shhhercommand.cpp

   1 /*
   2  *  shhher.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "shhhercommand.h"
  11
  12 #include "readcolumn.h"
  13 #include "readmatrix.hpp"
  14 #include "rabundvector.hpp"
  15 #include "sabundvector.hpp"
  16 #include "listvector.hpp"
  17 #include "cluster.hpp"
  18 #include "sparsematrix.hpp"
  19 #include <cfloat>
  20
  21 //**********************************************************************************************************************
  22 vector<string> ShhherCommand::setParameters(){
  23         try {
  24                 CommandParameter pflow("flow", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pflow);
  25                 CommandParameter pfile("file", "InputTypes", "", "", "none", "fileflow", "none",false,false); parameters.push_back(pfile);
  26                 CommandParameter plookup("lookup", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plookup);
  27                 CommandParameter pcutoff("cutoff", "Number", "", "0.01", "", "", "",false,false); parameters.push_back(pcutoff);
  28                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  29                 CommandParameter pmaxiter("maxiter", "Number", "", "1000", "", "", "",false,false); parameters.push_back(pmaxiter);
  30                 CommandParameter psigma("sigma", "Number", "", "60", "", "", "",false,false); parameters.push_back(psigma);
  31                 CommandParameter pmindelta("mindelta", "Number", "", "0.000001", "", "", "",false,false); parameters.push_back(pmindelta);
  32                 CommandParameter porder("order", "String", "", "", "", "", "",false,false); parameters.push_back(porder);
  33                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  34                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  35
  36                 vector<string> myArray;
  37                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  38                 return myArray;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "ShhherCommand", "setParameters");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 string ShhherCommand::getHelpString(){
  47         try {
  48                 string helpString = "";
  49                 helpString += "The shhh.seqs command reads a file containing flowgrams and creates a file of corrected sequences.\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "ShhherCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 ShhherCommand::ShhherCommand(){
  60         try {
  61                 abort = true; calledHelp = true;
  62                 setParameters();
  63
  64                 //initialize outputTypes
  65 //              vector<string> tempOutNames;
  66 //              outputTypes["pn.dist"] = tempOutNames;
  67
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "ShhherCommand", "ShhherCommand");
  71                 exit(1);
  72         }
  73 }
  74
  75 //**********************************************************************************************************************
  76
  77 ShhherCommand::ShhherCommand(string option) {
  78         try {
  79
  80 #ifdef USE_MPI
  81                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  82                 MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
  83
  84                 if(pid == 0){
  85 #endif
  86
  87
  88                 abort = false; calledHelp = false;
  89
  90
  91                 //allow user to run help
  92                 if(option == "help") { help(); abort = true; calledHelp = true; }
  93                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  94
  95                 else {
  96                         vector<string> myArray = setParameters();
  97
  98                         OptionParser parser(option);
  99                         map<string,string> parameters = parser.getParameters();
 100
 101                         ValidParameters validParameter;
 102                         map<string,string>::iterator it;
 103
 104                         //check to make sure all parameters are valid for command
 105                         for (it = parameters.begin(); it != parameters.end(); it++) {
 106                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 107                         }
 108
 109                         //initialize outputTypes
 110                         vector<string> tempOutNames;
 111 //                      outputTypes["pn.dist"] = tempOutNames;
 112                         //                      outputTypes["fasta"] = tempOutNames;
 113
 114                         //if the user changes the input directory command factory will send this info to us in the output parameter
 115                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 116                         if (inputDir == "not found"){   inputDir = "";          }
 117                         else {
 118                                 string path;
 119                                 it = parameters.find("flow");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 125                                 }
 126
 127                                 it = parameters.find("lookup");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["lookup"] = inputDir + it->second;           }
 133                                 }
 134
 135                                 it = parameters.find("file");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 141                                 }
 142                         }
 143
 144
 145                         //check for required parameters
 146                         flowFileName = validParameter.validFile(parameters, "flow", true);
 147                         flowFilesFileName = validParameter.validFile(parameters, "file", true);
 148                         if (flowFileName == "not found" && flowFilesFileName == "not found") {
 149                                 m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
 150                                 m->mothurOutEndLine();
 151                                 abort = true;
 152                         }
 153                         else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }
 154
 155                         if(flowFileName != "not found"){
 156                                 compositeFASTAFileName = "";
 157                                 compositeNamesFileName = "";
 158                         }
 159                         else{
 160                                 ofstream temp;
 161
 162                                 //flow.files = 9 character offset
 163                                 compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.fasta";
 164                                 m->openOutputFile(compositeFASTAFileName, temp);
 165                                 temp.close();
 166
 167                                 compositeNamesFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "shhh.names";
 168                                 m->openOutputFile(compositeNamesFileName, temp);
 169                                 temp.close();
 170                         }
 171
 172                         //if the user changes the output directory command factory will send this info to us in the output parameter
 173                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 174                                 outputDir = "";
 175                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 176                         }
 177
 178
 179                         //check for optional parameter and set defaults
 180                         // ...at some point should added some additional type checking...
 181                         string temp;
 182                         temp = validParameter.validFile(parameters, "lookup", true);
 183                         if (temp == "not found")        {
 184                                 lookupFileName = "LookUp_Titanium.pat";
 185
 186                                 int ableToOpen;
 187                                 ifstream in;
 188                                 ableToOpen = m->openInputFile(lookupFileName, in, "noerror");
 189                                 in.close();
 190
 191                                 //if you can't open it, try input location
 192                                 if (ableToOpen == 1) {
 193                                         if (inputDir != "") { //default path is set
 194                                                 string tryPath = inputDir + lookupFileName;
 195                                                 m->mothurOut("Unable to open " + lookupFileName + ". Trying input directory " + tryPath); m->mothurOutEndLine();
 196                                                 ifstream in2;
 197                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 198                                                 in2.close();
 199                                                 lookupFileName = tryPath;
 200                                         }
 201                                 }
 202
 203                                 //if you can't open it, try default location
 204                                 if (ableToOpen == 1) {
 205                                         if (m->getDefaultPath() != "") { //default path is set
 206                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(lookupFileName);
 207                                                 m->mothurOut("Unable to open " + lookupFileName + ". Trying default " + tryPath); m->mothurOutEndLine();
 208                                                 ifstream in2;
 209                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 210                                                 in2.close();
 211                                                 lookupFileName = tryPath;
 212                                         }
 213                                 }
 214
 215                                 //if you can't open it its not in current working directory or inputDir, try mothur excutable location
 216                                 if (ableToOpen == 1) {
 217                                         string exepath = m->argv;
 218                                         string tempPath = exepath;
 219                                         for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
 220                                         exepath = exepath.substr(0, (tempPath.find_last_of('m')));
 221
 222                                         string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
 223                                         m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
 224                                         ifstream in2;
 225                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 226                                         in2.close();
 227                                         lookupFileName = tryPath;
 228                                 }
 229
 230                                 if (ableToOpen == 1) {  m->mothurOut("Unable to open " + lookupFileName + "."); m->mothurOutEndLine(); abort=true;  }
 231                         }
 232                         else if(temp == "not open")     {
 233
 234                                 lookupFileName = validParameter.validFile(parameters, "lookup", false);
 235
 236                                 //if you can't open it its not inputDir, try mothur excutable location
 237                                 string exepath = m->argv;
 238                                 string tempPath = exepath;
 239                                 for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
 240                                 exepath = exepath.substr(0, (tempPath.find_last_of('m')));
 241
 242                                 string tryPath = m->getFullPathName(exepath) + lookupFileName;
 243                                 m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
 244                                 ifstream in2;
 245                                 int ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 246                                 in2.close();
 247                                 lookupFileName = tryPath;
 248
 249                                 if (ableToOpen == 1) {  m->mothurOut("Unable to open " + lookupFileName + "."); m->mothurOutEndLine(); abort=true;  }
 250                         }else                                           {       lookupFileName = temp;  }
 251
 252                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 253                         m->setProcessors(temp);
 254                         convert(temp, processors);
 255
 256                         temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.01";          }
 257                         convert(temp, cutoff);
 258
 259                         temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){       temp = "0.000001";      }
 260                         convert(temp, minDelta);
 261
 262                         temp = validParameter.validFile(parameters, "maxiter", false);  if (temp == "not found"){       temp = "1000";          }
 263                         convert(temp, maxIters);
 264
 265                         temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
 266                         convert(temp, sigma);
 267
 268                         flowOrder = validParameter.validFile(parameters, "order", false);
 269                         if (flowOrder == "not found"){ flowOrder = "TACG";              }
 270                         else if(flowOrder.length() != 4){
 271                                 m->mothurOut("The value of the order option must be four bases long\n");
 272                         }
 273
 274                 }
 275
 276 #ifdef USE_MPI
 277                 }
 278 #endif
 279
 280         }
 281         catch(exception& e) {
 282                 m->errorOut(e, "ShhherCommand", "ShhherCommand");
 283                 exit(1);
 284         }
 285 }
 286 //**********************************************************************************************************************
