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
  23 #define NUMBINS 1000
  24 #define HOMOPS 10
  25 #define MIN_COUNT 0.1
  26 #define MIN_WEIGHT 0.1
  27 #define MIN_TAU 0.0001
  28 #define MIN_ITER 10
  29
  30 //**********************************************************************************************************************
  31
  32 vector<string> ShhherCommand::getValidParameters(){
  33         try {
  34                 string Array[] =  {
  35                         "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"
  36                 };
  37
  38                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "ShhherCommand", "getValidParameters");
  43                 exit(1);
  44         }
  45 }
  46
  47 //**********************************************************************************************************************
  48
  49 ShhherCommand::ShhherCommand(){
  50         try {
  51                 abort = true; calledHelp = true;
  52
  53                 //initialize outputTypes
  54                 vector<string> tempOutNames;
  55                 outputTypes["pn.dist"] = tempOutNames;
  56
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "ShhherCommand", "ShhherCommand");
  60                 exit(1);
  61         }
  62 }
  63
  64 //**********************************************************************************************************************
  65
  66 vector<string> ShhherCommand::getRequiredParameters(){
  67         try {
  68                 string Array[] =  {"flow"};
  69                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  70                 return myArray;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "ShhherCommand", "getRequiredParameters");
  74                 exit(1);
  75         }
  76 }
  77
  78 //**********************************************************************************************************************
  79
  80 vector<string> ShhherCommand::getRequiredFiles(){
  81         try {
  82                 vector<string> myArray;
  83                 return myArray;
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "ShhherCommand", "getRequiredFiles");
  87                 exit(1);
  88         }
  89 }
  90
  91 //**********************************************************************************************************************
  92
  93 ShhherCommand::ShhherCommand(string option) {
  94         try {
  95
  96 #ifdef USE_MPI
  97                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
  98                 MPI_Comm_size(MPI_COMM_WORLD, &ncpus);
  99
 100                 if(pid == 0){
 101 #endif
 102
 103
 104                 abort = false; calledHelp = false;
 105
 106
 107                 //allow user to run help
 108                 if(option == "help") { help(); abort = true; calledHelp = true; }
 109
 110                 else {
 111
 112                         //valid paramters for this command
 113                         string AlignArray[] =  {
 114                                 "file", "flow", "lookup", "cutoff", "sigma", "outputdir","inputdir", "processors", "maxiter", "mindelta"
 115                         };
 116
 117                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
 118
 119                         OptionParser parser(option);
 120                         map<string,string> parameters = parser.getParameters();
 121
 122                         ValidParameters validParameter;
 123                         map<string,string>::iterator it;
 124
 125                         //check to make sure all parameters are valid for command
 126                         for (it = parameters.begin(); it != parameters.end(); it++) {
 127                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 128                         }
 129
 130                         //initialize outputTypes
 131                         vector<string> tempOutNames;
 132                         outputTypes["pn.dist"] = tempOutNames;
 133                         //                      outputTypes["fasta"] = tempOutNames;
 134
 135                         //if the user changes the input directory command factory will send this info to us in the output parameter
 136                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 137                         if (inputDir == "not found"){   inputDir = "";          }
 138                         else {
 139                                 string path;
 140                                 it = parameters.find("flow");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 146                                 }
 147
 148                                 it = parameters.find("lookup");
 149                                 //user has given a template file
 150                                 if(it != parameters.end()){
 151                                         path = m->hasPath(it->second);
 152                                         //if the user has not given a path then, add inputdir. else leave path alone.
 153                                         if (path == "") {       parameters["lookup"] = inputDir + it->second;           }
 154                                 }
 155
 156                                 it = parameters.find("file");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 162                                 }
 163                         }
 164
 165
 166                         //check for required parameters
 167                         flowFileName = validParameter.validFile(parameters, "flow", true);
 168                         flowFilesFileName = validParameter.validFile(parameters, "file", true);
 169                         if (flowFileName == "not found" && flowFilesFileName == "not found") {
 170                                 m->mothurOut("values for either flow or file must be provided for the shhh.seqs command.");
 171                                 m->mothurOutEndLine();
 172                                 abort = true;
 173                         }
 174                         else if (flowFileName == "not open" || flowFilesFileName == "not open") { abort = true; }
 175
 176                         if(flowFileName != "not found"){        compositeFASTAFileName = "";    }
 177                         else{
 178                                 compositeFASTAFileName = flowFilesFileName.substr(0, flowFilesFileName.length()-10) + "pn.fasta";
 179                                 ofstream temp;
 180                                 m->openOutputFile(compositeFASTAFileName, temp);
 181                                 temp.close();
 182                         }
 183
 184                         //if the user changes the output directory command factory will send this info to us in the output parameter
 185                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 186                                 outputDir = "";
 187                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 188                         }
 189
 190
 191                         //check for optional parameter and set defaults
 192                         // ...at some point should added some additional type checking...
 193                         string temp;
 194                         temp = validParameter.validFile(parameters, "lookup", true);
 195                         if (temp == "not found")        {       lookupFileName = "LookUp_Titanium.pat"; }
 196                         else if(temp == "not open")     {       abort = true;                   }
 197                         else                                            {       lookupFileName = temp;  }
 198
 199                         temp = validParameter.validFile(parameters, "processors", false);if (temp == "not found"){      temp = "1";                     }
 200                         convert(temp, processors);
 201
 202                         temp = validParameter.validFile(parameters, "cutoff", false);   if (temp == "not found"){       temp = "0.01";          }
 203                         convert(temp, cutoff);
 204
 205                         temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){       temp = "0.000001";      }
 206                         convert(temp, minDelta);
 207
 208                         temp = validParameter.validFile(parameters, "maxiter", false);  if (temp == "not found"){       temp = "1000";          }
 209                         convert(temp, maxIters);
 210
 211                         temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")    {       temp = "60";            }
 212                         convert(temp, sigma);
 213
 214                         globaldata = GlobalData::getInstance();
 215                 }
 216
 217 #ifdef USE_MPI
 218                 }
 219 #endif
 220
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "ShhherCommand", "ShhherCommand");
 224                 exit(1);
 225         }
 226 }
 227
 228 //**********************************************************************************************************************
 229
 230 ShhherCommand::~ShhherCommand(){}
 231
 232 //**********************************************************************************************************************
 233
 234 void ShhherCommand::help(){
 235         try {
 236                 m->mothurOut("The shhher command reads a file containing flowgrams and creates a file of corrected sequences.\n");
 237         }
 238         catch(exception& e) {
 239                 m->errorOut(e, "ShhherCommand", "help");
 240                 exit(1);
 241         }
 242 }
 243
 244 //**********************************************************************************************************************
 245 #ifdef USE_MPI
 246 int ShhherCommand::execute(){
 247         try {
 248                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 249
 250                 int tag = 1976;
 251                 MPI_Status status;
 252
 253                 double begClock = clock();
 254                 unsigned long int begTime = time(NULL);
 255
 256                 if(pid == 0){
 257
 258                         for(int i=1;i<ncpus;i++){
 259                                 MPI_Send(&abort, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 260                         }
 261                         if(abort == 1){ return 0;       }
 262
 263                         processors = ncpus;
 264
 265                         m->mothurOut("\nGetting preliminary data...\n");
 266                         getSingleLookUp();
 267                         getJointLookUp();
 268
 269                         vector<string> flowFileVector;
 270                         if(flowFilesFileName != "not found"){
 271                                 string fName;
 272
 273                                 ifstream flowFilesFile;
 274                                 m->openInputFile(flowFilesFileName, flowFilesFile);
 275                                 while(flowFilesFile){
 276                                         flowFilesFile >> fName;
 277                                         flowFileVector.push_back(fName);
 278                                         m->gobble(flowFilesFile);
 279                                 }
 280                         }
 281                         else{
 282                                 flowFileVector.push_back(flowFileName);
 283                         }
 284                         int numFiles = flowFileVector.size();
 285
 286                         for(int i=1;i<ncpus;i++){
 287                                 MPI_Send(&numFiles, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 288                         }
 289
 290                         for(int i=0;i<numFiles;i++){
 291                                 flowFileName = flowFileVector[i];
 292
 293
 294
 295                                 m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 296                                 m->mothurOut("Reading flowgrams...\n");
 297                                 getFlowData();
 298
 299                                 m->mothurOut("Identifying unique flowgrams...\n");
 300                                 getUniques();
 301
