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                         else { m->setSharedFile(sharedfile); }
 161
 162                         //if the user changes the output directory command factory will send this info to us in the output parameter
 163                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 164                                 outputDir = "";
 165                                 outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
 166                         }
 167
 168                         //check for optional parameter and set defaults
 169                         // ...at some point should added some additional type checking...
 170                         label = validParameter.validFile(parameters, "label", false);
 171                         if (label == "not found") { label = ""; }
 172                         else {
 173                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 174                                 else { allLines = 1;  }
 175                         }
 176
 177                         output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
 178                         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"; }
 179
 180                         groups = validParameter.validFile(parameters, "groups", false);
 181                         if (groups == "not found") { groups = ""; }
 182                         else {
 183                                 m->splitAtDash(groups, Groups);
 184                                 m->Groups = Groups;
 185                         }
 186
 187                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 188                         m->setProcessors(temp);
 189                         convert(temp, processors);
 190
 191                         calc = validParameter.validFile(parameters, "calc", false);
 192                         if (calc == "not found") { calc = "jclass-thetayc";  }
 193                         else {
 194                                  if (calc == "default")  {  calc = "jclass-thetayc";  }
 195                         }
 196                         m->splitAtDash(calc, Estimators);
 197                         if (m->inUsersGroups("citation", Estimators)) {
 198                                 ValidCalculators validCalc; validCalc.printCitations(Estimators);
 199                                 //remove citation from list of calcs
 200                                 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") {  Estimators.erase(Estimators.begin()+i); break; } }
 201                         }
 202
 203                         if (abort == false) {
 204
 205                                 ValidCalculators validCalculator;
 206
 207                                 int i;
 208                                 for (i=0; i<Estimators.size(); i++) {
 209                                         if (validCalculator.isValidCalculator("matrix", Estimators[i]) == true) {
 210                                                 if (Estimators[i] == "sharedsobs") {
 211                                                         matrixCalculators.push_back(new SharedSobsCS());
 212                                                 }else if (Estimators[i] == "sharedchao") {
 213                                                         matrixCalculators.push_back(new SharedChao1());
 214                                                 }else if (Estimators[i] == "sharedace") {
 215                                                         matrixCalculators.push_back(new SharedAce());
 216                                                 }else if (Estimators[i] == "jabund") {
 217                                                         matrixCalculators.push_back(new JAbund());
 218                                                 }else if (Estimators[i] == "sorabund") {
 219                                                         matrixCalculators.push_back(new SorAbund());
 220                                                 }else if (Estimators[i] == "jclass") {
 221                                                         matrixCalculators.push_back(new Jclass());
 222                                                 }else if (Estimators[i] == "sorclass") {
 223                                                         matrixCalculators.push_back(new SorClass());
 224                                                 }else if (Estimators[i] == "jest") {
 225                                                         matrixCalculators.push_back(new Jest());
 226                                                 }else if (Estimators[i] == "sorest") {
 227                                                         matrixCalculators.push_back(new SorEst());
 228                                                 }else if (Estimators[i] == "thetayc") {
 229                                                         matrixCalculators.push_back(new ThetaYC());
 230                                                 }else if (Estimators[i] == "thetan") {
 231                                                         matrixCalculators.push_back(new ThetaN());
 232                                                 }else if (Estimators[i] == "kstest") {
 233                                                         matrixCalculators.push_back(new KSTest());
 234                                                 }else if (Estimators[i] == "sharednseqs") {
 235                                                         matrixCalculators.push_back(new SharedNSeqs());
 236                                                 }else if (Estimators[i] == "ochiai") {
 237                                                         matrixCalculators.push_back(new Ochiai());
 238                                                 }else if (Estimators[i] == "anderberg") {
 239                                                         matrixCalculators.push_back(new Anderberg());
 240                                                 }else if (Estimators[i] == "kulczynski") {
 241                                                         matrixCalculators.push_back(new Kulczynski());
 242                                                 }else if (Estimators[i] == "kulczynskicody") {
 243                                                         matrixCalculators.push_back(new KulczynskiCody());
 244                                                 }else if (Estimators[i] == "lennon") {
 245                                                         matrixCalculators.push_back(new Lennon());
 246                                                 }else if (Estimators[i] == "morisitahorn") {
 247                                                         matrixCalculators.push_back(new MorHorn());