 287 #ifdef USE_MPI
 288 int ShhherCommand::execute(){
 289         try {
 290                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 291
 292                 int tag = 1976;
 293                 MPI_Status status;
 294
 295                 if(pid == 0){
 296
 297                         for(int i=1;i<ncpus;i++){
 298                                 MPI_Send(&abort, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 299                         }
 300                         if(abort == 1){ return 0;       }
 301
 302                         processors = ncpus;
 303
 304                         m->mothurOut("\nGetting preliminary data...\n");
 305                         getSingleLookUp();      if (m->control_pressed) { return 0; }
 306                         getJointLookUp();       if (m->control_pressed) { return 0; }
 307
 308                         vector<string> flowFileVector;
 309                         if(flowFilesFileName != "not found"){
 310                                 string fName;
 311
 312                                 ifstream flowFilesFile;
 313                                 m->openInputFile(flowFilesFileName, flowFilesFile);
 314                                 while(flowFilesFile){
 315                                         fName = m->getline(flowFilesFile);
 316                                         flowFileVector.push_back(fName);
 317                                         m->gobble(flowFilesFile);
 318                                 }
 319                         }
 320                         else{
 321                                 flowFileVector.push_back(flowFileName);
 322                         }
 323                         int numFiles = flowFileVector.size();
 324
 325                         for(int i=1;i<ncpus;i++){
 326                                 MPI_Send(&numFiles, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 327                         }
 328
 329                         for(int i=0;i<numFiles;i++){
 330
 331                                 if (m->control_pressed) { break; }
 332
 333                                 double begClock = clock();
 334                                 unsigned long long begTime = time(NULL);
 335
 336                                 flowFileName = flowFileVector[i];
 337
 338                                 m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 339                                 m->mothurOut("Reading flowgrams...\n");
 340                                 getFlowData();
 341
 342                                 if (m->control_pressed) { break; }
 343
 344                                 m->mothurOut("Identifying unique flowgrams...\n");
 345                                 getUniques();
 346
 347                                 if (m->control_pressed) { break; }
 348
 349                                 m->mothurOut("Calculating distances between flowgrams...\n");
 350                                 char fileName[1024];
 351                                 strcpy(fileName, flowFileName.c_str());
 352
 353                                 for(int i=1;i<ncpus;i++){
 354                                         MPI_Send(&fileName[0], 1024, MPI_CHAR, i, tag, MPI_COMM_WORLD);
 355
 356                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 357                                         MPI_Send(&numUniques, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 358                                         MPI_Send(&numFlowCells, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 359                                         MPI_Send(&flowDataIntI[0], numSeqs * numFlowCells, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 360                                         MPI_Send(&flowDataPrI[0], numSeqs * numFlowCells, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 361                                         MPI_Send(&mapUniqueToSeq[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 362                                         MPI_Send(&mapSeqToUnique[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 363                                         MPI_Send(&lengths[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 364                                         MPI_Send(&jointLookUp[0], NUMBINS * NUMBINS, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 365                                         MPI_Send(&cutoff, 1, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 366                                 }
 367
 368                                 string distFileName = flowDistMPI(0, int(sqrt(1.0/float(ncpus)) * numUniques));
 369
 370                                 if (m->control_pressed) { break; }
 371
 372                                 int done;
 373                                 for(int i=1;i<ncpus;i++){
 374                                         MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 375
 376                                         m->appendFiles((distFileName + ".temp." + toString(i)), distFileName);
 377                                         m->mothurRemove((distFileName + ".temp." + toString(i)));
 378                                 }
 379
 380                                 string namesFileName = createNamesFile();
 381
 382                                 if (m->control_pressed) { break; }
 383
 384                                 m->mothurOut("\nClustering flowgrams...\n");
 385                                 string listFileName = cluster(distFileName, namesFileName);
 386
 387                                 if (m->control_pressed) { break; }
 388
 389                                 getOTUData(listFileName);
 390
 391                                 m->mothurRemove(distFileName);
 392                                 m->mothurRemove(namesFileName);
 393                                 m->mothurRemove(listFileName);
 394
 395                                 if (m->control_pressed) { break; }
 396
 397                                 initPyroCluster();
 398
 399                                 if (m->control_pressed) { break; }
 400
 401                                 for(int i=1;i<ncpus;i++){
 402                                         MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 403                                         MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 404                                         MPI_Send(&uniqueFlowgrams[0], numFlowCells * numUniques, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 405                                         MPI_Send(&sigma, 1, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 406                                 }
 407
 408                                 if (m->control_pressed) { break; }
 409
 410                                 double maxDelta = 0;
 411                                 int iter = 0;
 412
 413                                 int numOTUsOnCPU = numOTUs / ncpus;
 414                                 int numSeqsOnCPU = numSeqs / ncpus;
 415                                 m->mothurOut("\nDenoising flowgrams...\n");
 416                                 m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 417
 418                                 while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 419
 420                                         double cycClock = clock();
 421                                         unsigned long long cycTime = time(NULL);
 422                                         fill();
 423
 424                                         if (m->control_pressed) { break; }
 425
 426                                         int total = singleTau.size();
 427                                         for(int i=1;i<ncpus;i++){
 428                                                 MPI_Send(&total, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 429                                                 MPI_Send(&change[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 430                                                 MPI_Send(&centroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 431
 432                                                 MPI_Send(&singleTau[0], total, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 433                                                 MPI_Send(&seqNumber[0], total, MPI_INT, i, tag, MPI_COMM_WORLD);
 434                                                 MPI_Send(&seqIndex[0], total, MPI_INT, i, tag, MPI_COMM_WORLD);
 435                                                 MPI_Send(&nSeqsPerOTU[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 436                                                 MPI_Send(&cumNumSeqs[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 437                                         }
 438
 439                                         calcCentroidsDriver(0, numOTUsOnCPU);
 440
 441                                         for(int i=1;i<ncpus;i++){
 442                                                 int otuStart = i * numOTUs / ncpus;
 443                                                 int otuStop = (i + 1) * numOTUs / ncpus;
 444
 445                                                 vector<int> tempCentroids(numOTUs, 0);
 446                                                 vector<short> tempChange(numOTUs, 0);
 447
 448                                                 MPI_Recv(&tempCentroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 449                                                 MPI_Recv(&tempChange[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD, &status);
 450
 451                                                 for(int j=otuStart;j<otuStop;j++){
 452                                                         centroids[j] = tempCentroids[j];
 453                                                         change[j] = tempChange[j];
 454                                                 }
 455                                         }
 456
 457                                         maxDelta = getNewWeights(); if (m->control_pressed) { break; }
 458                                         double nLL = getLikelihood(); if (m->control_pressed) { break; }
 459                                         checkCentroids(); if (m->control_pressed) { break; }
 460
 461                                         for(int i=1;i<ncpus;i++){
 462                                                 MPI_Send(&centroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 463                                                 MPI_Send(&weight[0], numOTUs, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 464                                                 MPI_Send(&change[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 465                                         }
 466
 467                                         calcNewDistancesParent(0, numSeqsOnCPU);
 468
 469                                         total = singleTau.size();
 470
 471                                         for(int i=1;i<ncpus;i++){
 472                                                 int childTotal;
 473                                                 int seqStart = i * numSeqs / ncpus;
 474                                                 int seqStop = (i + 1) * numSeqs / ncpus;
 475
 476                                                 MPI_Recv(&childTotal, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 477
 478                                                 vector<int> childSeqIndex(childTotal, 0);
 479                                                 vector<double> childSingleTau(childTotal, 0);
 480                                                 vector<double> childDist(numSeqs * numOTUs, 0);
 481                                                 vector<int> otuIndex(childTotal, 0);
 482
 483                                                 MPI_Recv(&childSeqIndex[0], childTotal, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 484                                                 MPI_Recv(&childSingleTau[0], childTotal, MPI_DOUBLE, i, tag, MPI_COMM_WORLD, &status);
 485                                                 MPI_Recv(&childDist[0], numOTUs * numSeqs, MPI_DOUBLE, i, tag, MPI_COMM_WORLD, &status);
 486                                                 MPI_Recv(&otuIndex[0], childTotal, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 487
 488                                                 int oldTotal = total;
 489                                                 total += childTotal;
 490                                                 singleTau.resize(total, 0);
 491                                                 seqIndex.resize(total, 0);
 492                                                 seqNumber.resize(total, 0);
 493
 494                                                 int childIndex = 0;
 495
 496                                                 for(int j=oldTotal;j<total;j++){
 497                                                         int otuI = otuIndex[childIndex];
 498                                                         int seqI = childSeqIndex[childIndex];
 499
 500                                                         singleTau[j] = childSingleTau[childIndex];
 501
 502                                                         aaP[otuI][nSeqsPerOTU[otuI]] = j;
 503                                                         aaI[otuI][nSeqsPerOTU[otuI]] = seqI;
 504                                                         nSeqsPerOTU[otuI]++;
 505                                                         childIndex++;
 506                                                 }
 507
 508                                                 int index = seqStart * numOTUs;
 509                                                 for(int j=seqStart;j<seqStop;j++){
 510                                                         for(int k=0;k<numOTUs;k++){
 511                                                                 dist[index] = childDist[index];
 512                                                                 index++;
 513                                                         }
 514                                                 }
