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 #include "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharednseqs.h"
  15 #include "sharedjabund.h"
  16 #include "sharedsorabund.h"
  17 #include "sharedjclass.h"
  18 #include "sharedsorclass.h"
  19 #include "sharedjest.h"
  20 #include "sharedsorest.h"
  21 #include "sharedthetayc.h"
  22 #include "sharedthetan.h"
  23 #include "sharedkstest.h"
  24 #include "whittaker.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "whittaker.h"
  34 #include "odum.h"
  35 #include "canberra.h"
  36 #include "structeuclidean.h"
  37 #include "structchord.h"
  38 #include "hellinger.h"
  39 #include "manhattan.h"
  40 #include "structpearson.h"
  41 #include "soergel.h"
  42 #include "spearman.h"
  43 #include "structkulczynski.h"
  44 #include "structchi2.h"
  45 #include "speciesprofile.h"
  46 #include "hamming.h"
  47 #include "gower.h"
  48 #include "memchi2.h"
  49 #include "memchord.h"
  50 #include "memeuclidean.h"
  51 #include "mempearson.h"
  52
  53 //**********************************************************************************************************************
  54 vector<string> MatrixOutputCommand::setParameters(){
  55         try {
  56                 CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
  57                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  58                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  59                 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);
  60                 CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
  61                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  62                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  63                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  64
  65                 vector<string> myArray;
  66                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  67                 return myArray;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "MatrixOutputCommand", "setParameters");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 string MatrixOutputCommand::getHelpString(){
  76         try {
  77                 string helpString = "";
  78                 ValidCalculators validCalculator;
  79                 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";
  80                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
  81                 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";
  82                 helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
  83                 helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
  84                 helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
  85                 helpString += "The default value for groups is all the groups in your groupfile.\n";
  86                 helpString += "The default value for calc is jclass and thetayc.\n";
  87                 helpString += validCalculator.printCalc("matrix");
  88                 helpString += "The dist.shared command outputs a .dist file for each calculator you specify at each distance you choose.\n";
  89                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  90                 return helpString;
  91         }
  92         catch(exception& e) {
  93                 m->errorOut(e, "MatrixOutputCommand", "getHelpString");
  94                 exit(1);
  95         }
  96 }
  97 //**********************************************************************************************************************
  98 MatrixOutputCommand::MatrixOutputCommand(){
  99         try {
 100                 abort = true; calledHelp = true;
 101                 setParameters();
 102                 vector<string> tempOutNames;
 103                 outputTypes["phylip"] = tempOutNames;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 107                 exit(1);
 108         }
 109 }
 110 //**********************************************************************************************************************
 111
 112 MatrixOutputCommand::MatrixOutputCommand(string option)  {
 113         try {
 114                 abort = false; calledHelp = false;
 115                 allLines = 1;
 116
 117                 //allow user to run help
 118                 if(option == "help") {  help(); abort = true; calledHelp = true; }
 119                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 120
 121                 else {
 122                         vector<string> myArray = setParameters();
 123
 124                         OptionParser parser(option);
 125                         map<string,string> parameters  = parser.getParameters();
 126                         map<string,string>::iterator it;
 127
 128                         ValidParameters validParameter;
 129
 130                         //check to make sure all parameters are valid for command
 131                         for (it = parameters.begin(); it != parameters.end(); it++) {
 132                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 133                         }
 134
 135                         //initialize outputTypes
 136                         vector<string> tempOutNames;
 137                         outputTypes["phylip"] = tempOutNames;
 138
 139                         //if the user changes the input directory command factory will send this info to us in the output parameter
 140                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 141                         if (inputDir == "not found"){   inputDir = "";          }
 142                         else {
 143                                 string path;
 144                                 it = parameters.find("shared");
 145                                 //user has given a template file
 146                                 if(it != parameters.end()){
 147                                         path = m->hasPath(it->second);
 148                                         //if the user has not given a path then, add inputdir. else leave path alone.