 248                                                 }else if (Estimators[i] == "braycurtis") {
 249                                                         matrixCalculators.push_back(new BrayCurtis());
 250                                                 }else if (Estimators[i] == "whittaker") {
 251                                                         matrixCalculators.push_back(new Whittaker());
 252                                                 }else if (Estimators[i] == "odum") {
 253                                                         matrixCalculators.push_back(new Odum());
 254                                                 }else if (Estimators[i] == "canberra") {
 255                                                         matrixCalculators.push_back(new Canberra());
 256                                                 }else if (Estimators[i] == "structeuclidean") {
 257                                                         matrixCalculators.push_back(new StructEuclidean());
 258                                                 }else if (Estimators[i] == "structchord") {
 259                                                         matrixCalculators.push_back(new StructChord());
 260                                                 }else if (Estimators[i] == "hellinger") {
 261                                                         matrixCalculators.push_back(new Hellinger());
 262                                                 }else if (Estimators[i] == "manhattan") {
 263                                                         matrixCalculators.push_back(new Manhattan());
 264                                                 }else if (Estimators[i] == "structpearson") {
 265                                                         matrixCalculators.push_back(new StructPearson());
 266                                                 }else if (Estimators[i] == "soergel") {
 267                                                         matrixCalculators.push_back(new Soergel());
 268                                                 }else if (Estimators[i] == "spearman") {
 269                                                         matrixCalculators.push_back(new Spearman());
 270                                                 }else if (Estimators[i] == "structkulczynski") {
 271                                                         matrixCalculators.push_back(new StructKulczynski());
 272                                                 }else if (Estimators[i] == "speciesprofile") {
 273                                                         matrixCalculators.push_back(new SpeciesProfile());
 274                                                 }else if (Estimators[i] == "hamming") {
 275                                                         matrixCalculators.push_back(new Hamming());
 276                                                 }else if (Estimators[i] == "structchi2") {
 277                                                         matrixCalculators.push_back(new StructChi2());
 278                                                 }else if (Estimators[i] == "gower") {
 279                                                         matrixCalculators.push_back(new Gower());
 280                                                 }else if (Estimators[i] == "memchi2") {
 281                                                         matrixCalculators.push_back(new MemChi2());
 282                                                 }else if (Estimators[i] == "memchord") {
 283                                                         matrixCalculators.push_back(new MemChord());
 284                                                 }else if (Estimators[i] == "memeuclidean") {
 285                                                         matrixCalculators.push_back(new MemEuclidean());
 286                                                 }else if (Estimators[i] == "mempearson") {
 287                                                         matrixCalculators.push_back(new MemPearson());
 288                                                 }
 289                                         }
 290                                 }
 291
 292                         }
 293                 }
 294
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
 298                 exit(1);
 299         }
 300 }
 301
 302 //**********************************************************************************************************************
 303
 304 MatrixOutputCommand::~MatrixOutputCommand(){}
 305
 306 //**********************************************************************************************************************
 307
 308 int MatrixOutputCommand::execute(){
 309         try {
 310
 311                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 312
 313                 //if the users entered no valid calculators don't execute command
 314                 if (matrixCalculators.size() == 0) { m->mothurOut("No valid calculators."); m->mothurOutEndLine();  return 0; }
 315
 316                 input = new InputData(sharedfile, "sharedfile");
 317                 lookup = input->getSharedRAbundVectors();
 318                 string lastLabel = lookup[0]->getLabel();
 319
 320                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 321                 set<string> processedLabels;
 322                 set<string> userLabels = labels;
 323
 324                 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;}
 325
 326                 numGroups = lookup.size();
 327                 lines.resize(processors);
 328                 for (int i = 0; i < processors; i++) {
 329                         lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
 330                         lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
 331                 }
 332
 333                 if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); return 0;  }
 334
 335                 //as long as you are not at the end of the file or done wih the lines you want
 336                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 337
 338                         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;  }
 339
 340                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 341                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 342                                 process(lookup);
 343
 344                                 processedLabels.insert(lookup[0]->getLabel());
 345                                 userLabels.erase(lookup[0]->getLabel());
 346                         }
 347