 515                                         }
 516
 517                                         iter++;
 518
 519                                         m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
 520
 521                                         if((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 522                                                 int live = 1;
 523                                                 for(int i=1;i<ncpus;i++){
 524                                                         MPI_Send(&live, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 525                                                 }
 526                                         }
 527                                         else{
 528                                                 int live = 0;
 529                                                 for(int i=1;i<ncpus;i++){
 530                                                         MPI_Send(&live, 1, MPI_INT, i, tag, MPI_COMM_WORLD); //send kill command
 531                                                 }
 532                                         }
 533
 534                                 }
 535
 536                                 if (m->control_pressed) { break; }
 537
 538                                 m->mothurOut("\nFinalizing...\n");
 539                                 fill();
 540
 541                                 if (m->control_pressed) { break; }
 542
 543                                 setOTUs();
 544
 545                                 vector<int> otuCounts(numOTUs, 0);
 546                                 for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
 547                                 calcCentroidsDriver(0, numOTUs);
 548
 549                                 if (m->control_pressed) { break; }
 550
 551                                 writeQualities(otuCounts);      if (m->control_pressed) { break; }
 552                                 writeSequences(otuCounts);      if (m->control_pressed) { break; }
 553                                 writeNames(otuCounts);          if (m->control_pressed) { break; }
 554                                 writeClusters(otuCounts);       if (m->control_pressed) { break; }
 555                                 writeGroups();                          if (m->control_pressed) { break; }
 556
 557
 558                                 m->mothurOut("Total time to process " + toString(flowFileName) + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 559                         }
 560                 }
 561                 else{
 562                         int abort = 1;
 563
 564                         MPI_Recv(&abort, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 565                         if(abort){      return 0;       }
 566
 567                         int numFiles;
 568                         MPI_Recv(&numFiles, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 569
 570                         for(int i=0;i<numFiles;i++){
 571
 572                                 if (m->control_pressed) { break; }
 573
 574                                 //Now into the pyrodist part
 575                                 bool live = 1;
 576
 577                                 char fileName[1024];
 578                                 MPI_Recv(&fileName, 1024, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
 579                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 580                                 MPI_Recv(&numUniques, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 581                                 MPI_Recv(&numFlowCells, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 582
 583                                 flowDataIntI.resize(numSeqs * numFlowCells);
 584                                 flowDataPrI.resize(numSeqs * numFlowCells);
 585                                 mapUniqueToSeq.resize(numSeqs);
 586                                 mapSeqToUnique.resize(numSeqs);
 587                                 lengths.resize(numSeqs);
 588                                 jointLookUp.resize(NUMBINS * NUMBINS);
 589
 590                                 MPI_Recv(&flowDataIntI[0], numSeqs * numFlowCells, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 591                                 MPI_Recv(&flowDataPrI[0], numSeqs * numFlowCells, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 592                                 MPI_Recv(&mapUniqueToSeq[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 593                                 MPI_Recv(&mapSeqToUnique[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 594                                 MPI_Recv(&lengths[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 595                                 MPI_Recv(&jointLookUp[0], NUMBINS * NUMBINS, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 596                                 MPI_Recv(&cutoff, 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 597
 598                                 flowFileName = string(fileName);
 599                                 int flowDistStart = int(sqrt(float(pid)/float(ncpus)) * numUniques);
 600                                 int flowDistEnd = int(sqrt(float(pid+1)/float(ncpus)) * numUniques);
 601
 602                                 string distanceStringChild = flowDistMPI(flowDistStart, flowDistEnd);
 603
 604                                 if (m->control_pressed) { break; }
 605
 606                                 int done = 1;
 607                                 MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 608
 609                                 //Now into the pyronoise part
 610                                 MPI_Recv(&numOTUs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 611
 612                                 singleLookUp.resize(HOMOPS * NUMBINS);
 613                                 uniqueFlowgrams.resize(numUniques * numFlowCells);
 614                                 weight.resize(numOTUs);
 615                                 centroids.resize(numOTUs);
 616                                 change.resize(numOTUs);
 617                                 dist.assign(numOTUs * numSeqs, 0);
 618                                 nSeqsPerOTU.resize(numOTUs);
 619                                 cumNumSeqs.resize(numOTUs);
 620
 621                                 MPI_Recv(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 622                                 MPI_Recv(&uniqueFlowgrams[0], uniqueFlowgrams.size(), MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 623                                 MPI_Recv(&sigma, 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 624
 625                                 int startOTU = pid * numOTUs / ncpus;
 626                                 int endOTU = (pid + 1) * numOTUs / ncpus;
 627
 628                                 int startSeq = pid * numSeqs / ncpus;
 629                                 int endSeq = (pid + 1) * numSeqs /ncpus;
 630
 631                                 int total;
 632
 633                                 while(live){
 634
 635                                         if (m->control_pressed) { break; }
 636
 637                                         MPI_Recv(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 638                                         singleTau.assign(total, 0.0000);
 639                                         seqNumber.assign(total, 0);
 640                                         seqIndex.assign(total, 0);
 641
 642                                         MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 643                                         MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 644                                         MPI_Recv(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 645                                         MPI_Recv(&seqNumber[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 646                                         MPI_Recv(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 647                                         MPI_Recv(&nSeqsPerOTU[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 648                                         MPI_Recv(&cumNumSeqs[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 649
 650                                         calcCentroidsDriver(startOTU, endOTU);
 651
 652                                         MPI_Send(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD);
 653                                         MPI_Send(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD);
 654
 655                                         MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 656                                         MPI_Recv(&weight[0], numOTUs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 657                                         MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 658
 659                                         vector<int> otuIndex(total, 0);
 660                                         calcNewDistancesChildMPI(startSeq, endSeq, otuIndex);
 661                                         total = otuIndex.size();
 662
 663                                         MPI_Send(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 664                                         MPI_Send(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD);
 665                                         MPI_Send(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
 666                                         MPI_Send(&dist[0], numOTUs * numSeqs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
 667                                         MPI_Send(&otuIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD);
 668
 669                                         MPI_Recv(&live, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 670                                 }
 671                         }
 672                 }
 673
 674                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 675
 676                 MPI_Barrier(MPI_COMM_WORLD);
 677
 678
 679                 if(compositeFASTAFileName != ""){
 680                         outputNames.push_back(compositeFASTAFileName);
 681                         outputNames.push_back(compositeNamesFileName);
 682                 }
 683
 684                 m->mothurOutEndLine();
 685                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 686                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 687                 m->mothurOutEndLine();
 688
 689                 return 0;
 690
 691         }
 692         catch(exception& e) {
 693                 m->errorOut(e, "ShhherCommand", "execute");
 694                 exit(1);
 695         }
 696 }
 697
 698 /**************************************************************************************************/
 699
 700 string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
 701         try{
 702                 ostringstream outStream;
 703                 outStream.setf(ios::fixed, ios::floatfield);
 704                 outStream.setf(ios::dec, ios::basefield);
 705                 outStream.setf(ios::showpoint);
 706                 outStream.precision(6);
 707
 708                 int begTime = time(NULL);
 709                 double begClock = clock();
 710
 711                 for(int i=startSeq;i<stopSeq;i++){
 712
 713                         if (m->control_pressed) { break; }
 714
 715                         for(int j=0;j<i;j++){
 716                                 float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
 717
 718                                 if(flowDistance < 1e-6){
 719                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
 720                                 }
 721                                 else if(flowDistance <= cutoff){
 722                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
 723                                 }
 724                         }
 725                         if(i % 100 == 0){
 726                                 m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 727                         }
 728                 }
 729
 730                 string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist";
 731                 if(pid != 0){   fDistFileName += ".temp." + toString(pid);      }
 732
 733                 if (m->control_pressed) { return fDistFileName; }
 734
 735                 m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 736
 737                 ofstream distFile(fDistFileName.c_str());
 738                 distFile << outStream.str();
 739                 distFile.close();
 740
 741                 return fDistFileName;
 742         }
 743         catch(exception& e) {
 744                 m->errorOut(e, "ShhherCommand", "flowDistParentFork");
 745                 exit(1);
 746         }
 747 }
 748
 749 #else
 750 //**********************************************************************************************************************
 751
 752 int ShhherCommand::execute(){
 753         try {
 754                 if (abort == true) { return 0; }
 755
 756                 getSingleLookUp();      if (m->control_pressed) { return 0; }
 757                 getJointLookUp();       if (m->control_pressed) { return 0; }
 758
 759
 760                 vector<string> flowFileVector;
 761                 if(flowFilesFileName != "not found"){
 762                         string fName;
 763
 764                         ifstream flowFilesFile;
 765                         m->openInputFile(flowFilesFileName, flowFilesFile);
 766                         while(flowFilesFile){
 767                                 fName = m->getline(flowFilesFile);
 768                                 flowFileVector.push_back(fName);
 769                                 m->gobble(flowFilesFile);
 770                         }
 771                 }
 772                 else{
 773                         flowFileVector.push_back(flowFileName);
 774                 }
 775                 int numFiles = flowFileVector.size();