 302                                 m->mothurOut("Calculating distances between flowgrams...\n");
 303                                 char fileName[1024];
 304                                 strcpy(fileName, flowFileName.c_str());
 305
 306                                 for(int i=1;i<ncpus;i++){
 307                                         MPI_Send(&fileName[0], 1024, MPI_CHAR, i, tag, MPI_COMM_WORLD);
 308
 309                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 310                                         MPI_Send(&numUniques, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 311                                         MPI_Send(&numFlowCells, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 312                                         MPI_Send(&flowDataIntI[0], numSeqs * numFlowCells, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 313                                         MPI_Send(&flowDataPrI[0], numSeqs * numFlowCells, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 314                                         MPI_Send(&mapUniqueToSeq[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 315                                         MPI_Send(&mapSeqToUnique[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 316                                         MPI_Send(&lengths[0], numSeqs, MPI_INT, i, tag, MPI_COMM_WORLD);
 317                                         MPI_Send(&jointLookUp[0], NUMBINS * NUMBINS, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 318                                         MPI_Send(&cutoff, 1, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 319                                 }
 320
 321                                 string distFileName = flowDistMPI(0, int(sqrt(1.0/float(ncpus)) * numUniques));
 322
 323                                 int done;
 324                                 for(int i=1;i<ncpus;i++){
 325                                         MPI_Recv(&done, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 326
 327                                         m->appendFiles((distFileName + ".temp." + toString(i)), distFileName);
 328                                         remove((distFileName + ".temp." + toString(i)).c_str());
 329                                 }
 330
 331                                 string namesFileName = createNamesFile();
 332
 333                                 m->mothurOut("\nClustering flowgrams...\n");
 334                                 string listFileName = cluster(distFileName, namesFileName);
 335
 336                                 getOTUData(listFileName);
 337                                 initPyroCluster();
 338
 339                                 for(int i=1;i<ncpus;i++){
 340                                         MPI_Send(&numOTUs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 341                                         MPI_Send(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 342                                         MPI_Send(&uniqueFlowgrams[0], numFlowCells * numUniques, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 343                                         MPI_Send(&sigma, 1, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 344                                 }
 345
 346
 347                                 double maxDelta = 0;
 348                                 int iter = 0;
 349
 350                                 int numOTUsOnCPU = numOTUs / ncpus;
 351                                 int numSeqsOnCPU = numSeqs / ncpus;
 352                                 m->mothurOut("\nDenoising flowgrams...\n");
 353                                 m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 354
 355                                 while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 356
 357                                         double cycClock = clock();
 358                                         unsigned long int cycTime = time(NULL);
 359                                         fill();
 360
 361                                         int total = singleTau.size();
 362                                         for(int i=1;i<ncpus;i++){
 363                                                 MPI_Send(&total, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 364                                                 MPI_Send(&change[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 365                                                 MPI_Send(&centroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 366
 367                                                 MPI_Send(&singleTau[0], total, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 368                                                 MPI_Send(&seqNumber[0], total, MPI_INT, i, tag, MPI_COMM_WORLD);
 369                                                 MPI_Send(&seqIndex[0], total, MPI_INT, i, tag, MPI_COMM_WORLD);
 370                                                 MPI_Send(&nSeqsPerOTU[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 371                                                 MPI_Send(&cumNumSeqs[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 372                                         }
 373
 374                                         calcCentroidsDriver(0, numOTUsOnCPU);
 375
 376                                         for(int i=1;i<ncpus;i++){
 377                                                 int otuStart = i * numOTUs / ncpus;
 378                                                 int otuStop = (i + 1) * numOTUs / ncpus;
 379
 380                                                 vector<int> tempCentroids(numOTUs, 0);
 381                                                 vector<short> tempChange(numOTUs, 0);
 382
 383                                                 MPI_Recv(&tempCentroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 384                                                 MPI_Recv(&tempChange[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD, &status);
 385
 386                                                 for(int j=otuStart;j<otuStop;j++){
 387                                                         centroids[j] = tempCentroids[j];
 388                                                         change[j] = tempChange[j];
 389                                                 }
 390                                         }
 391
 392                                         maxDelta = getNewWeights();
 393                                         double nLL = getLikelihood();
 394                                         checkCentroids();
 395
 396                                         for(int i=1;i<ncpus;i++){
 397                                                 MPI_Send(&centroids[0], numOTUs, MPI_INT, i, tag, MPI_COMM_WORLD);
 398                                                 MPI_Send(&weight[0], numOTUs, MPI_DOUBLE, i, tag, MPI_COMM_WORLD);
 399                                                 MPI_Send(&change[0], numOTUs, MPI_SHORT, i, tag, MPI_COMM_WORLD);
 400                                         }
 401
 402                                         calcNewDistancesParent(0, numSeqsOnCPU);
 403
 404                                         total = singleTau.size();
 405
 406                                         for(int i=1;i<ncpus;i++){
 407                                                 int childTotal;
 408                                                 int seqStart = i * numSeqs / ncpus;
 409                                                 int seqStop = (i + 1) * numSeqs / ncpus;
 410
 411                                                 MPI_Recv(&childTotal, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 412
 413                                                 vector<int> childSeqIndex(childTotal, 0);
 414                                                 vector<double> childSingleTau(childTotal, 0);
 415                                                 vector<double> childDist(numSeqs * numOTUs, 0);
 416                                                 vector<int> otuIndex(childTotal, 0);
 417
 418                                                 MPI_Recv(&childSeqIndex[0], childTotal, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 419                                                 MPI_Recv(&childSingleTau[0], childTotal, MPI_DOUBLE, i, tag, MPI_COMM_WORLD, &status);
 420                                                 MPI_Recv(&childDist[0], numOTUs * numSeqs, MPI_DOUBLE, i, tag, MPI_COMM_WORLD, &status);
 421                                                 MPI_Recv(&otuIndex[0], childTotal, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 422
 423                                                 int oldTotal = total;
 424                                                 total += childTotal;
 425                                                 singleTau.resize(total, 0);
 426                                                 seqIndex.resize(total, 0);
 427                                                 seqNumber.resize(total, 0);
 428
 429                                                 int childIndex = 0;
 430
 431                                                 for(int j=oldTotal;j<total;j++){
 432                                                         int otuI = otuIndex[childIndex];
 433                                                         int seqI = childSeqIndex[childIndex];
 434
 435                                                         singleTau[j] = childSingleTau[childIndex];
 436
 437                                                         aaP[otuI][nSeqsPerOTU[otuI]] = j;
 438                                                         aaI[otuI][nSeqsPerOTU[otuI]] = seqI;
 439                                                         nSeqsPerOTU[otuI]++;
 440                                                         childIndex++;
 441                                                 }
 442
 443                                                 int index = seqStart * numOTUs;
 444                                                 for(int j=seqStart;j<seqStop;j++){
 445                                                         for(int k=0;k<numOTUs;k++){
 446                                                                 dist[index] = childDist[index];
 447                                                                 index++;
 448                                                         }
 449                                                 }
 450                                         }
 451
 452                                         iter++;
 453
 454                                         m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
 455
 456                                         if((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 457                                                 int live = 1;
 458                                                 for(int i=1;i<ncpus;i++){
 459                                                         MPI_Send(&live, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 460                                                 }
 461                                         }
 462                                         else{
 463                                                 int live = 0;
 464                                                 for(int i=1;i<ncpus;i++){
 465                                                         MPI_Send(&live, 1, MPI_INT, i, tag, MPI_COMM_WORLD); //send kill command
 466                                                 }
 467                                         }
 468
 469                                 }
 470
 471                                 m->mothurOut("\nFinalizing...\n");
 472                                 fill();
 473                                 setOTUs();
 474                                 vector<int> otuCounts(numOTUs, 0);
 475                                 for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
 476                                 calcCentroidsDriver(0, numOTUs);
 477                                 writeQualities(otuCounts);
 478                                 writeSequences(otuCounts);
 479                                 writeNames(otuCounts);