 348                         if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 349                                 string saveLabel = lookup[0]->getLabel();
 350
 351                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 352                                 lookup = input->getSharedRAbundVectors(lastLabel);
 353
 354                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 355                                 process(lookup);
 356
 357                                 processedLabels.insert(lookup[0]->getLabel());
 358                                 userLabels.erase(lookup[0]->getLabel());
 359
 360                                 //restore real lastlabel to save below
 361                                 lookup[0]->setLabel(saveLabel);
 362                         }
 363
 364                         lastLabel = lookup[0]->getLabel();
 365
 366                         //get next line to process
 367                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 368                         lookup = input->getSharedRAbundVectors();
 369                 }
 370
 371                 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;  }
 372
 373                 //output error messages about any remaining user labels
 374                 set<string>::iterator it;
 375                 bool needToRun = false;
 376                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 377                         m->mothurOut("Your file does not include the label " + *it);
 378                         if (processedLabels.count(lastLabel) != 1) {
 379                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 380                                 needToRun = true;
 381                         }else {
 382                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 383                         }
 384                 }
 385
 386                 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;  }
 387
 388                 //run last label if you need to
 389                 if (needToRun == true)  {
 390                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {  delete lookup[i]; }  }
 391                         lookup = input->getSharedRAbundVectors(lastLabel);
 392
 393                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 394                         process(lookup);
 395                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 396                 }
 397
 398                 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;  }
 399
 400                 //reset groups parameter
 401                 m->Groups.clear();
 402
 403                 //set phylip file as new current phylipfile
 404                 string current = "";
 405                 itTypes = outputTypes.find("phylip");
 406                 if (itTypes != outputTypes.end()) {
 407                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setPhylipFile(current); }
 408                 }
 409
 410                 m->mothurOutEndLine();
 411                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 412                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 413                 m->mothurOutEndLine();
 414
 415
 416                 return 0;
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "MatrixOutputCommand", "execute");
 420                 exit(1);
 421         }
 422 }
 423 /***********************************************************/
 424 void MatrixOutputCommand::printSims(ostream& out, vector< vector<float> >& simMatrix) {
 425         try {
 426
 427                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 428
 429                 //output num seqs
 430                 out << simMatrix.size() << endl;
 431
 432                 if (output == "lt") {
 433                         for (int m = 0; m < simMatrix.size(); m++)      {
 434                                 out << lookup[m]->getGroup() << '\t';
 435                                 for (int n = 0; n < m; n++)     {
 436                                         out << simMatrix[m][n] << '\t';
 437                                 }
 438                                 out << endl;
 439                         }
 440                 }else{
 441                         for (int m = 0; m < simMatrix.size(); m++)      {
 442                                 out << lookup[m]->getGroup() << '\t';
 443                                 for (int n = 0; n < simMatrix[m].size(); n++)   {
 444                                         out << simMatrix[m][n] << '\t';
 445                                 }
 446                                 out << endl;
 447                         }
 448                 }
 449         }
 450         catch(exception& e) {
 451                 m->errorOut(e, "MatrixOutputCommand", "printSims");
 452                 exit(1);
 453         }
 454 }
 455 /***********************************************************/
 456 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
 457         try {
 458                 EstOutput data;
 459                 vector<SharedRAbundVector*> subset;
 460                 vector< vector<seqDist> > calcDists; calcDists.resize(matrixCalculators.size()); //one for each calc, this will be used to make .dist files
 461
 462         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 463                 if(processors == 1){
 464                         driver(thisLookup, 0, numGroups, calcDists);
 465                 }else{
 466                         int process = 1;
 467                         vector<int> processIDS;
 468
 469                         //loop through and create all the processes you want
 470                         while (process != processors) {
 471                                 int pid = fork();
 472
 473                                 if (pid > 0) {
 474                                         processIDS.push_back(pid);
 475                                         process++;
 476                                 }else if (pid == 0){
 477                                         driver(thisLookup, lines[process].start, lines[process].end, calcDists);
 478
 479                                         string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
 480                                         ofstream outtemp;
 481                                         m->openOutputFile(tempdistFileName, outtemp);
 482
 483                                         for (int i = 0; i < calcDists.size(); i++) {
 484                                                 outtemp << calcDists[i].size() << endl;
 485
 486                                                 for (int j = 0; j < calcDists[i].size(); j++) {