 776
 777
 778                 for(int i=0;i<numFiles;i++){
 779
 780                         if (m->control_pressed) { break; }
 781
 782                         flowFileName = flowFileVector[i];
 783
 784                         m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 785                         m->mothurOut("Reading flowgrams...\n");
 786                         getFlowData();
 787
 788                         if (m->control_pressed) { break; }
 789
 790                         m->mothurOut("Identifying unique flowgrams...\n");
 791                         getUniques();
 792
 793                         if (m->control_pressed) { break; }
 794
 795                         m->mothurOut("Calculating distances between flowgrams...\n");
 796                         string distFileName = createDistFile(processors);
 797                         string namesFileName = createNamesFile();
 798
 799                         if (m->control_pressed) { break; }
 800
 801                         m->mothurOut("\nClustering flowgrams...\n");
 802                         string listFileName = cluster(distFileName, namesFileName);
 803
 804                         if (m->control_pressed) { break; }
 805
 806                         getOTUData(listFileName);
 807
 808                         if (m->control_pressed) { break; }
 809
 810                         m->mothurRemove(distFileName);
 811                         m->mothurRemove(namesFileName);
 812                         m->mothurRemove(listFileName);
 813
 814                         initPyroCluster();
 815
 816                         if (m->control_pressed) { break; }
 817
 818                         double maxDelta = 0;
 819                         int iter = 0;
 820
 821                         double begClock = clock();
 822                         unsigned long long begTime = time(NULL);
 823
 824                         m->mothurOut("\nDenoising flowgrams...\n");
 825                         m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 826
 827                         while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 828
 829                                 if (m->control_pressed) { break; }
 830
 831                                 double cycClock = clock();
 832                                 unsigned long long cycTime = time(NULL);
 833                                 fill();
 834
 835                                 if (m->control_pressed) { break; }
 836
 837                                 calcCentroids();
 838
 839                                 if (m->control_pressed) { break; }
 840
 841                                 maxDelta = getNewWeights();  if (m->control_pressed) { break; }
 842                                 double nLL = getLikelihood(); if (m->control_pressed) { break; }
 843                                 checkCentroids();
 844
 845                                 if (m->control_pressed) { break; }
 846
 847                                 calcNewDistances();
 848
 849                                 if (m->control_pressed) { break; }
 850
 851                                 iter++;
 852
 853                                 m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
 854
 855                         }
 856
 857                         if (m->control_pressed) { break; }
 858
 859                         m->mothurOut("\nFinalizing...\n");
 860                         fill();
 861
 862                         if (m->control_pressed) { break; }
 863
 864                         setOTUs();
 865
 866                         if (m->control_pressed) { break; }
 867
 868                         vector<int> otuCounts(numOTUs, 0);
 869                         for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
 870
 871                         calcCentroidsDriver(0, numOTUs);        if (m->control_pressed) { break; }
 872                         writeQualities(otuCounts);                      if (m->control_pressed) { break; }
 873                         writeSequences(otuCounts);                      if (m->control_pressed) { break; }
 874                         writeNames(otuCounts);                          if (m->control_pressed) { break; }
 875                         writeClusters(otuCounts);                       if (m->control_pressed) { break; }
 876                         writeGroups();                                          if (m->control_pressed) { break; }
 877
 878                         m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 879                 }
 880
 881                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
 882
 883
 884                 if(compositeFASTAFileName != ""){
 885                         outputNames.push_back(compositeFASTAFileName);
 886                         outputNames.push_back(compositeNamesFileName);
 887                 }
 888
 889                 m->mothurOutEndLine();
 890                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 891                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 892                 m->mothurOutEndLine();
 893
 894                 return 0;
 895         }
 896         catch(exception& e) {
 897                 m->errorOut(e, "ShhherCommand", "execute");
 898                 exit(1);
 899         }
 900 }
 901 #endif
 902 /**************************************************************************************************/
 903
 904 void ShhherCommand::getFlowData(){
 905         try{
 906                 ifstream flowFile;
 907                 m->openInputFile(flowFileName, flowFile);
 908
 909                 string seqName;
 910                 seqNameVector.clear();
 911                 lengths.clear();
 912                 flowDataIntI.clear();
 913                 nameMap.clear();
 914
 915
 916                 int currentNumFlowCells;
 917
 918                 float intensity;
 919
 920                 flowFile >> numFlowCells;
 921                 int index = 0;//pcluster
 922                 while(!flowFile.eof()){
 923
 924                         if (m->control_pressed) { break; }
 925
 926                         flowFile >> seqName >> currentNumFlowCells;
 927                         lengths.push_back(currentNumFlowCells);
 928
 929                         seqNameVector.push_back(seqName);
 930                         nameMap[seqName] = index++;//pcluster
 931
 932                         for(int i=0;i<numFlowCells;i++){
 933                                 flowFile >> intensity;
 934                                 if(intensity > 9.99)    {       intensity = 9.99;       }
 935                                 int intI = int(100 * intensity + 0.0001);
 936                                 flowDataIntI.push_back(intI);
 937                         }
 938                         m->gobble(flowFile);
 939                 }
 940                 flowFile.close();
 941
 942                 numSeqs = seqNameVector.size();
 943
 944                 for(int i=0;i<numSeqs;i++){
 945
 946                         if (m->control_pressed) { break; }
 947
 948                         int iNumFlowCells = i * numFlowCells;
 949                         for(int j=lengths[i];j<numFlowCells;j++){
 950                                 flowDataIntI[iNumFlowCells + j] = 0;
 951                         }
 952                 }
 953
 954         }
 955         catch(exception& e) {
 956                 m->errorOut(e, "ShhherCommand", "getFlowData");
 957                 exit(1);
 958         }
 959 }
 960
 961 /**************************************************************************************************/
 962
 963 void ShhherCommand::getSingleLookUp(){
 964         try{
 965                 //      these are the -log probabilities that a signal corresponds to a particular homopolymer length
 966                 singleLookUp.assign(HOMOPS * NUMBINS, 0);
 967
 968                 int index = 0;
 969                 ifstream lookUpFile;
 970                 m->openInputFile(lookupFileName, lookUpFile);
 971
 972                 for(int i=0;i<HOMOPS;i++){
 973
 974                         if (m->control_pressed) { break; }
 975
 976                         float logFracFreq;
 977                         lookUpFile >> logFracFreq;
 978
 979                         for(int j=0;j<NUMBINS;j++)      {
 980                                 lookUpFile >> singleLookUp[index];
 981                                 index++;
 982                         }
 983                 }
 984                 lookUpFile.close();
 985         }
 986         catch(exception& e) {
 987                 m->errorOut(e, "ShhherCommand", "getSingleLookUp");
 988                 exit(1);
 989         }
 990 }
 991
 992 /**************************************************************************************************/
 993
 994 void ShhherCommand::getJointLookUp(){
 995         try{
 996
 997                 //      the most likely joint probability (-log) that two intenities have the same polymer length
 998                 jointLookUp.resize(NUMBINS * NUMBINS, 0);
 999
1000                 for(int i=0;i<NUMBINS;i++){
1001
1002                         if (m->control_pressed) { break; }
1003
1004                         for(int j=0;j<NUMBINS;j++){
1005
1006                                 double minSum = 100000000;
1007
1008                                 for(int k=0;k<HOMOPS;k++){
1009                                         double sum = singleLookUp[k * NUMBINS + i] + singleLookUp[k * NUMBINS + j];
1010
1011                                         if(sum < minSum)        {       minSum = sum;           }
1012                                 }
1013                                 jointLookUp[i * NUMBINS + j] = minSum;
1014                         }
1015                 }
1016         }
1017         catch(exception& e) {
1018                 m->errorOut(e, "ShhherCommand", "getJointLookUp");
1019                 exit(1);
1020         }
1021 }
1022
1023 /**************************************************************************************************/
1024
1025 double ShhherCommand::getProbIntensity(int intIntensity){
1026         try{
1027
1028                 double minNegLogProb = 100000000;
1029
1030
1031                 for(int i=0;i<HOMOPS;i++){//loop signal strength
1032
1033                         if (m->control_pressed) { break; }
1034
1035                         float negLogProb = singleLookUp[i * NUMBINS + intIntensity];
1036                         if(negLogProb < minNegLogProb)  {       minNegLogProb = negLogProb; }
1037                 }
1038
1039                 return minNegLogProb;
1040         }
1041         catch(exception& e) {
1042                 m->errorOut(e, "ShhherCommand", "getProbIntensity");
1043                 exit(1);
1044         }
1045 }
1046
1047 /**************************************************************************************************/
1048
1049 void ShhherCommand::getUniques(){
1050         try{
1051
1052
1053                 numUniques = 0;
1054                 uniqueFlowgrams.assign(numFlowCells * numSeqs, -1);
1055                 uniqueCount.assign(numSeqs, 0);                                                 //      anWeights
1056                 uniqueLengths.assign(numSeqs, 0);
1057                 mapSeqToUnique.assign(numSeqs, -1);
1058                 mapUniqueToSeq.assign(numSeqs, -1);
1059
1060                 vector<short> uniqueFlowDataIntI(numFlowCells * numSeqs, -1);
1061
1062                 for(int i=0;i<numSeqs;i++){
1063
1064                         if (m->control_pressed) { break; }
1065
1066                         int index = 0;
1067
1068                         vector<short> current(numFlowCells);
1069                         for(int j=0;j<numFlowCells;j++){
1070                                 current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0));
1071                         }
1072
1073                         for(int j=0;j<numUniques;j++){
1074                                 int offset = j * numFlowCells;
1075                                 bool toEnd = 1;
1076
1077                                 int shorterLength;
1078                                 if(lengths[i] < uniqueLengths[j])       {       shorterLength = lengths[i];                     }
1079                                 else                                                            {       shorterLength = uniqueLengths[j];       }
1080
1081                                 for(int k=0;k<shorterLength;k++){
1082                                         if(current[k] != uniqueFlowgrams[offset + k]){
1083                                                 toEnd = 0;
1084                                                 break;
1085                                         }
1086                                 }
1087
1088                                 if(toEnd){
1089                                         mapSeqToUnique[i] = j;
1090                                         uniqueCount[j]++;
1091                                         index = j;
1092                                         if(lengths[i] > uniqueLengths[j])       {       uniqueLengths[j] = lengths[i];  }
1093                                         break;
1094                                 }
1095                                 index++;
1096                         }
1097
1098                         if(index == numUniques){
1099                                 uniqueLengths[numUniques] = lengths[i];
1100                                 uniqueCount[numUniques] = 1;
1101                                 mapSeqToUnique[i] = numUniques;//anMap
1102                                 mapUniqueToSeq[numUniques] = i;//anF
1103
1104                                 for(int k=0;k<numFlowCells;k++){
1105                                         uniqueFlowgrams[numUniques * numFlowCells + k] = current[k];
1106                                         uniqueFlowDataIntI[numUniques * numFlowCells + k] = flowDataIntI[i * numFlowCells + k];
1107                                 }
1108
1109                                 numUniques++;
1110                         }