 480                                 writeClusters(otuCounts);
 481                                 writeGroups();
 482
 483                                 remove(distFileName.c_str());
 484                                 remove(namesFileName.c_str());
 485                                 remove(listFileName.c_str());
 486
 487                                 m->mothurOut("Total time to process " + toString(flowFileName) + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 488                         }
 489                 }
 490                 else{
 491                         int abort = 1;
 492                         bool live = 1;
 493
 494                         MPI_Recv(&abort, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 495                         if(abort){      return 0;       }
 496
 497                         int numFiles;
 498                         MPI_Recv(&numFiles, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 499
 500                         for(int i=0;i<numFiles;i++){
 501                                 //Now into the pyrodist part
 502                                 char fileName[1024];
 503                                 MPI_Recv(&fileName, 1024, MPI_CHAR, 0, tag, MPI_COMM_WORLD, &status);
 504                                 MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 505                                 MPI_Recv(&numUniques, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 506                                 MPI_Recv(&numFlowCells, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 507
 508                                 flowDataIntI.resize(numSeqs * numFlowCells);
 509                                 flowDataPrI.resize(numSeqs * numFlowCells);
 510                                 mapUniqueToSeq.resize(numSeqs);
 511                                 mapSeqToUnique.resize(numSeqs);
 512                                 lengths.resize(numSeqs);
 513                                 jointLookUp.resize(NUMBINS * NUMBINS);
 514
 515                                 MPI_Recv(&flowDataIntI[0], numSeqs * numFlowCells, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 516                                 MPI_Recv(&flowDataPrI[0], numSeqs * numFlowCells, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 517                                 MPI_Recv(&mapUniqueToSeq[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 518                                 MPI_Recv(&mapSeqToUnique[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 519                                 MPI_Recv(&lengths[0], numSeqs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 520                                 MPI_Recv(&jointLookUp[0], NUMBINS * NUMBINS, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 521                                 MPI_Recv(&cutoff, 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 522
 523                                 flowFileName = string(fileName);
 524                                 int flowDistStart = int(sqrt(float(pid)/float(ncpus)) * numUniques);
 525                                 int flowDistEnd = int(sqrt(float(pid+1)/float(ncpus)) * numUniques);
 526
 527                                 string distanceStringChild = flowDistMPI(flowDistStart, flowDistEnd);
 528
 529                                 int done = 1;
 530                                 MPI_Send(&done, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 531
 532                                 //Now into the pyronoise part
 533                                 MPI_Recv(&numOTUs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 534
 535                                 singleLookUp.resize(HOMOPS * NUMBINS);
 536                                 uniqueFlowgrams.resize(numUniques * numFlowCells);
 537                                 weight.resize(numOTUs);
 538                                 centroids.resize(numOTUs);
 539                                 change.resize(numOTUs);
 540                                 dist.assign(numOTUs * numSeqs, 0);
 541                                 nSeqsPerOTU.resize(numOTUs);
 542                                 cumNumSeqs.resize(numOTUs);
 543
 544                                 MPI_Recv(&singleLookUp[0], singleLookUp.size(), MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 545                                 MPI_Recv(&uniqueFlowgrams[0], uniqueFlowgrams.size(), MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 546                                 MPI_Recv(&sigma, 1, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 547
 548                                 int startOTU = pid * numOTUs / ncpus;
 549                                 int endOTU = (pid + 1) * numOTUs / ncpus;
 550
 551                                 int startSeq = pid * numSeqs / ncpus;
 552                                 int endSeq = (pid + 1) * numSeqs /ncpus;
 553
 554                                 int total;
 555
 556                                 while(live){
 557
 558                                         MPI_Recv(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 559                                         singleTau.assign(total, 0.0000);
 560                                         seqNumber.assign(total, 0);
 561                                         seqIndex.assign(total, 0);
 562
 563                                         MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 564                                         MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 565                                         MPI_Recv(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 566                                         MPI_Recv(&seqNumber[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 567                                         MPI_Recv(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 568                                         MPI_Recv(&nSeqsPerOTU[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 569                                         MPI_Recv(&cumNumSeqs[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 570
 571                                         calcCentroidsDriver(startOTU, endOTU);
 572
 573                                         MPI_Send(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD);
 574                                         MPI_Send(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD);
 575
 576
 577                                         MPI_Recv(&centroids[0], numOTUs, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 578                                         MPI_Recv(&weight[0], numOTUs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD, &status);
 579                                         MPI_Recv(&change[0], numOTUs, MPI_SHORT, 0, tag, MPI_COMM_WORLD, &status);
 580
 581                                         vector<int> otuIndex(total, 0);
 582                                         calcNewDistancesChildMPI(startSeq, endSeq, otuIndex);
 583                                         total = otuIndex.size();
 584
 585                                         MPI_Send(&total, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 586                                         MPI_Send(&seqIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD);
 587                                         MPI_Send(&singleTau[0], total, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
 588                                         MPI_Send(&dist[0], numOTUs * numSeqs, MPI_DOUBLE, 0, tag, MPI_COMM_WORLD);
 589                                         MPI_Send(&otuIndex[0], total, MPI_INT, 0, tag, MPI_COMM_WORLD);
 590
 591                                         MPI_Recv(&live, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 592                                 }
 593                         }
 594                 }
 595
 596                 MPI_Barrier(MPI_COMM_WORLD);
 597                 return 0;
 598
 599         }
 600         catch(exception& e) {
 601                 m->errorOut(e, "ShhherCommand", "execute");
 602                 exit(1);
 603         }
 604 }
 605
 606 /**************************************************************************************************/
 607
 608 string ShhherCommand::flowDistMPI(int startSeq, int stopSeq){
 609         try{
 610                 ostringstream outStream;
 611                 outStream.setf(ios::fixed, ios::floatfield);
 612                 outStream.setf(ios::dec, ios::basefield);
 613                 outStream.setf(ios::showpoint);
 614                 outStream.precision(6);
 615
 616                 int begTime = time(NULL);
 617                 double begClock = clock();
 618
 619                 for(int i=startSeq;i<stopSeq;i++){
 620                         for(int j=0;j<i;j++){
 621                                 float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
 622
 623                                 if(flowDistance < 1e-6){
 624                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
 625                                 }
 626                                 else if(flowDistance <= cutoff){
 627                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
 628                                 }
 629                         }
 630                         if(i % 100 == 0){
 631                                 m->mothurOut(toString(i) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 632                         }
 633                 }
 634
 635                 m->mothurOut(toString(stopSeq) + '\t' + toString(time(NULL) - begTime) + '\t' + toString((clock()-begClock)/CLOCKS_PER_SEC) + '\n');
 636
 637                 string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
 638                 if(pid != 0){   fDistFileName += ".temp." + toString(pid);      }
 639
 640                 ofstream distFile(fDistFileName.c_str());
 641                 distFile << outStream.str();
 642                 distFile.close();
 643
 644                 return fDistFileName;
 645         }
 646         catch(exception& e) {
 647                 m->errorOut(e, "ShhherCommand", "flowDistParentFork");
 648                 exit(1);
 649         }
 650 }
 651
 652 #else
 653 //**********************************************************************************************************************
 654
 655 int ShhherCommand::execute(){
 656         try {
 657                 if (abort == true) { return 0; }
 658
 659                 getSingleLookUp();
 660                 getJointLookUp();
 661
 662                 vector<string> flowFileVector;
 663                 if(flowFilesFileName != "not found"){
 664                         string fName;
 665
 666                         ifstream flowFilesFile;
 667                         m->openInputFile(flowFilesFileName, flowFilesFile);
 668                         while(flowFilesFile){
 669                                 flowFilesFile >> fName;
 670                                 flowFileVector.push_back(fName);
 671                                 m->gobble(flowFilesFile);
 672                         }
 673                 }
 674                 else{
 675                         flowFileVector.push_back(flowFileName);
 676                 }
 677                 int numFiles = flowFileVector.size();
 678
 679
 680                 for(int i=0;i<numFiles;i++){
 681                         flowFileName = flowFileVector[i];
 682
 683                         m->mothurOut("\n>>>>>\tProcessing " + flowFileName + " (file " + toString(i+1) + " of " + toString(numFiles) + ")\t<<<<<\n");
 684                         m->mothurOut("Reading flowgrams...\n");
 685                         getFlowData();
 686
 687                         m->mothurOut("Identifying unique flowgrams...\n");
 688                         getUniques();
 689
 690
 691                         m->mothurOut("Calculating distances between flowgrams...\n");
 692                         string distFileName = createDistFile(processors);
 693                         string namesFileName = createNamesFile();
 694
 695                         m->mothurOut("\nClustering flowgrams...\n");
 696                         string listFileName = cluster(distFileName, namesFileName);