 487                                                         outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
 488                                                 }
 489                                         }
 490                                         outtemp.close();
 491
 492                                         exit(0);
 493                                 }else {
 494                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 495                                         for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 496                                         exit(0);
 497                                 }
 498                         }
 499
 500                         //parent do your part
 501                         driver(thisLookup, lines[0].start, lines[0].end, calcDists);
 502
 503                         //force parent to wait until all the processes are done
 504                         for (int i = 0; i < processIDS.size(); i++) {
 505                                 int temp = processIDS[i];
 506                                 wait(&temp);
 507                         }
 508
 509                         for (int i = 0; i < processIDS.size(); i++) {
 510                                 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) +  ".dist";
 511                                 ifstream intemp;
 512                                 m->openInputFile(tempdistFileName, intemp);
 513
 514                                 for (int k = 0; k < calcDists.size(); k++) {
 515                                         int size = 0;
 516                                         intemp >> size; m->gobble(intemp);
 517
 518                                         for (int j = 0; j < size; j++) {
 519                                                 int seq1 = 0;
 520                                                 int seq2 = 0;
 521                                                 float dist = 1.0;
 522
 523                                                 intemp >> seq1 >> seq2 >> dist;   m->gobble(intemp);
 524
 525                                                 seqDist tempDist(seq1, seq2, dist);
 526                                                 calcDists[k].push_back(tempDist);
 527                                         }
 528                                 }
 529                                 intemp.close();
 530                                 remove(tempdistFileName.c_str());
 531                         }
 532
 533                 }
 534 #else
 535                 driver(thisLookup, 0, numGroups, calcDists);
 536 #endif
 537
 538                 for (int i = 0; i < calcDists.size(); i++) {
 539                         if (m->control_pressed) { break; }
 540
 541                         //initialize matrix
 542                         vector< vector<float> > matrix; //square matrix to represent the distance
 543                         matrix.resize(thisLookup.size());
 544                         for (int k = 0; k < thisLookup.size(); k++) {  matrix[k].resize(thisLookup.size(), 0.0); }
 545
 546                         for (int j = 0; j < calcDists[i].size(); j++) {
 547                                 int row = calcDists[i][j].seq1;
 548                                 int column = calcDists[i][j].seq2;
 549                                 float dist = calcDists[i][j].dist;
 550
 551                                 matrix[row][column] = dist;
 552                                 matrix[column][row] = dist;
 553                         }
 554
 555                         string distFileName = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel()  + "." + output + ".dist";
 556                         outputNames.push_back(distFileName); outputTypes["phylip"].push_back(distFileName);
 557                         ofstream outDist;
 558                         m->openOutputFile(distFileName, outDist);
 559                         outDist.setf(ios::fixed, ios::floatfield); outDist.setf(ios::showpoint);
 560
 561                         printSims(outDist, matrix);
 562
 563                         outDist.close();
 564                 }
 565
 566                 return 0;
 567         }
 568         catch(exception& e) {
 569                 m->errorOut(e, "MatrixOutputCommand", "process");
 570                 exit(1);
 571         }
 572 }
 573 /**************************************************************************************************/
 574 int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
 575         try {
 576
 577                 vector<SharedRAbundVector*> subset;
 578                 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
 579
 580                         for (int l = 0; l < k; l++) {
 581
 582                                 if (k != l) { //we dont need to similiarity of a groups to itself
 583                                         subset.clear(); //clear out old pair of sharedrabunds
 584                                         //add new pair of sharedrabunds
 585                                         subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
 586
 587                                         for(int i=0;i<matrixCalculators.size();i++) {
 588
 589                                                 //if this calc needs all groups to calculate the pair load all groups
 590                                                 if (matrixCalculators[i]->getNeedsAll()) {
 591                                                         //load subset with rest of lookup for those calcs that need everyone to calc for a pair
 592                                                         for (int w = 0; w < thisLookup.size(); w++) {
 593                                                                 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
 594                                                         }
 595                                                 }
 596
 597                                                 vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
 598
 599                                                 if (m->control_pressed) { return 1; }
 600
 601                                                 seqDist temp(l, k, tempdata[0]);
 602                                                 calcDists[i].push_back(temp);
 603                                         }
 604                                 }
 605                         }
 606                 }
 607
 608                 return 0;
 609         }
 610         catch(exception& e) {
 611                 m->errorOut(e, "MatrixOutputCommand", "driver");
 612                 exit(1);
 613         }
 614 }
 615 /***********************************************************/
 616
 617
 618