1111                 }
1112                 uniqueFlowDataIntI.resize(numFlowCells * numUniques);
1113                 uniqueLengths.resize(numUniques);
1114
1115                 flowDataPrI.resize(numSeqs * numFlowCells, 0);
1116                 for(int i=0;i<flowDataPrI.size();i++)   {       if (m->control_pressed) { break; } flowDataPrI[i] = getProbIntensity(flowDataIntI[i]);          }
1117         }
1118         catch(exception& e) {
1119                 m->errorOut(e, "ShhherCommand", "getUniques");
1120                 exit(1);
1121         }
1122 }
1123
1124 /**************************************************************************************************/
1125
1126 float ShhherCommand::calcPairwiseDist(int seqA, int seqB){
1127         try{
1128                 int minLength = lengths[mapSeqToUnique[seqA]];
1129                 if(lengths[seqB] < minLength){  minLength = lengths[mapSeqToUnique[seqB]];      }
1130
1131                 int ANumFlowCells = seqA * numFlowCells;
1132                 int BNumFlowCells = seqB * numFlowCells;
1133
1134                 float dist = 0;
1135
1136                 for(int i=0;i<minLength;i++){
1137
1138                         if (m->control_pressed) { break; }
1139
1140                         int flowAIntI = flowDataIntI[ANumFlowCells + i];
1141                         float flowAPrI = flowDataPrI[ANumFlowCells + i];
1142
1143                         int flowBIntI = flowDataIntI[BNumFlowCells + i];
1144                         float flowBPrI = flowDataPrI[BNumFlowCells + i];
1145                         dist += jointLookUp[flowAIntI * NUMBINS + flowBIntI] - flowAPrI - flowBPrI;
1146                 }
1147
1148                 dist /= (float) minLength;
1149                 return dist;
1150         }
1151         catch(exception& e) {
1152                 m->errorOut(e, "ShhherCommand", "calcPairwiseDist");
1153                 exit(1);
1154         }
1155 }
1156
1157 /**************************************************************************************************/
1158
1159 void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int stopSeq){
1160         try{
1161
1162                 ostringstream outStream;
1163                 outStream.setf(ios::fixed, ios::floatfield);
1164                 outStream.setf(ios::dec, ios::basefield);
1165                 outStream.setf(ios::showpoint);
1166                 outStream.precision(6);
1167
1168                 int begTime = time(NULL);
1169                 double begClock = clock();
1170
1171                 for(int i=startSeq;i<stopSeq;i++){
1172
1173                         if (m->control_pressed) { break; }
1174
1175                         for(int j=0;j<i;j++){
1176                                 float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
1177
1178                                 if(flowDistance < 1e-6){
1179                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
1180                                 }
1181                                 else if(flowDistance <= cutoff){
1182                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
1183                                 }
1184                         }
1185                         if(i % 100 == 0){
1186                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime));
1187                                 m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
1188                                 m->mothurOutEndLine();
1189                         }
1190                 }
1191
1192                 ofstream distFile(distFileName.c_str());
1193                 distFile << outStream.str();
1194                 distFile.close();
1195
1196                 if (m->control_pressed) {}
1197                 else {
1198                         m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
1199                         m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
1200                         m->mothurOutEndLine();
1201                 }
1202         }
1203         catch(exception& e) {
1204                 m->errorOut(e, "ShhherCommand", "flowDistParentFork");
1205                 exit(1);
1206         }
1207 }
1208
1209 /**************************************************************************************************/
1210
1211 string ShhherCommand::createDistFile(int processors){
1212         try{
1213 //////////////////////// until I figure out the shared memory issue //////////////////////
1214 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1215 #else
1216                 processors=1;
1217 #endif
1218 //////////////////////// until I figure out the shared memory issue //////////////////////
1219
1220                 string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.dist";
1221
1222                 unsigned long long begTime = time(NULL);
1223                 double begClock = clock();
1224
1225                 if (numSeqs < processors){      processors = 1; }
1226
1227                 if(processors == 1)     {       flowDistParentFork(fDistFileName, 0, numUniques);               }
1228
1229                 else{ //you have multiple processors
1230
1231                         vector<int> start(processors, 0);
1232                         vector<int> end(processors, 0);
1233
1234                         int process = 1;
1235                         vector<int> processIDs;
1236
1237                         for (int i = 0; i < processors; i++) {
1238                                 start[i] = int(sqrt(float(i)/float(processors)) * numUniques);
1239                                 end[i] = int(sqrt(float(i+1)/float(processors)) * numUniques);
1240                         }
1241
1242 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1243
1244                         //loop through and create all the processes you want
1245                         while (process != processors) {
1246                                 int pid = fork();
1247
1248                                 if (pid > 0) {
1249                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1250                                         process++;
1251                                 }else if (pid == 0){
1252                                         flowDistParentFork(fDistFileName + toString(getpid()) + ".temp", start[process], end[process]);
1253                                         exit(0);
1254                                 }else {
1255                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1256                                         perror(" : ");
1257                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1258                                         exit(0);
1259                                 }
1260                         }
1261
1262                         //parent does its part
1263                         flowDistParentFork(fDistFileName, start[0], end[0]);
1264
1265                         //force parent to wait until all the processes are done
1266                         for (int i=0;i<processIDs.size();i++) {
1267                                 int temp = processIDs[i];
1268                                 wait(&temp);
1269                         }
1270 #else
1271                         //////////////////////////////////////////////////////////////////////////////////////////////////////
1272                         //Windows version shared memory, so be careful when passing variables through the flowDistParentForkData struct.
1273                         //Above fork() will clone, so memory is separate, but that's not the case with windows,
1274                         //////////////////////////////////////////////////////////////////////////////////////////////////////
1275
1276                         vector<flowDistParentForkData*> pDataArray;
1277                         DWORD   dwThreadIdArray[processors-1];
1278                         HANDLE  hThreadArray[processors-1];
1279
1280                         //Create processor worker threads.
1281                         for(int i = 0; i < processors-1; i++){
1282                                 // Allocate memory for thread data.
1283                                 string extension = extension = toString(i) + ".temp";
1284
1285                                 flowDistParentForkData* tempdist = new flowDistParentForkData((fDistFileName + extension), mapUniqueToSeq, mapSeqToUnique, lengths, flowDataIntI, flowDataPrI, jointLookUp, m, start[i+1], end[i+1], numFlowCells, cutoff, i);
1286                                 pDataArray.push_back(tempdist);
1287                                 processIDs.push_back(i);
1288
1289                                 //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
1290                                 //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1291                                 hThreadArray[i] = CreateThread(NULL, 0, MyflowDistParentForkThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1292                         }
1293
1294                         //parent does its part
1295                         flowDistParentFork(fDistFileName, start[0], end[0]);
1296
1297                         //Wait until all threads have terminated.
1298                         WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1299
1300                         //Close all thread handles and free memory allocations.
1301                         for(int i=0; i < pDataArray.size(); i++){
1302                                 CloseHandle(hThreadArray[i]);
1303                                 delete pDataArray[i];
1304                         }
1305
1306 #endif
1307
1308                         //append and remove temp files
1309                         for (int i=0;i<processIDs.size();i++) {
1310                                 m->appendFiles((fDistFileName + toString(processIDs[i]) + ".temp"), fDistFileName);
1311                                 m->mothurRemove((fDistFileName + toString(processIDs[i]) + ".temp"));
1312                         }
1313
1314                 }
1315
1316                 m->mothurOutEndLine();
1317                 m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
1318
1319                 return fDistFileName;
1320         }
1321         catch(exception& e) {
1322                 m->errorOut(e, "ShhherCommand", "createDistFile");
1323                 exit(1);
1324         }
1325
1326 }
1327
1328 /**************************************************************************************************/
1329
1330 string ShhherCommand::createNamesFile(){
1331         try{
1332
1333                 vector<string> duplicateNames(numUniques, "");
1334                 for(int i=0;i<numSeqs;i++){
1335                         duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
1336                 }
1337
1338                 string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
1339
1340                 ofstream nameFile;
1341                 m->openOutputFile(nameFileName, nameFile);
1342
1343                 for(int i=0;i<numUniques;i++){
1344
1345                         if (m->control_pressed) { break; }
1346
1347 //                      nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
1348                         nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
1349                 }
1350
1351                 nameFile.close();
1352                 return  nameFileName;
1353         }
1354         catch(exception& e) {
1355                 m->errorOut(e, "ShhherCommand", "createNamesFile");
1356                 exit(1);
1357         }
1358 }
1359
1360 //**********************************************************************************************************************
1361
1362 string ShhherCommand::cluster(string distFileName, string namesFileName){
1363         try {
1364
1365                 ReadMatrix* read = new ReadColumnMatrix(distFileName);
1366                 read->setCutoff(cutoff);
1367
1368                 NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
1369                 clusterNameMap->readMap();
1370                 read->read(clusterNameMap);
1371
1372                 ListVector* list = read->getListVector();
1373                 SparseMatrix* matrix = read->getMatrix();
1374
1375                 delete read;
1376                 delete clusterNameMap;
1377
1378                 RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
1379
1380                 Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest");
1381                 string tag = cluster->getTag();
1382
1383                 double clusterCutoff = cutoff;
1384                 while (matrix->getSmallDist() <= clusterCutoff && matrix->getNNodes() > 0){
1385
1386                         if (m->control_pressed) { break; }
1387
1388                         cluster->update(clusterCutoff);
1389                 }
1390
1391                 list->setLabel(toString(cutoff));
1392
1393                 string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.list";
1394                 ofstream listFile;
1395                 m->openOutputFile(listFileName, listFile);
1396                 list->print(listFile);
1397                 listFile.close();
1398
1399                 delete matrix;  delete cluster; delete rabund; delete list;
1400
1401                 return listFileName;
1402         }
1403         catch(exception& e) {
1404                 m->errorOut(e, "ShhherCommand", "cluster");
1405                 exit(1);
1406         }
1407 }
1408
1409 /**************************************************************************************************/
1410
1411 void ShhherCommand::getOTUData(string listFileName){
1412         try {
1413
1414                 ifstream listFile;
1415                 m->openInputFile(listFileName, listFile);
1416                 string label;
1417
1418                 listFile >> label >> numOTUs;
1419
1420                 otuData.assign(numSeqs, 0);
1421                 cumNumSeqs.assign(numOTUs, 0);
1422                 nSeqsPerOTU.assign(numOTUs, 0);
1423                 aaP.clear();aaP.resize(numOTUs);
1424
1425                 seqNumber.clear();
1426                 aaI.clear();