 697                         getOTUData(listFileName);
 698
 699                         initPyroCluster();
 700
 701                         double maxDelta = 0;
 702                         int iter = 0;
 703
 704                         double begClock = clock();
 705                         unsigned long int begTime = time(NULL);
 706
 707
 708                         cout << numOTUs << endl;
 709
 710
 711                         m->mothurOut("\nDenoising flowgrams...\n");
 712                         m->mothurOut("iter\tmaxDelta\tnLL\t\tcycletime\n");
 713
 714                         while((maxIters == 0 && maxDelta > minDelta) || iter < MIN_ITER || (maxDelta > minDelta && iter < maxIters)){
 715
 716                                 double cycClock = clock();
 717                                 unsigned long int cycTime = time(NULL);
 718                                 fill();
 719
 720                                 calcCentroids();
 721
 722                                 maxDelta = getNewWeights();
 723                                 double nLL = getLikelihood();
 724                                 checkCentroids();
 725
 726                                 calcNewDistances();
 727
 728                                 iter++;
 729
 730                                 m->mothurOut(toString(iter) + '\t' + toString(maxDelta) + '\t' + toString(nLL) + '\t' + toString(time(NULL) - cycTime) + '\t' + toString((clock() - cycClock)/(double)CLOCKS_PER_SEC) + '\n');
 731
 732                         }
 733
 734                         m->mothurOut("\nFinalizing...\n");
 735                         fill();
 736                         setOTUs();
 737
 738                         vector<int> otuCounts(numOTUs, 0);
 739                         for(int i=0;i<numSeqs;i++)      {       otuCounts[otuData[i]]++;        }
 740
 741                         calcCentroidsDriver(0, numOTUs);
 742                         writeQualities(otuCounts);
 743                         writeSequences(otuCounts);
 744                         writeNames(otuCounts);
 745                         writeClusters(otuCounts);
 746                         writeGroups();
 747
 748                         remove(distFileName.c_str());
 749                         remove(namesFileName.c_str());
 750                         remove(listFileName.c_str());
 751
 752                         m->mothurOut("Total time to process " + flowFileName + ":\t" + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/(double)CLOCKS_PER_SEC) + '\n');
 753                 }
 754                 return 0;
 755         }
 756         catch(exception& e) {
 757                 m->errorOut(e, "ShhherCommand", "execute");
 758                 exit(1);
 759         }
 760 }
 761 #endif
 762 /**************************************************************************************************/
 763
 764 void ShhherCommand::getFlowData(){
 765         try{
 766                 ifstream flowFile;
 767                 m->openInputFile(flowFileName, flowFile);
 768
 769                 string seqName;
 770                 seqNameVector.clear();
 771                 lengths.clear();
 772                 flowDataIntI.clear();
 773                 nameMap.clear();
 774
 775
 776                 int currentNumFlowCells;
 777
 778                 float intensity;
 779
 780                 flowFile >> numFlowCells;
 781                 int index = 0;//pcluster
 782                 while(!flowFile.eof()){
 783                         flowFile >> seqName >> currentNumFlowCells;
 784                         lengths.push_back(currentNumFlowCells);
 785
 786                         seqNameVector.push_back(seqName);
 787                         nameMap[seqName] = index++;//pcluster
 788
 789                         for(int i=0;i<numFlowCells;i++){
 790                                 flowFile >> intensity;
 791                                 if(intensity > 9.99)    {       intensity = 9.99;       }
 792                                 int intI = int(100 * intensity + 0.0001);
 793                                 flowDataIntI.push_back(intI);
 794                         }
 795                         m->gobble(flowFile);
 796                 }
 797                 flowFile.close();
 798
 799                 numSeqs = seqNameVector.size();
 800
 801                 for(int i=0;i<numSeqs;i++){
 802                         int iNumFlowCells = i * numFlowCells;
 803                         for(int j=lengths[i];j<numFlowCells;j++){
 804                                 flowDataIntI[iNumFlowCells + j] = 0;
 805                         }
 806                 }
 807
 808         }
 809         catch(exception& e) {
 810                 m->errorOut(e, "ShhherCommand", "getFlowData");
 811                 exit(1);
 812         }
 813 }
 814
 815 /**************************************************************************************************/
 816
 817 void ShhherCommand::getSingleLookUp(){
 818         try{
 819                 //      these are the -log probabilities that a signal corresponds to a particular homopolymer length
 820                 singleLookUp.assign(HOMOPS * NUMBINS, 0);
 821
 822                 int index = 0;
 823                 ifstream lookUpFile;
 824                 m->openInputFile(lookupFileName, lookUpFile);
 825
 826                 for(int i=0;i<HOMOPS;i++){
 827                         float logFracFreq;
 828                         lookUpFile >> logFracFreq;
 829
 830                         for(int j=0;j<NUMBINS;j++)      {
 831                                 lookUpFile >> singleLookUp[index];
 832                                 index++;
 833                         }
 834                 }
 835                 lookUpFile.close();
 836         }
 837         catch(exception& e) {
 838                 m->errorOut(e, "ShhherCommand", "getSingleLookUp");
 839                 exit(1);
 840         }
 841 }
 842
 843 /**************************************************************************************************/
 844
 845 void ShhherCommand::getJointLookUp(){
 846         try{
 847
 848                 //      the most likely joint probability (-log) that two intenities have the same polymer length
 849                 jointLookUp.resize(NUMBINS * NUMBINS, 0);
 850
 851                 for(int i=0;i<NUMBINS;i++){
 852                         for(int j=0;j<NUMBINS;j++){
 853
 854                                 double minSum = 100000000;
 855
 856                                 for(int k=0;k<HOMOPS;k++){
 857                                         double sum = singleLookUp[k * NUMBINS + i] + singleLookUp[k * NUMBINS + j];
 858
 859                                         if(sum < minSum)        {       minSum = sum;           }
 860                                 }
 861                                 jointLookUp[i * NUMBINS + j] = minSum;
 862                         }
 863                 }
 864         }
 865         catch(exception& e) {
 866                 m->errorOut(e, "ShhherCommand", "getJointLookUp");
 867                 exit(1);
 868         }
 869 }
 870
 871 /**************************************************************************************************/
 872
 873 double ShhherCommand::getProbIntensity(int intIntensity){
 874         try{
 875
 876                 double minNegLogProb = 100000000;
 877
 878
 879                 for(int i=0;i<HOMOPS;i++){//loop signal strength
 880                         float negLogProb = singleLookUp[i * NUMBINS + intIntensity];
 881                         if(negLogProb < minNegLogProb)  {       minNegLogProb = negLogProb; }
 882                 }
 883
 884                 return minNegLogProb;
 885         }
 886         catch(exception& e) {
 887                 m->errorOut(e, "ShhherCommand", "getProbIntensity");
 888                 exit(1);
 889         }
 890 }
 891
 892 /**************************************************************************************************/
 893
 894 void ShhherCommand::getUniques(){
 895         try{
 896
 897
 898                 numUniques = 0;
 899                 uniqueFlowgrams.assign(numFlowCells * numSeqs, -1);
 900                 uniqueCount.assign(numSeqs, 0);                                                 //      anWeights
 901                 uniqueLengths.assign(numSeqs, 0);
 902                 mapSeqToUnique.assign(numSeqs, -1);
 903                 mapUniqueToSeq.assign(numSeqs, -1);
 904
 905                 vector<short> uniqueFlowDataIntI(numFlowCells * numSeqs, -1);
 906
 907                 for(int i=0;i<numSeqs;i++){
 908                         int index = 0;
 909
 910                         vector<short> current(numFlowCells);
 911                         for(int j=0;j<numFlowCells;j++){
 912                                 current[j] = short(((flowDataIntI[i * numFlowCells + j] + 50.0)/100.0));
 913                         }
 914
 915                         for(int j=0;j<numUniques;j++){
 916                                 int offset = j * numFlowCells;
 917                                 bool toEnd = 1;
 918
 919                                 int shorterLength;
 920                                 if(lengths[i] < uniqueLengths[j])       {       shorterLength = lengths[i];                     }
 921                                 else                                                            {       shorterLength = uniqueLengths[j];       }
 922
 923                                 for(int k=0;k<shorterLength;k++){
 924                                         if(current[k] != uniqueFlowgrams[offset + k]){
 925                                                 toEnd = 0;
 926                                                 break;
 927                                         }
 928                                 }
 929
 930                                 if(toEnd){
 931                                         mapSeqToUnique[i] = j;
 932                                         uniqueCount[j]++;
 933                                         index = j;
 934                                         if(lengths[i] > uniqueLengths[j])       {       uniqueLengths[j] = lengths[i];  }
 935                                         break;
 936                                 }
 937                                 index++;
 938                         }
 939
 940                         if(index == numUniques){
 941                                 uniqueLengths[numUniques] = lengths[i];
 942                                 uniqueCount[numUniques] = 1;
 943                                 mapSeqToUnique[i] = numUniques;//anMap
 944                                 mapUniqueToSeq[numUniques] = i;//anF
 945
 946                                 for(int k=0;k<numFlowCells;k++){
 947                                         uniqueFlowgrams[numUniques * numFlowCells + k] = current[k];
 948                                         uniqueFlowDataIntI[numUniques * numFlowCells + k] = flowDataIntI[i * numFlowCells + k];
 949                                 }
 950
 951                                 numUniques++;
 952                         }
 953                 }
 954                 uniqueFlowDataIntI.resize(numFlowCells * numUniques);
 955                 uniqueLengths.resize(numUniques);
 956
 957                 flowDataPrI.resize(numSeqs * numFlowCells, 0);
 958                 for(int i=0;i<flowDataPrI.size();i++)   {       flowDataPrI[i] = getProbIntensity(flowDataIntI[i]);             }
 959         }
 960         catch(exception& e) {
 961                 m->errorOut(e, "ShhherCommand", "getUniques");
 962                 exit(1);
 963         }
 964 }
 965
 966 /**************************************************************************************************/
 967
 968 float ShhherCommand::calcPairwiseDist(int seqA, int seqB){
 969         try{
 970                 int minLength = lengths[mapSeqToUnique[seqA]];
 971                 if(lengths[seqB] < minLength){  minLength = lengths[mapSeqToUnique[seqB]];      }
 972
 973                 int ANumFlowCells = seqA * numFlowCells;
 974                 int BNumFlowCells = seqB * numFlowCells;
 975