 149                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 150                                 }
 151                         }
 152
 153                         sharedfile = validParameter.validFile(parameters, "shared", true);
 154                         if (sharedfile == "not found") {
 155                                 //if there is a current shared file, use it
 156                                 sharedfile = m->getSharedFile();
 157                                 if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 158                                 else {  m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
 159                         }else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 160
 161                         //if the user changes the output directory command factory will send this info to us in the output parameter
 162                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 163                                 outputDir = "";
 164                                 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 165                         }
 166
 167                         //check for optional parameter and set defaults
 168                         // ...at some point should added some additional type checking...
 169                         label = validParameter.validFile(parameters, "label", false);
 170                         if (label == "not found") { label = ""; }
 171                         else {
 172                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 173                                 else { allLines = 1;  }
 174                         }
 175
 176                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
 177                         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"; }
 178
 179                         groups = validParameter.validFile(parameters, "groups", false);
 180                         if (groups == "not found") { groups = ""; }
 181                         else {
 182                                 m->splitAtDash(groups, Groups);
 183                                 m->Groups = Groups;
 184                         }
 185
 186                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 187                         m->setProcessors(temp);
 188                         convert(temp, processors);
 189
 190                         calc = validParameter.validFile(parameters, "calc", false);
 191                         if (calc == "not found") { calc = "jclass-thetayc";  }
 192                         else {
 193                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 194                         }
 195                         m->splitAtDash(calc, Estimators);
 196                         if (m->inUsersGroups("citation", Estimators)) {
 197                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 198                                 //remove citation from list of calcs
 199                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 200                         }
 201
 202                         if (abort == false) {
 203
 204                                 ValidCalculators validCalculator;
 205
 206                                 int i;
 207                                 for (i=0; i<Estimators.size(); i++) {
 208                                         if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
 209                                                 if (Estimators[i] == "sharedsobs") {
 210                                                         matrixCalculators.push_back(new SharedSobsCS());
 211                                                 }else if (Estimators[i] == "sharedchao") {
 212                                                         matrixCalculators.push_back(new SharedChao1());
 213                                                 }else if (Estimators[i] == "sharedace") {
 214                                                         matrixCalculators.push_back(new SharedAce());
 215                                                 }else if (Estimators[i] == "jabund") {
 216                                                         matrixCalculators.push_back(new JAbund());
 217                                                 }else if (Estimators[i] == "sorabund") {
 218                                                         matrixCalculators.push_back(new SorAbund());
 219                                                 }else if (Estimators[i] == "jclass") {
 220                                                         matrixCalculators.push_back(new Jclass());
 221                                                 }else if (Estimators[i] == "sorclass") {
 222                                                         matrixCalculators.push_back(new SorClass());
 223                                                 }else if (Estimators[i] == "jest") {
 224                                                         matrixCalculators.push_back(new Jest());
 225                                                 }else if (Estimators[i] == "sorest") {
 226                                                         matrixCalculators.push_back(new SorEst());
 227                                                 }else if (Estimators[i] == "thetayc") {
 228                                                         matrixCalculators.push_back(new ThetaYC());
 229                                                 }else if (Estimators[i] == "thetan") {
 230                                                         matrixCalculators.push_back(new ThetaN());
 231                                                 }else if (Estimators[i] == "kstest") {
 232                                                         matrixCalculators.push_back(new KSTest());
 233                                                 }else if (Estimators[i] == "sharednseqs") {
 234                                                         matrixCalculators.push_back(new SharedNSeqs());
 235                                                 }else if (Estimators[i] == "ochiai") {
 236                                                         matrixCalculators.push_back(new Ochiai());
 237                                                 }else if (Estimators[i] == "anderberg") {
 238                                                         matrixCalculators.push_back(new Anderberg());
 239                                                 }else if (Estimators[i] == "kulczynski") {
 240                                                         matrixCalculators.push_back(new Kulczynski());
 241                                                 }else if (Estimators[i] == "kulczynskicody") {
 242                                                         matrixCalculators.push_back(new KulczynskiCody());