1427                 seqIndex.clear();
1428
1429                 string singleOTU = "";
1430
1431                 for(int i=0;i<numOTUs;i++){
1432
1433                         if (m->control_pressed) { break; }
1434
1435                         listFile >> singleOTU;
1436
1437                         istringstream otuString(singleOTU);
1438
1439                         while(otuString){
1440
1441                                 string seqName = "";
1442
1443                                 for(int j=0;j<singleOTU.length();j++){
1444                                         char letter = otuString.get();
1445
1446                                         if(letter != ','){
1447                                                 seqName += letter;
1448                                         }
1449                                         else{
1450                                                 map<string,int>::iterator nmIt = nameMap.find(seqName);
1451                                                 int index = nmIt->second;
1452
1453                                                 nameMap.erase(nmIt);
1454
1455                                                 otuData[index] = i;
1456                                                 nSeqsPerOTU[i]++;
1457                                                 aaP[i].push_back(index);
1458                                                 seqName = "";
1459                                         }
1460                                 }
1461
1462                                 map<string,int>::iterator nmIt = nameMap.find(seqName);
1463
1464                                 int index = nmIt->second;
1465                                 nameMap.erase(nmIt);
1466
1467                                 otuData[index] = i;
1468                                 nSeqsPerOTU[i]++;
1469                                 aaP[i].push_back(index);
1470
1471                                 otuString.get();
1472                         }
1473
1474                         sort(aaP[i].begin(), aaP[i].end());
1475                         for(int j=0;j<nSeqsPerOTU[i];j++){
1476                                 seqNumber.push_back(aaP[i][j]);
1477                         }
1478                         for(int j=nSeqsPerOTU[i];j<numSeqs;j++){
1479                                 aaP[i].push_back(0);
1480                         }
1481
1482
1483                 }
1484
1485                 for(int i=1;i<numOTUs;i++){
1486                         cumNumSeqs[i] = cumNumSeqs[i-1] + nSeqsPerOTU[i-1];
1487                 }
1488                 aaI = aaP;
1489                 seqIndex = seqNumber;
1490
1491                 listFile.close();
1492
1493         }
1494         catch(exception& e) {
1495                 m->errorOut(e, "ShhherCommand", "getOTUData");
1496                 exit(1);
1497         }
1498 }
1499
1500 /**************************************************************************************************/
1501
1502 void ShhherCommand::initPyroCluster(){
1503         try{
1504
1505                 if (numOTUs < processors) { processors = 1; }
1506
1507                 dist.assign(numSeqs * numOTUs, 0);
1508                 change.assign(numOTUs, 1);
1509                 centroids.assign(numOTUs, -1);
1510                 weight.assign(numOTUs, 0);
1511                 singleTau.assign(numSeqs, 1.0);
1512
1513                 nSeqsBreaks.assign(processors+1, 0);
1514                 nOTUsBreaks.assign(processors+1, 0);
1515
1516                 nSeqsBreaks[0] = 0;
1517                 for(int i=0;i<processors;i++){
1518                         nSeqsBreaks[i+1] = nSeqsBreaks[i] + (int)((double) numSeqs / (double) processors);
1519                         nOTUsBreaks[i+1] = nOTUsBreaks[i] + (int)((double) numOTUs / (double) processors);
1520                 }
1521                 nSeqsBreaks[processors] = numSeqs;
1522                 nOTUsBreaks[processors] = numOTUs;
1523         }
1524         catch(exception& e) {
1525                 m->errorOut(e, "ShhherCommand", "initPyroCluster");
1526                 exit(1);
1527         }
1528 }
1529
1530 /**************************************************************************************************/
1531
1532 void ShhherCommand::fill(){
1533         try {
1534                 int index = 0;
1535                 for(int i=0;i<numOTUs;i++){
1536
1537                         if (m->control_pressed) { break; }
1538
1539                         cumNumSeqs[i] = index;
1540                         for(int j=0;j<nSeqsPerOTU[i];j++){
1541                                 seqNumber[index] = aaP[i][j];
1542                                 seqIndex[index] = aaI[i][j];
1543
1544                                 index++;
1545                         }
1546                 }
1547         }
1548         catch(exception& e) {
1549                 m->errorOut(e, "ShhherCommand", "fill");
1550                 exit(1);
1551         }
1552 }
1553
1554 /**************************************************************************************************/
1555
1556 void ShhherCommand::calcCentroids(){
1557         try{
1558
1559 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1560
1561                 if(processors == 1)     {
1562                         calcCentroidsDriver(0, numOTUs);
1563                 }
1564                 else{ //you have multiple processors
1565                         if (numOTUs < processors){      processors = 1; }
1566
1567                         int process = 1;
1568                         vector<int> processIDs;
1569
1570                         //loop through and create all the processes you want
1571                         while (process != processors) {
1572                                 int pid = vfork();
1573
1574                                 if (pid > 0) {
1575                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1576                                         process++;
1577                                 }else if (pid == 0){
1578                                         calcCentroidsDriver(nOTUsBreaks[process], nOTUsBreaks[process+1]);
1579                                         exit(0);
1580                                 }else {
1581                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1582                                         perror(" : ");
1583                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1584                                         exit(0);
1585                                 }
1586                         }
1587
1588                         //parent does its part
1589                         calcCentroidsDriver(nOTUsBreaks[0], nOTUsBreaks[1]);
1590
1591                         //force parent to wait until all the processes are done
1592                         for (int i=0;i<processIDs.size();i++) {
1593                                 int temp = processIDs[i];
1594                                 wait(&temp);
1595                         }
1596                 }
1597
1598 #else
1599                 calcCentroidsDriver(0, numOTUs);
1600 #endif
1601         }
1602         catch(exception& e) {
1603                 m->errorOut(e, "ShhherCommand", "calcCentroidsDriver");
1604                 exit(1);
1605         }
1606 }
1607
1608 /**************************************************************************************************/
1609
1610 void ShhherCommand::calcCentroidsDriver(int start, int finish){
1611
1612         //this function gets the most likely homopolymer length at a flow position for a group of sequences
1613         //within an otu
1614
1615         try{
1616
1617                 for(int i=start;i<finish;i++){
1618
1619                         if (m->control_pressed) { break; }
1620
1621                         double count = 0;
1622                         int position = 0;
1623                         int minFlowGram = 100000000;
1624                         double minFlowValue = 1e8;
1625                         change[i] = 0; //FALSE
1626
1627                         for(int j=0;j<nSeqsPerOTU[i];j++){
1628                                 count += singleTau[seqNumber[cumNumSeqs[i] + j]];
1629                         }
1630
1631                         if(nSeqsPerOTU[i] > 0 && count > MIN_COUNT){
1632                                 vector<double> adF(nSeqsPerOTU[i]);
1633                                 vector<int> anL(nSeqsPerOTU[i]);
1634
1635                                 for(int j=0;j<nSeqsPerOTU[i];j++){
1636                                         int index = cumNumSeqs[i] + j;
1637                                         int nI = seqIndex[index];
1638                                         int nIU = mapSeqToUnique[nI];
1639
1640                                         int k;
1641                                         for(k=0;k<position;k++){
1642                                                 if(nIU == anL[k]){
1643                                                         break;
1644                                                 }
1645                                         }
1646                                         if(k == position){
1647                                                 anL[position] = nIU;
1648                                                 adF[position] = 0.0000;
1649                                                 position++;
1650                                         }
1651                                 }
1652
1653                                 for(int j=0;j<nSeqsPerOTU[i];j++){
1654                                         int index = cumNumSeqs[i] + j;
1655                                         int nI = seqIndex[index];
1656
1657                                         double tauValue = singleTau[seqNumber[index]];
1658
1659                                         for(int k=0;k<position;k++){
1660                                                 double dist = getDistToCentroid(anL[k], nI, lengths[nI]);
1661                                                 adF[k] += dist * tauValue;
1662                                         }
1663                                 }
1664
1665                                 for(int j=0;j<position;j++){
1666                                         if(adF[j] < minFlowValue){
1667                                                 minFlowGram = j;
1668                                                 minFlowValue = adF[j];
1669                                         }
1670                                 }
1671
1672                                 if(centroids[i] != anL[minFlowGram]){
1673                                         change[i] = 1;
1674                                         centroids[i] = anL[minFlowGram];
1675                                 }
1676                         }
1677                         else if(centroids[i] != -1){
1678                                 change[i] = 1;
1679                                 centroids[i] = -1;
1680                         }
1681                 }
1682         }
1683         catch(exception& e) {
1684                 m->errorOut(e, "ShhherCommand", "calcCentroidsDriver");
1685                 exit(1);
1686         }
1687 }
1688
1689 /**************************************************************************************************/
1690
1691 double ShhherCommand::getDistToCentroid(int cent, int flow, int length){
1692         try{
1693
1694                 int flowAValue = cent * numFlowCells;
1695                 int flowBValue = flow * numFlowCells;
1696
1697                 double dist = 0;
1698
1699                 for(int i=0;i<length;i++){
1700                         dist += singleLookUp[uniqueFlowgrams[flowAValue] * NUMBINS + flowDataIntI[flowBValue]];
1701                         flowAValue++;
1702                         flowBValue++;
1703                 }
1704
1705                 return dist / (double)length;
1706         }
1707         catch(exception& e) {
1708                 m->errorOut(e, "ShhherCommand", "getDistToCentroid");
1709                 exit(1);
1710         }
1711 }
1712
1713 /**************************************************************************************************/
1714
1715 double ShhherCommand::getNewWeights(){
1716         try{
1717
1718                 double maxChange = 0;
1719
1720                 for(int i=0;i<numOTUs;i++){
1721
1722                         if (m->control_pressed) { break; }
1723
1724                         double difference = weight[i];
1725                         weight[i] = 0;
1726
1727                         for(int j=0;j<nSeqsPerOTU[i];j++){
1728                                 int index = cumNumSeqs[i] + j;
1729                                 double tauValue = singleTau[seqNumber[index]];
1730                                 weight[i] += tauValue;
1731                         }
1732
1733                         difference = fabs(weight[i] - difference);
1734                         if(difference > maxChange){     maxChange = difference; }
1735                 }
1736                 return maxChange;
1737         }
1738         catch(exception& e) {
1739                 m->errorOut(e, "ShhherCommand", "getNewWeights");
1740                 exit(1);
1741         }
1742 }
1743
1744 /**************************************************************************************************/
1745
1746 double ShhherCommand::getLikelihood(){
1747
1748         try{
1749
1750                 vector<long double> P(numSeqs, 0);
1751                 int effNumOTUs = 0;
1752
1753                 for(int i=0;i<numOTUs;i++){
1754                         if(weight[i] > MIN_WEIGHT){
1755                                 effNumOTUs++;
1756                         }
1757                 }
1758
1759                 string hold;
1760                 for(int i=0;i<numOTUs;i++){
1761
1762                         if (m->control_pressed) { break; }
1763
1764                         for(int j=0;j<nSeqsPerOTU[i];j++){
1765                                 int index = cumNumSeqs[i] + j;
1766                                 int nI = seqIndex[index];
1767                                 double singleDist = dist[seqNumber[index]];