 976                 float dist = 0;
 977
 978                 for(int i=0;i<minLength;i++){
 979                         int flowAIntI = flowDataIntI[ANumFlowCells + i];
 980                         float flowAPrI = flowDataPrI[ANumFlowCells + i];
 981
 982                         int flowBIntI = flowDataIntI[BNumFlowCells + i];
 983                         float flowBPrI = flowDataPrI[BNumFlowCells + i];
 984                         dist += jointLookUp[flowAIntI * NUMBINS + flowBIntI] - flowAPrI - flowBPrI;
 985                 }
 986
 987                 dist /= (float) minLength;
 988                 return dist;
 989         }
 990         catch(exception& e) {
 991                 m->errorOut(e, "ShhherCommand", "calcPairwiseDist");
 992                 exit(1);
 993         }
 994 }
 995
 996 /**************************************************************************************************/
 997
 998 void ShhherCommand::flowDistParentFork(string distFileName, int startSeq, int stopSeq){
 999         try{
1000
1001                 ostringstream outStream;
1002                 outStream.setf(ios::fixed, ios::floatfield);
1003                 outStream.setf(ios::dec, ios::basefield);
1004                 outStream.setf(ios::showpoint);
1005                 outStream.precision(6);
1006
1007                 int begTime = time(NULL);
1008                 double begClock = clock();
1009
1010                 for(int i=startSeq;i<stopSeq;i++){
1011                         for(int j=0;j<i;j++){
1012                                 float flowDistance = calcPairwiseDist(mapUniqueToSeq[i], mapUniqueToSeq[j]);
1013
1014                                 if(flowDistance < 1e-6){
1015                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << 0.000000 << endl;
1016                                 }
1017                                 else if(flowDistance <= cutoff){
1018                                         outStream << mapUniqueToSeq[i] << '\t' << mapUniqueToSeq[j] << '\t' << flowDistance << endl;
1019                                 }
1020                         }
1021                         if(i % 100 == 0){
1022                                 m->mothurOut(toString(i) + "\t" + toString(time(NULL) - begTime));
1023                                 m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
1024                                 m->mothurOutEndLine();
1025                         }
1026                 }
1027                 m->mothurOut(toString(stopSeq-1) + "\t" + toString(time(NULL) - begTime));
1028                 m->mothurOut("\t" + toString((clock()-begClock)/CLOCKS_PER_SEC));
1029                 m->mothurOutEndLine();
1030
1031                 ofstream distFile(distFileName.c_str());
1032                 distFile << outStream.str();
1033                 distFile.close();
1034         }
1035         catch(exception& e) {
1036                 m->errorOut(e, "ShhherCommand", "flowDistParentFork");
1037                 exit(1);
1038         }
1039 }
1040
1041 /**************************************************************************************************/
1042
1043 string ShhherCommand::createDistFile(int processors){
1044         try{
1045                 string fDistFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.dist";
1046
1047                 unsigned long int begTime = time(NULL);
1048                 double begClock = clock();
1049
1050                 vector<int> start;
1051                 vector<int> end;
1052
1053 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1054                 if(processors == 1)     {       flowDistParentFork(fDistFileName, 0, numUniques);               }
1055                 else{ //you have multiple processors
1056
1057                         if (numSeqs < processors){      processors = 1; }
1058
1059                         vector<int> start(processors, 0);
1060                         vector<int> end(processors, 0);
1061
1062                         for (int i = 0; i < processors; i++) {
1063                                 start[i] = int(sqrt(float(i)/float(processors)) * numUniques);
1064                                 end[i] = int(sqrt(float(i+1)/float(processors)) * numUniques);
1065                         }
1066
1067                         int process = 1;
1068                         vector<int> processIDs;
1069
1070                         //loop through and create all the processes you want
1071                         while (process != processors) {
1072                                 int pid = fork();
1073
1074                                 if (pid > 0) {
1075                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1076                                         process++;
1077                                 }else if (pid == 0){
1078                                         flowDistParentFork(fDistFileName + toString(getpid()) + ".temp", start[process], end[process]);
1079                                         exit(0);
1080                                 }else {
1081                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1082                                         perror(" : ");
1083                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1084                                         exit(0);
1085                                 }
1086                         }
1087
1088                         //parent does its part
1089                         flowDistParentFork(fDistFileName, start[0], end[0]);
1090
1091                         //force parent to wait until all the processes are done
1092                         for (int i=0;i<processIDs.size();i++) {
1093                                 int temp = processIDs[i];
1094                                 wait(&temp);
1095                         }
1096
1097                         //append and remove temp files
1098                         for (int i=0;i<processIDs.size();i++) {
1099                                 m->appendFiles((fDistFileName + toString(processIDs[i]) + ".temp"), fDistFileName);
1100                                 remove((fDistFileName + toString(processIDs[i]) + ".temp").c_str());
1101                         }
1102
1103                 }
1104
1105 #else
1106                 flowDistParentFork(fDistFileName, 0, numUniques);
1107 #endif
1108
1109                 m->mothurOutEndLine();
1110
1111                 m->mothurOut("Total time: " + toString(time(NULL) - begTime) + '\t' + toString((clock() - begClock)/CLOCKS_PER_SEC) + '\n');
1112
1113
1114                 return fDistFileName;
1115         }
1116         catch(exception& e) {
1117                 m->errorOut(e, "ShhherCommand", "createDistFile");
1118                 exit(1);
1119         }
1120
1121 }
1122
1123 /**************************************************************************************************/
1124
1125 string ShhherCommand::createNamesFile(){
1126         try{
1127
1128                 vector<string> duplicateNames(numUniques, "");
1129                 for(int i=0;i<numSeqs;i++){
1130                         duplicateNames[mapSeqToUnique[i]] += seqNameVector[i] + ',';
1131                 }
1132
1133                 string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.names";
1134
1135                 ofstream nameFile;
1136                 m->openOutputFile(nameFileName, nameFile);
1137
1138                 for(int i=0;i<numUniques;i++){
1139 //                      nameFile << seqNameVector[mapUniqueToSeq[i]] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
1140                         nameFile << mapUniqueToSeq[i] << '\t' << duplicateNames[i].substr(0, duplicateNames[i].find_last_of(',')) << endl;
1141                 }
1142
1143                 nameFile.close();
1144                 return  nameFileName;
1145         }
1146         catch(exception& e) {
1147                 m->errorOut(e, "ShhherCommand", "createNamesFile");
1148                 exit(1);
1149         }
1150 }
1151
1152 //**********************************************************************************************************************
1153
1154 string ShhherCommand::cluster(string distFileName, string namesFileName){
1155         try {
1156
1157
1158                 globaldata->setNameFile(namesFileName);
1159                 globaldata->setColumnFile(distFileName);
1160                 globaldata->setFormat("column");
1161
1162                 ReadMatrix* read = new ReadColumnMatrix(distFileName);
1163                 read->setCutoff(cutoff);
1164
1165                 NameAssignment* clusterNameMap = new NameAssignment(namesFileName);
1166                 clusterNameMap->readMap();
1167                 read->read(clusterNameMap);
1168
1169                 ListVector* list = read->getListVector();
1170                 SparseMatrix* matrix = read->getMatrix();
1171
1172                 delete read;
1173                 delete clusterNameMap;
1174
1175                 RAbundVector* rabund = new RAbundVector(list->getRAbundVector());
1176
1177                 Cluster* cluster = new CompleteLinkage(rabund, list, matrix, cutoff, "furthest");
1178                 string tag = cluster->getTag();
1179
1180                 double clusterCutoff = cutoff;
1181                 while (matrix->getSmallDist() <= clusterCutoff && matrix->getNNodes() > 0){
1182                         cluster->update(clusterCutoff);
1183                 }
1184
1185                 list->setLabel(toString(cutoff));
1186
1187                 string listFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.list";
1188                 ofstream listFile;
1189                 m->openOutputFile(listFileName, listFile);
1190                 list->print(listFile);
1191                 listFile.close();
1192
1193                 delete matrix;  delete cluster; delete rabund; delete list;
1194
1195                 return listFileName;
1196         }
1197         catch(exception& e) {
1198                 m->errorOut(e, "ShhherCommand", "cluster");
1199                 exit(1);
1200         }
1201 }
1202
1203 /**************************************************************************************************/
1204
1205 void ShhherCommand::getOTUData(string listFileName){
1206         try {
1207
1208                 ifstream listFile;
1209                 m->openInputFile(listFileName, listFile);
1210                 string label;
1211
1212                 listFile >> label >> numOTUs;
1213
1214                 otuData.assign(numSeqs, 0);
1215                 cumNumSeqs.assign(numOTUs, 0);
1216                 nSeqsPerOTU.assign(numOTUs, 0);
1217                 aaP.clear();aaP.resize(numOTUs);
1218
1219                 seqNumber.clear();
1220                 aaI.clear();
1221                 seqIndex.clear();
1222
1223                 string singleOTU = "";
1224
1225                 for(int i=0;i<numOTUs;i++){
1226
1227                         listFile >> singleOTU;
1228
1229                         istringstream otuString(singleOTU);
1230
1231                         while(otuString){
1232
1233                                 string seqName = "";
1234
1235                                 for(int j=0;j<singleOTU.length();j++){
1236                                         char letter = otuString.get();
1237
1238                                         if(letter != ','){
1239                                                 seqName += letter;
1240                                         }
1241                                         else{
1242                                                 map<string,int>::iterator nmIt = nameMap.find(seqName);
1243                                                 int index = nmIt->second;
1244
1245                                                 nameMap.erase(nmIt);
1246
1247                                                 otuData[index] = i;
1248                                                 nSeqsPerOTU[i]++;
1249                                                 aaP[i].push_back(index);
1250                                                 seqName = "";
1251                                         }
1252                                 }
1253
1254                                 map<string,int>::iterator nmIt = nameMap.find(seqName);
