process(lookup);
 302
 303                                 processedLabels.insert(lookup[0]->getLabel());
 304                                 userLabels.erase(lookup[0]->getLabel());
 305                         }
 306
 307                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 308                                 string saveLabel = lookup[0]->getLabel();
 309
 310                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 311                                 lookup = input->getSharedRAbundVectors(lastLabel);
 312
 313                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 314                                 process(lookup);
 315
 316                                 processedLabels.insert(lookup[0]->getLabel());
 317                                 userLabels.erase(lookup[0]->getLabel());
 318
 319                                 //restore real lastlabel to save below
 320                                 lookup[0]->setLabel(saveLabel);
 321                         }
 322
 323                         lastLabel = lookup[0]->getLabel();
 324
 325                         //get next line to process
 326                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 327                         lookup = input->getSharedRAbundVectors();
 328                 }
 329
 330                 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 331
 332                 //output error messages about any remaining user labels
 333                 set<string>::iterator it;
 334                 bool needToRun = false;
 335                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 336                         m->mothurOut("Your file does not include the label " + *it);
 337                         if (processedLabels.count(lastLabel) != 1) {
 338                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 339                                 needToRun = true;
 340                         }else {
 341                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 342                         }
 343                 }
 344
 345                 if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 346
 347                 //run last label if you need to
 348                 if (needToRun == true)  {
 349                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  }
 350                         lookup = input->getSharedRAbundVectors(lastLabel);
 351
 352                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 353                         process(lookup);
 354                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 355                 }
 356
 357                 if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0;  }
 358
 359                 //reset groups parameter
 360                 m->clearGroups();
 361
 362                 //set phylip file as new current phylipfile
 363                 string current = "";
 364                 itTypes = outputTypes.find("phylip");
 365                 if (itTypes != outputTypes.end()) {
 366                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 367                 }
 368
 369                 m->mothurOutEndLine();
 370                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 371                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 372                 m->mothurOutEndLine();
 373
 374
 375                 return 0;
 376         }
 377         catch(exception& e) {
 378                 m->errorOut(e, "MatrixOutputCommand", "execute");
 379                 exit(1);
 380         }
 381 }
 382 /***********************************************************/
 383 void MatrixOutputCommand::printSims(ostream& out, vector< vector<float> >& simMatrix) {
 384         try {
 385
 386                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 387
 388                 //output num seqs
 389                 out << simMatrix.size() << endl;
 390
 391                 if (output == "lt") {
 392                         for (int m = 0; m < simMatrix.size(); m++)      {
 393                                 out << lookup[m]->getGroup() << '\t';
 394                                 for (int n = 0; n < m; n++)     {
 395                                         out << simMatrix[m][n] << '\t';
 396                                 }
 397                                 out << endl;
 398                         }
 399                 }else{
 400                         for (int m = 0; m < simMatrix.size(); m++)      {
 401                                 out << lookup[m]->getGroup() << '\t';
 402                                 for (int n = 0; n < simMatrix[m].size(); n++)   {
 403                                         out << simMatrix[m][n] << '\t';
 404                                 }
 405                                 out << endl;
 406                         }
 407                 }
 408         }
 409         catch(exception& e) {
 410                 m->errorOut(e, "MatrixOutputCommand", "printSims");
 411                 exit(1);
 412         }
 413 }
 414 /***********************************************************/
 415 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 416         try {
 417                 EstOutput data;
 418                 vector<SharedRAbundVector*> subset;
 419                 vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files
 420
 421
 422                 if(processors == 1){
 423                         driver(thisLookup, 0, numGroups, calcDists);
 424                 }else{
 425                         int process = 1;
 426                         vector<int> processIDS;
 427
 428                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 429                         //loop through and create all the processes you want
 430                         while (process != processors) {
 431                                 int pid = fork();
 432
 433                                 if (pid > 0) {
 434                                         processIDS.push_back(pid);
 435                                         process++;
 436                                 }else if (pid == 0){
 437                                         driver(thisLookup, lines[process].start, lines[process].end, calcDists);
 438
 439                                         string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
 440                                         ofstream outtemp;
 441                                         m->openOutputFile(tempdistFileName, outtemp);
 442
 443                                         for (int i = 0; i < calcDists.size(); i++) {
 444                                                 outtemp << calcDists[i].size() << endl;
 445
 446                                                 for (int j = 0; j < calcDists[i].size(); j++) {
 447                                                         outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
 448                                                 }
 449                                         }
 450                                         outtemp.close();
 451
 452                                         exit(0);
 453                                 }else {
 454                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 455                                         for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 456                                         exit(0);
 457                                 }
 458                         }
 459
 460                         //parent do your part
 461                         driver(thisLookup, lines[0].start, lines[0].end, calcDists);
 462
 463                         //force parent to wait until all the processes are done
 464                         for (int i = 0; i < processIDS.size(); i++) {
 465                                 int temp = processIDS[i];
 466                                 wait(&temp);
 467                         }
 468
 469                         for (int i = 0; i < processIDS.size(); i++) {
 470                                 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
 471                                 ifstream intemp;
 472                                 m->openInputFile(tempdistFileName, intemp);
 473
 474                                 for (int k = 0; k < calcDists.size(); k++) {
 475                                         int size = 0;
 476                                         intemp >> size; m->gobble(intemp);
 477
 478                                         for (int j = 0; j < size; j++) {
 479                                                 int seq1 = 0;
 480                                                 int seq2 = 0;
 481                                                 float dist = 1.0;
 482
 483                                                 intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 484
 485                                                 seqDist tempDist(seq1, seq2, dist);
 486                                                 calcDists[k].push_back(tempDist);
 487                                         }
 488                                 }
 489                                 intemp.close();
 490                                 m->mothurRemove(tempdistFileName);
 491                         }
 492             #else
 493             //////////////////////////////////////////////////////////////////////////////////////////////////////
 494             //Windows version shared memory, so be careful when passing variables through the distSharedData struct.