 243                                                 }else if (Estimators[i] == "lennon") {
 244                                                         matrixCalculators.push_back(new Lennon());
 245                                                 }else if (Estimators[i] == "morisitahorn") {
 246                                                         matrixCalculators.push_back(new MorHorn());
 247                                                 }else if (Estimators[i] == "braycurtis") {
 248                                                         matrixCalculators.push_back(new BrayCurtis());
 249                                                 }else if (Estimators[i] == "whittaker") {
 250                                                         matrixCalculators.push_back(new Whittaker());
 251                                                 }else if (Estimators[i] == "odum") {
 252                                                         matrixCalculators.push_back(new Odum());
 253                                                 }else if (Estimators[i] == "canberra") {
 254                                                         matrixCalculators.push_back(new Canberra());
 255                                                 }else if (Estimators[i] == "structeuclidean") {
 256                                                         matrixCalculators.push_back(new StructEuclidean());
 257                                                 }else if (Estimators[i] == "structchord") {
 258                                                         matrixCalculators.push_back(new StructChord());
 259                                                 }else if (Estimators[i] == "hellinger") {
 260                                                         matrixCalculators.push_back(new Hellinger());
 261                                                 }else if (Estimators[i] == "manhattan") {
 262                                                         matrixCalculators.push_back(new Manhattan());
 263                                                 }else if (Estimators[i] == "structpearson") {
 264                                                         matrixCalculators.push_back(new StructPearson());
 265                                                 }else if (Estimators[i] == "soergel") {
 266                                                         matrixCalculators.push_back(new Soergel());
 267                                                 }else if (Estimators[i] == "spearman") {
 268                                                         matrixCalculators.push_back(new Spearman());
 269                                                 }else if (Estimators[i] == "structkulczynski") {
 270                                                         matrixCalculators.push_back(new StructKulczynski());
 271                                                 }else if (Estimators[i] == "speciesprofile") {
 272                                                         matrixCalculators.push_back(new SpeciesProfile());
 273                                                 }else if (Estimators[i] == "hamming") {
 274                                                         matrixCalculators.push_back(new Hamming());
 275                                                 }else if (Estimators[i] == "structchi2") {
 276                                                         matrixCalculators.push_back(new StructChi2());
 277                                                 }else if (Estimators[i] == "gower") {
 278                                                         matrixCalculators.push_back(new Gower());
 279                                                 }else if (Estimators[i] == "memchi2") {
 280                                                         matrixCalculators.push_back(new MemChi2());
 281                                                 }else if (Estimators[i] == "memchord") {
 282                                                         matrixCalculators.push_back(new MemChord());
 283                                                 }else if (Estimators[i] == "memeuclidean") {
 284                                                         matrixCalculators.push_back(new MemEuclidean());
 285                                                 }else if (Estimators[i] == "mempearson") {
 286                                                         matrixCalculators.push_back(new MemPearson());
 287                                                 }
 288                                         }
 289                                 }
 290
 291                         }
 292                 }
 293
 294         }
 295         catch(exception& e) {
 296                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 297                 exit(1);
 298         }
 299 }
 300
 301 //**********************************************************************************************************************
 302
 303 MatrixOutputCommand::~MatrixOutputCommand(){}
 304
 305 //**********************************************************************************************************************
 306
 307 int MatrixOutputCommand::execute(){
 308         try {
 309
 310                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 311
 312                 //if the users entered no valid calculators don't execute command
 313                 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }
 314
 315                 input = new InputData(sharedfile, "sharedfile");
 316                 lookup = input->getSharedRAbundVectors();
 317                 string lastLabel = lookup[0]->getLabel();
 318
 319                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 320                 set<string> processedLabels;
 321                 set<string> userLabels = labels;
 322
 323                 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;}
 324
 325                 numGroups = lookup.size();
 326                 lines.resize(processors);
 327                 for (int i = 0; i < processors; i++) {
 328                         lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
 329                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 330                 }
 331
 332                 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0;  }
 333
 334                 //as long as you are not at the end of the file or done wih the lines you want
 335                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 336
 337                         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++) {     remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 338
 339                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 340                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 341                                 process(lookup);