1255
1256                                 int index = nmIt->second;
1257                                 nameMap.erase(nmIt);
1258
1259                                 otuData[index] = i;
1260                                 nSeqsPerOTU[i]++;
1261                                 aaP[i].push_back(index);
1262
1263                                 otuString.get();
1264                         }
1265
1266                         sort(aaP[i].begin(), aaP[i].end());
1267                         for(int j=0;j<nSeqsPerOTU[i];j++){
1268                                 seqNumber.push_back(aaP[i][j]);
1269                         }
1270                         for(int j=nSeqsPerOTU[i];j<numSeqs;j++){
1271                                 aaP[i].push_back(0);
1272                         }
1273
1274
1275                 }
1276
1277                 for(int i=1;i<numOTUs;i++){
1278                         cumNumSeqs[i] = cumNumSeqs[i-1] + nSeqsPerOTU[i-1];
1279                 }
1280                 aaI = aaP;
1281                 seqIndex = seqNumber;
1282
1283                 listFile.close();
1284
1285                 for(int i=0;i<seqNumber.size();i++){
1286                         cout << seqNumber[i] << ' ';
1287                 }
1288                 cout << endl;
1289
1290
1291         }
1292         catch(exception& e) {
1293                 m->errorOut(e, "ShhherCommand", "getOTUData");
1294                 exit(1);
1295         }
1296 }
1297
1298 /**************************************************************************************************/
1299
1300 void ShhherCommand::initPyroCluster(){
1301         try{
1302                 dist.assign(numSeqs * numOTUs, 0);
1303                 change.assign(numOTUs, 1);
1304                 centroids.assign(numOTUs, -1);
1305                 weight.assign(numOTUs, 0);
1306                 singleTau.assign(numSeqs, 1.0);
1307
1308                 nSeqsBreaks.assign(processors+1, 0);
1309                 nOTUsBreaks.assign(processors+1, 0);
1310
1311                 cout << numSeqs << '\t' << numOTUs << '\t' << processors << endl;
1312
1313                 nSeqsBreaks[0] = 0;
1314                 for(int i=0;i<processors;i++){
1315                         nSeqsBreaks[i+1] = nSeqsBreaks[i] + (int)((double) numSeqs / (double) processors);
1316                         nOTUsBreaks[i+1] = nOTUsBreaks[i] + (int)((double) numOTUs / (double) processors);
1317                 }
1318                 nSeqsBreaks[processors] = numSeqs;
1319                 nOTUsBreaks[processors] = numOTUs;
1320         }
1321         catch(exception& e) {
1322                 m->errorOut(e, "ShhherCommand", "initPyroCluster");
1323                 exit(1);
1324         }
1325 }
1326
1327 /**************************************************************************************************/
1328
1329 void ShhherCommand::fill(){
1330         try {
1331                 int index = 0;
1332                 for(int i=0;i<numOTUs;i++){
1333                         cumNumSeqs[i] = index;
1334                         for(int j=0;j<nSeqsPerOTU[i];j++){
1335                                 seqNumber[index] = aaP[i][j];
1336                                 seqIndex[index] = aaI[i][j];
1337
1338                                 index++;
1339                         }
1340                 }
1341         }
1342         catch(exception& e) {
1343                 m->errorOut(e, "ShhherCommand", "fill");
1344                 exit(1);
1345         }
1346 }
1347
1348 /**************************************************************************************************/
1349
1350 void ShhherCommand::calcCentroids(){
1351         try{
1352
1353 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1354
1355                 if(processors == 1)     {
1356                         calcCentroidsDriver(0, numOTUs);
1357                 }
1358                 else{ //you have multiple processors
1359                         if (numOTUs < processors){      processors = 1; }
1360
1361                         int process = 1;
1362                         vector<int> processIDs;
1363
1364                         //loop through and create all the processes you want
1365                         while (process != processors) {
1366                                 int pid = vfork();
1367
1368                                 if (pid > 0) {
1369                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1370                                         process++;
1371                                 }else if (pid == 0){
1372                                         calcCentroidsDriver(nOTUsBreaks[process], nOTUsBreaks[process+1]);
1373                                         exit(0);
1374                                 }else {
1375                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1376                                         perror(" : ");
1377                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1378                                         exit(0);
1379                                 }
1380                         }
1381
1382                         //parent does its part
1383                         calcCentroidsDriver(nOTUsBreaks[0], nOTUsBreaks[1]);
1384
1385                         //force parent to wait until all the processes are done
1386                         for (int i=0;i<processIDs.size();i++) {
1387                                 int temp = processIDs[i];
1388                                 wait(&temp);
1389                         }
1390                 }
1391
1392 #else
1393                 calcCentroidsDriver(0, numOTUs);
1394 #endif
1395         }
1396         catch(exception& e) {
1397                 m->errorOut(e, "ShhherCommand", "calcCentroidsDriver");
1398                 exit(1);
1399         }
1400 }
1401
1402 /**************************************************************************************************/
1403
1404 void ShhherCommand::calcCentroidsDriver(int start, int finish){
1405
1406         //this function gets the most likely homopolymer length at a flow position for a group of sequences
1407         //within an otu
1408
1409         try{
1410
1411 //              for(int i=0;i<seqNumber.size();i++){
1412 //                      cout << seqNumber[i] << ' ';
1413 //              }cout << endl;
1414
1415                 for(int i=start;i<finish;i++){
1416
1417                         double count = 0;
1418                         int position = 0;
1419                         int minFlowGram = 100000000;
1420                         double minFlowValue = 1e8;
1421                         change[i] = 0; //FALSE
1422
1423                         for(int j=0;j<nSeqsPerOTU[i];j++){
1424                                 count += singleTau[seqNumber[cumNumSeqs[i] + j]];
1425                         }
1426
1427                         if(nSeqsPerOTU[i] > 0 && count > MIN_COUNT){
1428                                 vector<double> adF(nSeqsPerOTU[i]);
1429                                 vector<int> anL(nSeqsPerOTU[i]);
1430
1431                                 for(int j=0;j<nSeqsPerOTU[i];j++){
1432                                         int index = cumNumSeqs[i] + j;
1433                                         int nI = seqIndex[index];
1434                                         int nIU = mapSeqToUnique[nI];
1435
1436                                         int k;
1437                                         for(k=0;k<position;k++){
1438                                                 if(nIU == anL[k]){
1439                                                         break;
1440                                                 }
1441                                         }
1442                                         if(k == position){
1443                                                 anL[position] = nIU;
1444                                                 adF[position] = 0.0000;
1445                                                 position++;
1446                                         }
1447                                 }
1448
1449                                 for(int j=0;j<nSeqsPerOTU[i];j++){
1450                                         int index = cumNumSeqs[i] + j;
1451                                         int nI = seqIndex[index];
1452
1453                                         double tauValue = singleTau[seqNumber[index]];
1454
1455                                         for(int k=0;k<position;k++){
1456                                                 double dist = getDistToCentroid(anL[k], nI, lengths[nI]);
1457                                                 adF[k] += dist * tauValue;
1458                                         }
1459                                 }
1460
1461                                 for(int j=0;j<position;j++){
1462                                         if(adF[j] < minFlowValue){
1463                                                 minFlowGram = j;
1464                                                 minFlowValue = adF[j];
1465                                         }
1466                                 }
1467
1468                                 if(centroids[i] != anL[minFlowGram]){
1469                                         change[i] = 1;
1470                                         centroids[i] = anL[minFlowGram];
1471                                 }
1472                         }
1473                         else if(centroids[i] != -1){
1474                                 change[i] = 1;
1475                                 centroids[i] = -1;
1476                         }
1477                 }
1478         }
1479         catch(exception& e) {
1480                 m->errorOut(e, "ShhherCommand", "calcCentroidsDriver");
1481                 exit(1);
1482         }
1483 }
1484
1485 /**************************************************************************************************/
1486
1487 double ShhherCommand::getDistToCentroid(int cent, int flow, int length){
1488         try{
1489
1490                 int flowAValue = cent * numFlowCells;
1491                 int flowBValue = flow * numFlowCells;
1492
1493                 double dist = 0;
1494
1495                 for(int i=0;i<length;i++){
1496                         dist += singleLookUp[uniqueFlowgrams[flowAValue] * NUMBINS + flowDataIntI[flowBValue]];
1497                         flowAValue++;
1498                         flowBValue++;
1499                 }
1500
1501                 return dist / (double)length;
1502         }
1503         catch(exception& e) {
1504                 m->errorOut(e, "ShhherCommand", "getDistToCentroid");
1505                 exit(1);
1506         }
1507 }
1508
1509 /**************************************************************************************************/
1510
1511 double ShhherCommand::getNewWeights(){
1512         try{
1513
1514                 double maxChange = 0;
1515
1516                 for(int i=0;i<numOTUs;i++){
1517
1518                         double difference = weight[i];
1519                         weight[i] = 0;
1520
1521                         for(int j=0;j<nSeqsPerOTU[i];j++){
1522                                 int index = cumNumSeqs[i] + j;
1523                                 double tauValue = singleTau[seqNumber[index]];
1524                                 weight[i] += tauValue;
1525                         }
1526
1527                         difference = fabs(weight[i] - difference);
1528                         if(difference > maxChange){     maxChange = difference; }
1529                 }
1530                 return maxChange;
1531         }
1532         catch(exception& e) {
1533                 m->errorOut(e, "ShhherCommand", "getNewWeights");
1534                 exit(1);
1535         }
1536 }
1537
1538 /**************************************************************************************************/
1539
1540 double ShhherCommand::getLikelihood(){
1541
1542         try{
1543
1544                 vector<long double> P(numSeqs, 0);
1545                 int effNumOTUs = 0;
1546
1547                 for(int i=0;i<numOTUs;i++){
1548                         if(weight[i] > MIN_WEIGHT){
1549                                 effNumOTUs++;