 495             //Above fork() will clone, so memory is separate, but that's not the case with windows,
 496             //Taking advantage of shared memory to pass results vectors.
 497             //////////////////////////////////////////////////////////////////////////////////////////////////////
 498
 499             vector<distSharedData*> pDataArray;
 500             DWORD   dwThreadIdArray[processors-1];
 501             HANDLE  hThreadArray[processors-1];
 502
 503             //Create processor worker threads.
 504             for( int i=1; i<processors; i++ ){
 505
 506                 //make copy of lookup so we don't get access violations
 507                 vector<SharedRAbundVector*> newLookup;
 508                 for (int k = 0; k < thisLookup.size(); k++) {
 509                     SharedRAbundVector* temp = new SharedRAbundVector();
 510                     temp->setLabel(thisLookup[k]->getLabel());
 511                     temp->setGroup(thisLookup[k]->getGroup());
 512                     newLookup.push_back(temp);
 513                 }
 514
 515                 //for each bin
 516                 for (int k = 0; k < thisLookup[0]->getNumBins(); k++) {
 517                     if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
 518                     for (int j = 0; j < thisLookup.size(); j++) { newLookup[j]->push_back(thisLookup[j]->getAbundance(k), thisLookup[j]->getGroup()); }
 519                 }
 520
 521                 // Allocate memory for thread data.
 522                 distSharedData* tempSum = new distSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
 523                 pDataArray.push_back(tempSum);
 524                 processIDS.push_back(i);
 525
 526                 hThreadArray[i-1] = CreateThread(NULL, 0, MyDistSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
 527             }
 528
 529             //parent do your part
 530             driver(thisLookup, lines[0].start, lines[0].end, calcDists);
 531
 532             //Wait until all threads have terminated.
 533             WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 534
 535             //Close all thread handles and free memory allocations.
 536             for(int i=0; i < pDataArray.size(); i++){
 537                 for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) {  delete pDataArray[i]->thisLookup[j];  }
 538
 539                 for (int k = 0; k < calcDists.size(); k++) {
 540                     int size = pDataArray[i]->calcDists[k].size();
 541                     for (int j = 0; j < size; j++) {    calcDists[k].push_back(pDataArray[i]->calcDists[k][j]);    }
 542                 }
 543
 544                 CloseHandle(hThreadArray[i]);
 545                 delete pDataArray[i];
 546             }
 547
 548             #endif
 549                 }
 550
 551
 552
 553                 for (int i = 0; i < calcDists.size(); i++) {
 554                         if (m->control_pressed) { break; }
 555
 556                         //initialize matrix
 557                         vector< vector<float> > matrix; //square matrix to represent the distance
 558                         matrix.resize(thisLookup.size());
 559                         for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 560
 561                         for (int j = 0; j < calcDists[i].size(); j++) {
 562                                 int row = calcDists[i][j].seq1;
 563                                 int column = calcDists[i][j].seq2;
 564                                 float dist = calcDists[i][j].dist;
 565
 566                                 matrix[row][column] = dist;
 567                                 matrix[column][row] = dist;
 568                         }
 569
 570                         string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".dist";
 571                         outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
 572                         ofstream outDist;
 573                         m->openOutputFile(distFileName, outDist);
 574                         outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
 575
 576                         printSims(outDist, matrix);
 577
 578                         outDist.close();
 579                 }
 580
 581                 return 0;
 582         }
 583         catch(exception& e) {
 584                 m->errorOut(e, "MatrixOutputCommand", "process");
 585                 exit(1);
 586         }
 587 }
 588 /**************************************************************************************************/
 589 int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
 590         try {
 591
 592                 vector<SharedRAbundVector*> subset;
 593                 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
 594
 595                         for (int l = 0; l < k; l++) {
 596
 597                                 if (k != l) { //we dont need to similiarity of a groups to itself
 598                                         subset.clear(); //clear out old pair of sharedrabunds
 599                                         //add new pair of sharedrabunds
 600                                         subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 601
 602                                         for(int i=0;i<matrixCalculators.size();i++) {
 603
 604                                                 //if this calc needs all groups to calculate the pair load all groups
 605                                                 if (matrixCalculators[i]->getNeedsAll()) {
 606                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 607                                                         for (int w = 0; w < thisLookup.size(); w++) {
 608                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
 609                                                         }
 610                                                 }
 611
 612                                                 vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 613
 614                                                 if (m->control_pressed) { return 1; }
 615
 616                                                 seqDist temp(l, k, tempdata[0]);
 617                                                 calcDists[i].push_back(temp);
 618                                         }
 619                                 }
 620                         }
 621                 }
 622
 623                 return 0;
 624         }
 625         catch(exception& e) {
 626                 m->errorOut(e, "MatrixOutputCommand", "driver");
 627                 exit(1);
 628         }
 629 }
 630 /***********************************************************/
 631
 632
 633