 342
 343                                 processedLabels.insert(lookup[0]->getLabel());
 344                                 userLabels.erase(lookup[0]->getLabel());
 345                         }
 346
 347                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 348                                 string saveLabel = lookup[0]->getLabel();
 349
 350                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 351                                 lookup = input->getSharedRAbundVectors(lastLabel);
 352
 353                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 354                                 process(lookup);
 355
 356                                 processedLabels.insert(lookup[0]->getLabel());
 357                                 userLabels.erase(lookup[0]->getLabel());
 358
 359                                 //restore real lastlabel to save below
 360                                 lookup[0]->setLabel(saveLabel);
 361                         }
 362
 363                         lastLabel = lookup[0]->getLabel();
 364
 365                         //get next line to process
 366                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 367                         lookup = input->getSharedRAbundVectors();
 368                 }
 369
 370                 if (m->control_pressed) { outputTypes.clear(); delete input; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 371
 372                 //output error messages about any remaining user labels
 373                 set<string>::iterator it;
 374                 bool needToRun = false;
 375                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 376                         m->mothurOut("Your file does not include the label " + *it);
 377                         if (processedLabels.count(lastLabel) != 1) {
 378                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 379                                 needToRun = true;
 380                         }else {
 381                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 382                         }
 383                 }
 384
 385                 if (m->control_pressed) { outputTypes.clear(); delete input;  for (int i = 0; i < outputNames.size(); i++) {    remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 386
 387                 //run last label if you need to
 388                 if (needToRun == true)  {
 389                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  }
 390                         lookup = input->getSharedRAbundVectors(lastLabel);
 391
 392                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 393                         process(lookup);
 394                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 395                 }
 396
 397                 if (m->control_pressed) { outputTypes.clear();  delete input;  for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str()); } m->Groups.clear(); return 0;  }
 398
 399                 //reset groups parameter
 400                 m->Groups.clear();
 401
 402                 //set phylip file as new current phylipfile
 403                 string current = "";
 404                 itTypes = outputTypes.find("phylip");
 405                 if (itTypes != outputTypes.end()) {
 406                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 407                 }
 408
 409                 m->mothurOutEndLine();
 410                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 411                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 412                 m->mothurOutEndLine();
 413
 414
 415                 return 0;
 416         }
 417         catch(exception& e) {
 418                 m->errorOut(e, "MatrixOutputCommand", "execute");
 419                 exit(1);
 420         }
 421 }
 422 /***********************************************************/
 423 void MatrixOutputCommand::printSims(ostream& out, vector< vector<float> >& simMatrix) {
 424         try {
 425
 426                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 427
 428                 //output num seqs
 429                 out << simMatrix.size() << endl;
 430
 431                 if (output == "lt") {
 432                         for (int m = 0; m < simMatrix.size(); m++)      {
 433                                 out << lookup[m]->getGroup() << '\t';
 434                                 for (int n = 0; n < m; n++)     {
 435                                         out << simMatrix[m][n] << '\t';
 436                                 }
 437                                 out << endl;
 438                         }
 439                 }else{
 440                         for (int m = 0; m < simMatrix.size(); m++)      {
 441                                 out << lookup[m]->getGroup() << '\t';
 442                                 for (int n = 0; n < simMatrix[m].size(); n++)   {
 443                                         out << simMatrix[m][n] << '\t';
 444                                 }
 445                                 out << endl;
 446                         }
 447                 }
 448         }
 449         catch(exception& e) {
 450                 m->errorOut(e, "MatrixOutputCommand", "printSims");
 451                 exit(1);
 452         }
 453 }
 454 /***********************************************************/
 455 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 456         try {
 457                 EstOutput data;
 458                 vector<SharedRAbundVector*> subset;
 459                 vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files
 460
 461         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 462                 if(processors == 1){
 463                         driver(thisLookup, 0, numGroups, calcDists);
 464                 }else{
 465                         int process = 1;
 466                         vector<int> processIDS;
 467
 468                         //loop through and create all the processes you want
 469                         while (process != processors) {
 470                                 int pid = fork();
 471
 472                                 if (pid > 0) {
 473                                         processIDS.push_back(pid);
 474                                         process++;
 475                                 }else if (pid == 0){
 476                                         driver(thisLookup, lines[process].start, lines[process].end, calcDists);
 477
 478                                         string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
 479                                         ofstream outtemp;
 480                                         m->openOutputFile(tempdistFileName, outtemp);