1550                         }
1551                 }
1552
1553                 string hold;
1554                 for(int i=0;i<numOTUs;i++){
1555                         for(int j=0;j<nSeqsPerOTU[i];j++){
1556                                 int index = cumNumSeqs[i] + j;
1557                                 int nI = seqIndex[index];
1558                                 double singleDist = dist[seqNumber[index]];
1559
1560                                 P[nI] += weight[i] * exp(-singleDist * sigma);
1561                         }
1562                 }
1563                 double nLL = 0.00;
1564                 for(int i=0;i<numSeqs;i++){
1565                         if(P[i] == 0){  P[i] = DBL_EPSILON;     }
1566
1567                         nLL += -log(P[i]);
1568                 }
1569
1570                 nLL = nLL -(double)numSeqs * log(sigma);
1571
1572                 return nLL;
1573         }
1574         catch(exception& e) {
1575                 m->errorOut(e, "ShhherCommand", "getNewWeights");
1576                 exit(1);
1577         }
1578 }
1579
1580 /**************************************************************************************************/
1581
1582 void ShhherCommand::checkCentroids(){
1583         try{
1584                 vector<int> unique(numOTUs, 1);
1585
1586                 for(int i=0;i<numOTUs;i++){
1587                         if(centroids[i] == -1 || weight[i] < MIN_WEIGHT){
1588                                 unique[i] = -1;
1589                         }
1590                 }
1591
1592                 for(int i=0;i<numOTUs;i++){
1593                         if(unique[i] == 1){
1594                                 for(int j=i+1;j<numOTUs;j++){
1595                                         if(unique[j] == 1){
1596
1597                                                 if(centroids[j] == centroids[i]){
1598                                                         unique[j] = 0;
1599                                                         centroids[j] = -1;
1600
1601                                                         weight[i] += weight[j];
1602                                                         weight[j] = 0.0;
1603                                                 }
1604                                         }
1605                                 }
1606                         }
1607                 }
1608         }
1609         catch(exception& e) {
1610                 m->errorOut(e, "ShhherCommand", "checkCentroids");
1611                 exit(1);
1612         }
1613 }
1614
1615 /**************************************************************************************************/
1616
1617 void ShhherCommand::calcNewDistances(){
1618         try{
1619
1620 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1621
1622                 if(processors == 1)     {
1623                         calcNewDistancesParent(0, numSeqs);
1624                 }
1625                 else{ //you have multiple processors
1626                         if (numSeqs < processors){      processors = 1; }
1627
1628                         vector<vector<int> > child_otuIndex(processors);
1629                         vector<vector<int> > child_seqIndex(processors);
1630                         vector<vector<double> > child_singleTau(processors);
1631                         vector<int> totals(processors);
1632
1633                         int process = 1;
1634                         vector<int> processIDs;
1635
1636                         //loop through and create all the processes you want
1637                         while (process != processors) {
1638                                 int pid = vfork();
1639
1640                                 if (pid > 0) {
1641                                         processIDs.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1642                                         process++;
1643                                 }else if (pid == 0){
1644                                         calcNewDistancesChild(nSeqsBreaks[process], nSeqsBreaks[process+1], child_otuIndex[process], child_seqIndex[process], child_singleTau[process]);
1645                                         totals[process] = child_otuIndex[process].size();
1646
1647                                         exit(0);
1648                                 }else {
1649                                         m->mothurOut("[ERROR]: unable to spawn the necessary processes. Error code: " + toString(pid)); m->mothurOutEndLine();
1650                                         perror(" : ");
1651                                         for (int i=0;i<processIDs.size();i++) {  int temp = processIDs[i]; kill (temp, SIGINT); }
1652                                         exit(0);
1653                                 }
1654                         }
1655
1656                         //parent does its part
1657                         calcNewDistancesParent(nSeqsBreaks[0], nSeqsBreaks[1]);
1658                         int total = seqIndex.size();
1659
1660                         //force parent to wait until all the processes are done
1661                         for (int i=0;i<processIDs.size();i++) {
1662                                 int temp = processIDs[i];
1663                                 wait(&temp);
1664                         }
1665
1666                         for(int i=1;i<processors;i++){
1667                                 int oldTotal = total;
1668                                 total += totals[i];
1669
1670                                 singleTau.resize(total, 0);
1671                                 seqIndex.resize(total, 0);
1672                                 seqNumber.resize(total, 0);
1673
1674                                 int childIndex = 0;
1675
1676                                 for(int j=oldTotal;j<total;j++){
1677                                         int otuI = child_otuIndex[i][childIndex];
1678                                         int seqI = child_seqIndex[i][childIndex];
1679
1680                                         singleTau[j] = child_singleTau[i][childIndex];
1681                                         aaP[otuI][nSeqsPerOTU[otuI]] = j;
1682                                         aaI[otuI][nSeqsPerOTU[otuI]] = seqI;
1683                                         nSeqsPerOTU[otuI]++;
1684
1685                                         childIndex++;
1686                                 }
1687                         }
1688                 }
1689 #else
1690                 calcNewDistancesParent(0, numSeqs);
1691 #endif
1692         }
1693         catch(exception& e) {
1694                 m->errorOut(e, "ShhherCommand", "calcNewDistances");
1695                 exit(1);
1696         }
1697 }
1698
1699 /**************************************************************************************************/
1700 #ifdef USE_MPI
1701 void ShhherCommand::calcNewDistancesChildMPI(int startSeq, int stopSeq, vector<int>& otuIndex){
1702
1703         try{
1704                 vector<double> newTau(numOTUs,0);
1705                 vector<double> norms(numSeqs, 0);
1706                 otuIndex.clear();
1707                 seqIndex.clear();
1708                 singleTau.clear();
1709
1710
1711
1712                 for(int i=startSeq;i<stopSeq;i++){
1713                         double offset = 1e8;
1714                         int indexOffset = i * numOTUs;
1715
1716                         for(int j=0;j<numOTUs;j++){
1717
1718                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1719                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1720                                 }
1721                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1722                                         offset = dist[indexOffset + j];
1723                                 }
1724                         }
1725
1726                         for(int j=0;j<numOTUs;j++){
1727                                 if(weight[j] > MIN_WEIGHT){
1728                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1729                                         norms[i] += newTau[j];
1730                                 }
1731                                 else{
1732                                         newTau[j] = 0.0;
1733                                 }
1734                         }
1735
1736                         for(int j=0;j<numOTUs;j++){
1737
1738                                 newTau[j] /= norms[i];
1739
1740                                 if(newTau[j] > MIN_TAU){
1741                                         otuIndex.push_back(j);
1742                                         seqIndex.push_back(i);
1743                                         singleTau.push_back(newTau[j]);
1744                                 }
1745                         }
1746
1747                 }
1748         }
1749         catch(exception& e) {
1750                 m->errorOut(e, "ShhherCommand", "calcNewDistancesChildMPI");
1751                 exit(1);
1752         }
1753 }
1754 #endif
1755 /**************************************************************************************************/
1756
1757 void ShhherCommand::calcNewDistancesChild(int startSeq, int stopSeq, vector<int>& child_otuIndex, vector<int>& child_seqIndex, vector<double>& child_singleTau){
1758
1759         try{
1760                 vector<double> newTau(numOTUs,0);
1761                 vector<double> norms(numSeqs, 0);
1762                 child_otuIndex.resize(0);
1763                 child_seqIndex.resize(0);
1764                 child_singleTau.resize(0);
1765
1766                 for(int i=startSeq;i<stopSeq;i++){
1767                         double offset = 1e8;
1768                         int indexOffset = i * numOTUs;
1769
1770
1771                         for(int j=0;j<numOTUs;j++){
1772                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1773                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1774                                 }
1775
1776                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1777                                         offset = dist[indexOffset + j];
1778                                 }
1779                         }
1780
1781                         for(int j=0;j<numOTUs;j++){
1782                                 if(weight[j] > MIN_WEIGHT){
1783                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1784                                         norms[i] += newTau[j];
1785                                 }
1786                                 else{
1787                                         newTau[j] = 0.0;
1788                                 }
1789                         }
1790
1791                         for(int j=0;j<numOTUs;j++){
1792                                 newTau[j] /= norms[i];
1793
1794                                 if(newTau[j] > MIN_TAU){
1795                                         child_otuIndex.push_back(j);
1796                                         child_seqIndex.push_back(i);
1797                                         child_singleTau.push_back(newTau[j]);
1798                                 }
1799                         }
1800                 }
1801         }
1802         catch(exception& e) {
1803                 m->errorOut(e, "ShhherCommand", "calcNewDistancesChild");
1804                 exit(1);
1805         }
1806 }
1807
1808 /**************************************************************************************************/
1809
1810 void ShhherCommand::calcNewDistancesParent(int startSeq, int stopSeq){
1811
1812         try{
1813
1814                 int total = 0;
1815                 vector<double> newTau(numOTUs,0);
1816                 vector<double> norms(numSeqs, 0);
1817                 nSeqsPerOTU.assign(numOTUs, 0);
1818
1819                 for(int i=startSeq;i<stopSeq;i++){
1820                         int indexOffset = i * numOTUs;
1821
1822                         double offset = 1e8;
1823
1824                         for(int j=0;j<numOTUs;j++){
1825                                 if(weight[j] > MIN_WEIGHT && change[j] == 1){
1826                                         dist[indexOffset + j] = getDistToCentroid(centroids[j], i, lengths[i]);