1768
1769                                 P[nI] += weight[i] * exp(-singleDist * sigma);
1770                         }
1771                 }
1772                 double nLL = 0.00;
1773                 for(int i=0;i<numSeqs;i++){
1774                         if(P[i] == 0){  P[i] = DBL_EPSILON;     }
1775
1776                         nLL += -log(P[i]);
1777                 }
1778
1779                 nLL = nLL -(double)numSeqs * log(sigma);
1780
1781                 return nLL;
1782         }
1783         catch(exception& e) {
1784                 m->errorOut(e, "ShhherCommand", "getNewWeights");
1785                 exit(1);
1786         }
1787 }
1788
1789 /**************************************************************************************************/
1790
1791 void ShhherCommand::checkCentroids(){
1792         try{
1793                 vector<int> unique(numOTUs, 1);
1794
1795                 for(int i=0;i<numOTUs;i++){
1796                         if(centroids[i] == -1 || weight[i] < MIN_WEIGHT){
1797                                 unique[i] = -1;
1798                         }
1799                 }
1800
1801                 for(int i=0;i<numOTUs;i++){
1802
1803                         if (m->control_pressed) { break; }
1804
1805                         if(unique[i] == 1){
1806                                 for(int j=i+1;j<numOTUs;j++){
1807                                         if(unique[j] == 1){
1808
1809                                                 if(centroids[j] == centroids[i]){
1810                                                         unique[j] = 0;
1811                                                         centroids[j] = -1;
1812
1813                                                         weight[i] += weight[j];
1814                                                         weight[j] = 0.0;
1815                                                 }
1816                                         }
1817                                 }
1818                         }
1819                 }
1820         }
1821         catch(exception& e) {
1822                 m->errorOut(e, "ShhherCommand", "checkCentroids");
1823                 exit(1);
1824         }
1825 }
1826
1827 /**************************************************************************************************/
1828
1829 void ShhherCommand::calcNewDistances(){
1830         try{
1831
1832 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1833
1834                 if(processors == 1)     {
1835                         calcNewDistancesParent(0, numSeqs);
1836                 }
1837                 else{ //you have multiple processors
1838                         if (numSeqs < processors){      processors = 1; }
1839
1840                         vector<vector<int> > child_otuIndex(processors);
1841                         vector<vector<int> > child_seqIndex(processors);
1842                         vector<vector<double> > child_singleTau(processors);
1843                         vector<int> totals(processors);
1844
1845                         int process = 1;
1846                         vector<int> processIDs;
1847
1848                         //loop through and create all the processes you want
1849                         while (process != processors) {
1850                                 int pid = vfork();
1851
1852                                 if (pid > 0) {
1853                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1854                                         process++;
1855                                 }else if (pid == 0){
1856                                         calcNewDistancesChild(nSeqsBreaks[process], nSeqsBreaks[process+1], child_otuIndex[process], child_seqIndex[process], child_singleTau[process]);
1857                                         totals[process] = child_otuIndex[process].size();
1858
1859                                         exit(0);
1860                                 }else {
1861                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1862                                         perror(" : ");
1863                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1864                                         exit(0);
1865                                 }
1866                         }
1867
1868                         //parent does its part
1869                         calcNewDistancesParent(nSeqsBreaks[0], nSeqsBreaks[1]);
1870                         int total = seqIndex.size();
1871
1872                         //force parent to wait until all the processes are done
1873                         for (int i=0;i<processIDs.size();i++) {
1874                                 int temp = processIDs[i];
1875                                 wait(&temp);
1876                         }
1877
1878                         for(int i=1;i<processors;i++){
1879                                 int oldTotal = total;
1880                                 total += totals[i];
1881
1882                                 singleTau.resize(total, 0);
1883                                 seqIndex.resize(total, 0);
1884                                 seqNumber.resize(total, 0);
1885
1886                                 int childIndex = 0;
1887
1888                                 for(int j=oldTotal;j<total;j++){
1889                                         int otuI = child_otuIndex[i][childIndex];
1890                                         int seqI = child_seqIndex[i][childIndex];
1891
1892                                         singleTau[j] = child_singleTau[i][childIndex];
1893                                         aaP[otuI][nSeqsPerOTU[otuI]] = j;
1894                                         aaI[otuI][nSeqsPerOTU[otuI]] = seqI;
1895                                         nSeqsPerOTU[otuI]++;
1896
1897                                         childIndex++;
1898                                 }
1899                         }
1900                 }
1901 #else
1902                 calcNewDistancesParent(0, numSeqs);
1903 #endif
1904         }
1905         catch(exception& e) {
1906                 m->errorOut(e, "ShhherCommand", "calcNewDistances");
1907                 exit(1);
1908         }
1909 }
1910
1911 /**************************************************************************************************/
1912 #ifdef USE_MPI
1913 void ShhherCommand::calcNewDistancesChildMPI(int startSeq, int stopSeq, vector<int>& otuIndex){
1914
1915         try{
1916                 vector<double> newTau(numOTUs,0);
1917                 vector<double> norms(numSeqs, 0);
1918                 otuIndex.clear();
1919                 seqIndex.clear();
1920                 singleTau.clear();
1921
1922                 for(int i=startSeq;i<stopSeq;i++){
1923
1924                         if (m->control_pressed) { break; }
1925
1926                         double offset = 1e8;
1927                         int indexOffset = i * numOTUs;
1928
1929                         for(int j=0;j<numOTUs;j++){
1930
1931                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1932                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1933                                 }
1934                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1935                                         offset = dist[indexOffset + j];
1936                                 }
1937                         }
1938
1939                         for(int j=0;j<numOTUs;j++){
1940                                 if(weight[j] > MIN_WEIGHT){
1941                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1942                                         norms[i] += newTau[j];
1943                                 }
1944                                 else{
1945                                         newTau[j] = 0.0;
1946                                 }
1947                         }
1948
1949                         for(int j=0;j<numOTUs;j++){
1950
1951                                 newTau[j] /= norms[i];
1952
1953                                 if(newTau[j] > MIN_TAU){
1954                                         otuIndex.push_back(j);
1955                                         seqIndex.push_back(i);
1956                                         singleTau.push_back(newTau[j]);
1957                                 }
1958                         }
1959
1960                 }
1961         }
1962         catch(exception& e) {
1963                 m->errorOut(e, "ShhherCommand", "calcNewDistancesChildMPI");
1964                 exit(1);
1965         }
1966 }
1967 #endif
1968 /**************************************************************************************************/
1969
1970 void ShhherCommand::calcNewDistancesChild(int startSeq, int stopSeq, vector<int>& child_otuIndex, vector<int>& child_seqIndex, vector<double>& child_singleTau){
1971
1972         try{
1973                 vector<double> newTau(numOTUs,0);
1974                 vector<double> norms(numSeqs, 0);
1975                 child_otuIndex.resize(0);
1976                 child_seqIndex.resize(0);
1977                 child_singleTau.resize(0);
1978
1979                 for(int i=startSeq;i<stopSeq;i++){
1980
1981                         if (m->control_pressed) { break; }
1982
1983                         double offset = 1e8;
1984                         int indexOffset = i * numOTUs;
1985
1986
1987                         for(int j=0;j<numOTUs;j++){
1988                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1989                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1990                                 }
1991
1992                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1993                                         offset = dist[indexOffset + j];
1994                                 }
1995                         }
1996
1997                         for(int j=0;j<numOTUs;j++){
1998                                 if(weight[j] > MIN_WEIGHT){
1999                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
2000                                         norms[i] += newTau[j];
2001                                 }
2002                                 else{
2003                                         newTau[j] = 0.0;
2004                                 }
2005                         }
2006
2007                         for(int j=0;j<numOTUs;j++){
2008                                 newTau[j] /= norms[i];
2009
2010                                 if(newTau[j] > MIN_TAU){
2011                                         child_otuIndex.push_back(j);
2012                                         child_seqIndex.push_back(i);
2013                                         child_singleTau.push_back(newTau[j]);
2014                                 }
2015                         }
2016                 }
2017         }
2018         catch(exception& e) {
2019                 m->errorOut(e, "ShhherCommand", "calcNewDistancesChild");
2020                 exit(1);
2021         }
2022 }
2023
2024 /**************************************************************************************************/
2025
2026 void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){
2027
2028         try{
2029
2030                 int total = 0;
2031                 vector<double> newTau(numOTUs,0);
2032                 vector<double> norms(numSeqs, 0);
2033                 nSeqsPerOTU.assign(numOTUs, 0);
2034
2035                 for(int i=startSeq;i<stopSeq;i++){
2036
2037                         if (m->control_pressed) { break; }
2038
2039                         int indexOffset = i * numOTUs;
2040
2041                         double offset = 1e8;
2042
2043                         for(int j=0;j<numOTUs;j++){
2044
2045                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
2046                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
2047                                 }
2048
2049                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
2050                                         offset = dist[indexOffset + j];
2051                                 }
2052                         }
2053
2054                         for(int j=0;j<numOTUs;j++){
2055                                 if(weight[j] > MIN_WEIGHT){
2056                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
2057                                         norms[i] += newTau[j];
2058                                 }
2059                                 else{
2060                                         newTau[j] = 0.0;
2061                                 }
2062                         }
2063
2064                         for(int j=0;j<numOTUs;j++){
2065                                 newTau[j] /= norms[i];
2066                         }
2067
2068                         for(int j=0;j<numOTUs;j++){
2069                                 if(newTau[j] > MIN_TAU){
2070
2071                                         int oldTotal = total;
2072
2073                                         total++;
2074
2075                                         singleTau.resize(total, 0);
2076                                         seqNumber.resize(total, 0);
2077                                         seqIndex.resize(total, 0);
2078
2079                                         singleTau[oldTotal] = newTau[j];
2080
2081                                         aaP[j][nSeqsPerOTU[j]] = oldTotal;
2082                                         aaI[j][nSeqsPerOTU[j]] = i;
2083                                         nSeqsPerOTU[j]++;
2084                                 }
2085                         }
2086
2087                 }
2088
2089         }
2090         catch(exception& e) {
2091                 m->errorOut(e, "ShhherCommand", "calcNewDistancesParent");
2092                 exit(1);
2093         }
2094 }
2095
2096 /**************************************************************************************************/
2097
2098 void ShhherCommand::setOTUs(){
2099
2100         try {
2101                 vector<double> bigTauMatrix(numOTUs * numSeqs, 0.0000);
2102
2103                 for(int i=0;i<numOTUs;i++){