 481
 482                                         for (int i = 0; i < calcDists.size(); i++) {
 483                                                 outtemp << calcDists[i].size() << endl;
 484
 485                                                 for (int j = 0; j < calcDists[i].size(); j++) {
 486                                                         outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
 487                                                 }
 488                                         }
 489                                         outtemp.close();
 490
 491                                         exit(0);
 492                                 }else {
 493                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 494                                         for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 495                                         exit(0);
 496                                 }
 497                         }
 498
 499                         //parent do your part
 500                         driver(thisLookup, lines[0].start, lines[0].end, calcDists);
 501
 502                         //force parent to wait until all the processes are done
 503                         for (int i = 0; i < processIDS.size(); i++) {
 504                                 int temp = processIDS[i];
 505                                 wait(&temp);
 506                         }
 507
 508                         for (int i = 0; i < processIDS.size(); i++) {
 509                                 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
 510                                 ifstream intemp;
 511                                 m->openInputFile(tempdistFileName, intemp);
 512
 513                                 for (int k = 0; k < calcDists.size(); k++) {
 514                                         int size = 0;
 515                                         intemp >> size; m->gobble(intemp);
 516
 517                                         for (int j = 0; j < size; j++) {
 518                                                 int seq1 = 0;
 519                                                 int seq2 = 0;
 520                                                 float dist = 1.0;
 521
 522                                                 intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 523
 524                                                 seqDist tempDist(seq1, seq2, dist);
 525                                                 calcDists[k].push_back(tempDist);
 526                                         }
 527                                 }
 528                                 intemp.close();
 529                                 remove(tempdistFileName.c_str());
 530                         }
 531
 532                 }
 533 #else
 534                 driver(thisLookup, 0, numGroups, calcDists);
 535 #endif
 536
 537                 for (int i = 0; i < calcDists.size(); i++) {
 538                         if (m->control_pressed) { break; }
 539
 540                         //initialize matrix
 541                         vector< vector<float> > matrix; //square matrix to represent the distance
 542                         matrix.resize(thisLookup.size());
 543                         for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 544
 545                         for (int j = 0; j < calcDists[i].size(); j++) {
 546                                 int row = calcDists[i][j].seq1;
 547                                 int column = calcDists[i][j].seq2;
 548                                 float dist = calcDists[i][j].dist;
 549
 550                                 matrix[row][column] = dist;
 551                                 matrix[column][row] = dist;
 552                         }
 553
 554                         string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".dist";
 555                         outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
 556                         ofstream outDist;
 557                         m->openOutputFile(distFileName, outDist);
 558                         outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
 559
 560                         printSims(outDist, matrix);
 561
 562                         outDist.close();
 563                 }
 564
 565                 return 0;
 566         }
 567         catch(exception& e) {
 568                 m->errorOut(e, "MatrixOutputCommand", "process");
 569                 exit(1);
 570         }
 571 }
 572 /**************************************************************************************************/
 573 int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
 574         try {
 575
 576                 vector<SharedRAbundVector*> subset;
 577                 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
 578
 579                         for (int l = 0; l < k; l++) {
 580
 581                                 if (k != l) { //we dont need to similiarity of a groups to itself
 582                                         subset.clear(); //clear out old pair of sharedrabunds
 583                                         //add new pair of sharedrabunds
 584                                         subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 585
 586                                         for(int i=0;i<matrixCalculators.size();i++) {
 587
 588                                                 //if this calc needs all groups to calculate the pair load all groups
 589                                                 if (matrixCalculators[i]->getNeedsAll()) {
 590                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 591                                                         for (int w = 0; w < thisLookup.size(); w++) {
 592                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
 593                                                         }
 594                                                 }
 595
 596                                                 vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 597
 598                                                 if (m->control_pressed) { return 1; }
 599
 600                                                 seqDist temp(l, k, (1.0 - tempdata[0]));
 601                                                 calcDists[i].push_back(temp);
 602                                         }
 603                                 }
 604                         }
 605                 }
 606
 607                 return 0;
 608         }
 609         catch(exception& e) {
 610                 m->errorOut(e, "MatrixOutputCommand", "driver");
 611                 exit(1);
 612         }
 613 }
 614 /***********************************************************/
 615
 616
 617