2104
2105                         if (m->control_pressed) { break; }
2106
2107                         for(int j=0;j<nSeqsPerOTU[i];j++){
2108                                 int index = cumNumSeqs[i] + j;
2109                                 double tauValue = singleTau[seqNumber[index]];
2110                                 int sIndex = seqIndex[index];
2111                                 bigTauMatrix[sIndex * numOTUs + i] = tauValue;
2112                         }
2113                 }
2114
2115                 for(int i=0;i<numSeqs;i++){
2116                         double maxTau = -1.0000;
2117                         int maxOTU = -1;
2118                         for(int j=0;j<numOTUs;j++){
2119                                 if(bigTauMatrix[i * numOTUs + j] > maxTau){
2120                                         maxTau = bigTauMatrix[i * numOTUs + j];
2121                                         maxOTU = j;
2122                                 }
2123                         }
2124
2125                         otuData[i] = maxOTU;
2126                 }
2127
2128                 nSeqsPerOTU.assign(numOTUs, 0);
2129
2130                 for(int i=0;i<numSeqs;i++){
2131                         int index = otuData[i];
2132
2133                         singleTau[i] = 1.0000;
2134                         dist[i] = 0.0000;
2135
2136                         aaP[index][nSeqsPerOTU[index]] = i;
2137                         aaI[index][nSeqsPerOTU[index]] = i;
2138
2139                         nSeqsPerOTU[index]++;
2140                 }
2141                 fill();
2142         }
2143         catch(exception& e) {
2144                 m->errorOut(e, "ShhherCommand", "calcNewDistances");
2145                 exit(1);
2146         }
2147 }
2148
2149 /**************************************************************************************************/
2150
2151 void ShhherCommand::writeQualities(vector<int> otuCounts){
2152
2153         try {
2154                 string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
2155
2156                 ofstream qualityFile;
2157                 m->openOutputFile(qualityFileName, qualityFile);
2158
2159                 qualityFile.setf(ios::fixed, ios::floatfield);
2160                 qualityFile.setf(ios::showpoint);
2161                 qualityFile << setprecision(6);
2162
2163                 vector<vector<int> > qualities(numOTUs);
2164                 vector<double> pr(HOMOPS, 0);
2165
2166
2167                 for(int i=0;i<numOTUs;i++){
2168
2169                         if (m->control_pressed) { break; }
2170
2171                         int index = 0;
2172                         int base = 0;
2173
2174                         if(nSeqsPerOTU[i] > 0){
2175                                 qualities[i].assign(1024, -1);
2176
2177                                 while(index < numFlowCells){
2178                                         double maxPrValue = 1e8;
2179                                         short maxPrIndex = -1;
2180                                         double count = 0.0000;
2181
2182                                         pr.assign(HOMOPS, 0);
2183
2184                                         for(int j=0;j<nSeqsPerOTU[i];j++){
2185                                                 int lIndex = cumNumSeqs[i] + j;
2186                                                 double tauValue = singleTau[seqNumber[lIndex]];
2187                                                 int sequenceIndex = aaI[i][j];
2188                                                 short intensity = flowDataIntI[sequenceIndex * numFlowCells + index];
2189
2190                                                 count += tauValue;
2191
2192                                                 for(int s=0;s<HOMOPS;s++){
2193                                                         pr[s] += tauValue * singleLookUp[s * NUMBINS + intensity];
2194                                                 }
2195                                         }
2196
2197                                         maxPrIndex = uniqueFlowgrams[centroids[i] * numFlowCells + index];
2198                                         maxPrValue = pr[maxPrIndex];
2199
2200                                         if(count > MIN_COUNT){
2201                                                 double U = 0.0000;
2202                                                 double norm = 0.0000;
2203
2204                                                 for(int s=0;s<HOMOPS;s++){
2205                                                         norm += exp(-(pr[s] - maxPrValue));
2206                                                 }
2207
2208                                                 for(int s=1;s<=maxPrIndex;s++){
2209                                                         int value = 0;
2210                                                         double temp = 0.0000;
2211
2212                                                         U += exp(-(pr[s-1]-maxPrValue))/norm;
2213
2214                                                         if(U>0.00){
2215                                                                 temp = log10(U);
2216                                                         }
2217                                                         else{
2218                                                                 temp = -10.1;
2219                                                         }
2220                                                         temp = floor(-10 * temp);
2221                                                         value = (int)floor(temp);
2222                                                         if(value > 100){        value = 100;    }
2223
2224                                                         qualities[i][base] = (int)value;
2225                                                         base++;
2226                                                 }
2227                                         }
2228
2229                                         index++;
2230                                 }
2231                         }
2232
2233
2234                         if(otuCounts[i] > 0){
2235                                 qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
2236
2237                                 int j=4;        //need to get past the first four bases
2238                                 while(qualities[i][j] != -1){
2239                                         qualityFile << qualities[i][j] << ' ';
2240                                         j++;
2241                                 }
2242                                 qualityFile << endl;
2243                         }
2244                 }
2245                 qualityFile.close();
2246                 outputNames.push_back(qualityFileName);
2247
2248         }
2249         catch(exception& e) {
2250                 m->errorOut(e, "ShhherCommand", "writeQualities");
2251                 exit(1);
2252         }
2253 }
2254
2255 /**************************************************************************************************/
2256
2257 void ShhherCommand::writeSequences(vector<int> otuCounts){
2258         try {
2259
2260                 string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
2261                 ofstream fastaFile;
2262                 m->openOutputFile(fastaFileName, fastaFile);
2263
2264                 vector<string> names(numOTUs, "");
2265
2266                 for(int i=0;i<numOTUs;i++){
2267
2268                         if (m->control_pressed) { break; }
2269
2270                         int index = centroids[i];
2271
2272                         if(otuCounts[i] > 0){
2273                                 fastaFile << '>' << seqNameVector[aaI[i][0]] << endl;
2274
2275                                 string newSeq = "";
2276
2277                                 for(int j=0;j<numFlowCells;j++){
2278
2279                                         char base = flowOrder[j % 4];
2280                                         for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
2281                                                 newSeq += base;
2282                                         }
2283                                 }
2284
2285                                 fastaFile << newSeq.substr(4) << endl;
2286                         }
2287                 }
2288                 fastaFile.close();
2289
2290                 outputNames.push_back(fastaFileName);
2291
2292                 if(compositeFASTAFileName != ""){
2293                         m->appendFiles(fastaFileName, compositeFASTAFileName);
2294                 }
2295         }
2296         catch(exception& e) {
2297                 m->errorOut(e, "ShhherCommand", "writeSequences");
2298                 exit(1);
2299         }
2300 }
2301
2302 /**************************************************************************************************/
2303
2304 void ShhherCommand::writeNames(vector<int> otuCounts){
2305         try {
2306                 string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
2307                 ofstream nameFile;
2308                 m->openOutputFile(nameFileName, nameFile);
2309
2310                 for(int i=0;i<numOTUs;i++){
2311
2312                         if (m->control_pressed) { break; }
2313
2314                         if(otuCounts[i] > 0){
2315                                 nameFile << seqNameVector[aaI[i][0]] << '\t' << seqNameVector[aaI[i][0]];
2316
2317                                 for(int j=1;j<nSeqsPerOTU[i];j++){
2318                                         nameFile << ',' << seqNameVector[aaI[i][j]];
2319                                 }
2320
2321                                 nameFile << endl;
2322                         }
2323                 }
2324                 nameFile.close();
2325                 outputNames.push_back(nameFileName);
2326
2327
2328                 if(compositeNamesFileName != ""){
2329                         m->appendFiles(nameFileName, compositeNamesFileName);
2330                 }
2331         }
2332         catch(exception& e) {
2333                 m->errorOut(e, "ShhherCommand", "writeNames");
2334                 exit(1);
2335         }
2336 }
2337
2338 /**************************************************************************************************/
2339
2340 void ShhherCommand::writeGroups(){
2341         try {
2342                 string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
2343                 string groupFileName = fileRoot + ".shhh.groups";
2344                 ofstream groupFile;
2345                 m->openOutputFile(groupFileName, groupFile);
2346
2347                 for(int i=0;i<numSeqs;i++){
2348                         if (m->control_pressed) { break; }
2349                         groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
2350                 }
2351                 groupFile.close();
2352                 outputNames.push_back(groupFileName);
2353
2354         }
2355         catch(exception& e) {
2356                 m->errorOut(e, "ShhherCommand", "writeGroups");
2357                 exit(1);
2358         }
2359 }
2360
2361 /**************************************************************************************************/
2362
2363 void ShhherCommand::writeClusters(vector<int> otuCounts){
2364         try {
2365                 string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
2366                 ofstream otuCountsFile;
2367                 m->openOutputFile(otuCountsFileName, otuCountsFile);
2368
2369                 string bases = flowOrder;
2370
2371                 for(int i=0;i<numOTUs;i++){
2372
2373                         if (m->control_pressed) {
2374                                 break;
2375                         }
2376                         //output the translated version of the centroid sequence for the otu
2377                         if(otuCounts[i] > 0){
2378                                 int index = centroids[i];
2379
2380                                 otuCountsFile << "ideal\t";
2381                                 for(int j=8;j<numFlowCells;j++){
2382                                         char base = bases[j % 4];
2383                                         for(int s=0;s<uniqueFlowgrams[index * numFlowCells + j];s++){
2384                                                 otuCountsFile << base;
2385                                         }
2386                                 }
2387                                 otuCountsFile << endl;
2388
2389                                 for(int j=0;j<nSeqsPerOTU[i];j++){
2390                                         int sequence = aaI[i][j];
2391                                         otuCountsFile << seqNameVector[sequence] << '\t';
2392
2393                                         string newSeq = "";
2394
2395                                         for(int k=0;k<lengths[sequence];k++){
2396                                                 char base = bases[k % 4];
2397                                                 int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
2398
2399                                                 for(int s=0;s<freq;s++){
2400                                                         newSeq += base;
2401                                                         //otuCountsFile << base;
2402                                                 }
2403                                         }
2404                                         otuCountsFile << newSeq.substr(4) << endl;
2405                                 }
2406                                 otuCountsFile << endl;
2407                         }
2408                 }
2409                 otuCountsFile.close();
2410                 outputNames.push_back(otuCountsFileName);
2411
2412         }
2413         catch(exception& e) {
2414                 m->errorOut(e, "ShhherCommand", "writeClusters");
2415                 exit(1);
2416         }
2417 }
2418
2419 //**********************************************************************************************************************