1827                                 }
1828
1829                                 if(weight[j] > MIN_WEIGHT && dist[indexOffset + j] < offset){
1830                                         offset = dist[indexOffset + j];
1831                                 }
1832                         }
1833
1834                         for(int j=0;j<numOTUs;j++){
1835                                 if(weight[j] > MIN_WEIGHT){
1836                                         newTau[j] = exp(sigma * (-dist[indexOffset + j] + offset)) * weight[j];
1837                                         norms[i] += newTau[j];
1838                                 }
1839                                 else{
1840                                         newTau[j] = 0.0;
1841                                 }
1842                         }
1843
1844                         for(int j=0;j<numOTUs;j++){
1845                                 newTau[j] /= norms[i];
1846                         }
1847
1848                         for(int j=0;j<numOTUs;j++){
1849                                 if(newTau[j] > MIN_TAU){
1850
1851                                         int oldTotal = total;
1852
1853                                         total++;
1854
1855                                         singleTau.resize(total, 0);
1856                                         seqNumber.resize(total, 0);
1857                                         seqIndex.resize(total, 0);
1858
1859                                         singleTau[oldTotal] = newTau[j];
1860
1861                                         aaP[j][nSeqsPerOTU[j]] = oldTotal;
1862                                         aaI[j][nSeqsPerOTU[j]] = i;
1863                                         nSeqsPerOTU[j]++;
1864                                 }
1865                         }
1866                 }
1867         }
1868         catch(exception& e) {
1869                 m->errorOut(e, "ShhherCommand", "calcNewDistancesParent");
1870                 exit(1);
1871         }
1872 }
1873
1874 /**************************************************************************************************/
1875
1876 void ShhherCommand::setOTUs(){
1877
1878         try {
1879                 vector<double> bigTauMatrix(numOTUs * numSeqs, 0.0000);
1880
1881                 for(int i=0;i<numOTUs;i++){
1882                         for(int j=0;j<nSeqsPerOTU[i];j++){
1883                                 int index = cumNumSeqs[i] + j;
1884                                 double tauValue = singleTau[seqNumber[index]];
1885                                 int sIndex = seqIndex[index];
1886                                 bigTauMatrix[sIndex * numOTUs + i] = tauValue;
1887                         }
1888                 }
1889
1890                 for(int i=0;i<numSeqs;i++){
1891                         double maxTau = -1.0000;
1892                         int maxOTU = -1;
1893                         for(int j=0;j<numOTUs;j++){
1894                                 if(bigTauMatrix[i * numOTUs + j] > maxTau){
1895                                         maxTau = bigTauMatrix[i * numOTUs + j];
1896                                         maxOTU = j;
1897                                 }
1898                         }
1899
1900                         otuData[i] = maxOTU;
1901                 }
1902
1903                 nSeqsPerOTU.assign(numOTUs, 0);
1904
1905                 for(int i=0;i<numSeqs;i++){
1906                         int index = otuData[i];
1907
1908                         singleTau[i] = 1.0000;
1909                         dist[i] = 0.0000;
1910
1911                         aaP[index][nSeqsPerOTU[index]] = i;
1912                         aaI[index][nSeqsPerOTU[index]] = i;
1913
1914                         nSeqsPerOTU[index]++;
1915                 }
1916                 fill();
1917         }
1918         catch(exception& e) {
1919                 m->errorOut(e, "ShhherCommand", "calcNewDistances");
1920                 exit(1);
1921         }
1922 }
1923
1924 /**************************************************************************************************/
1925
1926 void ShhherCommand::writeQualities(vector<int> otuCounts){
1927
1928         try {
1929                 string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.qual";
1930
1931                 ofstream qualityFile;
1932                 m->openOutputFile(qualityFileName, qualityFile);
1933
1934                 qualityFile.setf(ios::fixed, ios::floatfield);
1935                 qualityFile.setf(ios::showpoint);
1936                 qualityFile << setprecision(6);
1937
1938                 vector<vector<int> > qualities(numOTUs);
1939                 vector<double> pr(HOMOPS, 0);
1940
1941
1942                 for(int i=0;i<numOTUs;i++){
1943                         int index = 0;
1944                         int base = 0;
1945
1946                         if(nSeqsPerOTU[i] > 0){
1947                                 qualities[i].assign(1024, -1);
1948
1949                                 while(index < numFlowCells){
1950                                         double maxPrValue = 1e8;
1951                                         short maxPrIndex = -1;
1952                                         double count = 0.0000;
1953
1954                                         pr.assign(HOMOPS, 0);
1955
1956                                         for(int j=0;j<nSeqsPerOTU[i];j++){
1957                                                 int lIndex = cumNumSeqs[i] + j;
1958                                                 double tauValue = singleTau[seqNumber[lIndex]];
1959                                                 int sequenceIndex = aaI[i][j];
1960                                                 short intensity = flowDataIntI[sequenceIndex * numFlowCells + index];
1961
1962                                                 count += tauValue;
1963
1964                                                 for(int s=0;s<HOMOPS;s++){
1965                                                         pr[s] += tauValue * singleLookUp[s * NUMBINS + intensity];
1966                                                 }
1967                                         }
1968
1969                                         maxPrIndex = uniqueFlowgrams[centroids[i] * numFlowCells + index];
1970                                         maxPrValue = pr[maxPrIndex];
1971
1972                                         if(count > MIN_COUNT){
1973                                                 double U = 0.0000;
1974                                                 double norm = 0.0000;
1975
1976                                                 for(int s=0;s<HOMOPS;s++){
1977                                                         norm += exp(-(pr[s] - maxPrValue));
1978                                                 }
1979
1980                                                 for(int s=1;s<=maxPrIndex;s++){
1981                                                         int value = 0;
1982                                                         double temp = 0.0000;
1983
1984                                                         U += exp(-(pr[s-1]-maxPrValue))/norm;
1985
1986                                                         if(U>0.00){
1987                                                                 temp = log10(U);
1988                                                         }
1989                                                         else{
1990                                                                 temp = -10.1;
1991                                                         }
1992                                                         temp = floor(-10 * temp);
1993                                                         value = (int)floor(temp);
1994                                                         if(value > 100){        value = 100;    }
1995
1996                                                         qualities[i][base] = (int)value;
1997                                                         base++;
1998                                                 }
1999                                         }
2000
2001                                         index++;
2002                                 }
2003                         }
2004
2005
2006                         if(otuCounts[i] > 0){
2007                                 qualityFile << '>' << seqNameVector[mapUniqueToSeq[i]] << endl;
2008
2009                                 int j=4;        //need to get past the first four bases
2010                                 while(qualities[i][j] != -1){
2011                                         qualityFile << qualities[i][j] << ' ';
2012                                         j++;
2013                                 }
2014                                 qualityFile << endl;
2015                         }
2016                 }
2017                 qualityFile.close();
2018
2019         }
2020         catch(exception& e) {
2021                 m->errorOut(e, "ShhherCommand", "writeQualities");
2022                 exit(1);
2023         }
2024 }
2025
2026 /**************************************************************************************************/
2027
2028 void ShhherCommand::writeSequences(vector<int> otuCounts){
2029         try {
2030                 string bases = "TACG";
2031
2032                 string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.fasta";
2033                 ofstream fastaFile;
2034                 m->openOutputFile(fastaFileName, fastaFile);
2035
2036                 vector<string> names(numOTUs, "");
2037
2038                 for(int i=0;i<numOTUs;i++){
2039                         int index = centroids[i];
2040
2041                         if(otuCounts[i] > 0){
2042                                 fastaFile << '>' << seqNameVector[aaI[i][0]] << endl;
2043
2044                                 for(int j=8;j<numFlowCells;j++){
2045
2046                                         char base = bases[j % 4];
2047                                         for(int k=0;k<uniqueFlowgrams[index * numFlowCells + j];k++){
2048                                                 fastaFile << base;
2049                                         }
2050                                 }
2051                                 fastaFile << endl;
2052                         }
2053                 }
2054                 fastaFile.close();
2055
2056                 if(compositeFASTAFileName != ""){
2057                         m->appendFiles(fastaFileName, compositeFASTAFileName);
2058                 }
2059         }
2060         catch(exception& e) {
2061                 m->errorOut(e, "ShhherCommand", "writeSequences");
2062                 exit(1);
2063         }
2064 }
2065
2066 /**************************************************************************************************/
2067
2068 void ShhherCommand::writeNames(vector<int> otuCounts){
2069         try {
2070                 string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.final.names";
2071                 ofstream nameFile;
2072                 m->openOutputFile(nameFileName, nameFile);
2073
2074                 for(int i=0;i<numOTUs;i++){
2075                         if(otuCounts[i] > 0){
2076                                 nameFile << seqNameVector[aaI[i][0]] << '\t' << seqNameVector[aaI[i][0]];
2077
2078                                 for(int j=1;j<nSeqsPerOTU[i];j++){
2079                                         nameFile << ',' << seqNameVector[aaI[i][j]];
2080                                 }
2081
2082                                 nameFile << endl;
2083                         }
2084                 }
2085                 nameFile.close();
2086         }
2087         catch(exception& e) {
2088                 m->errorOut(e, "ShhherCommand", "writeNames");
2089                 exit(1);
2090         }
2091 }
2092
2093 /**************************************************************************************************/
2094
2095 void ShhherCommand::writeGroups(){
2096         try {
2097                 string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
2098                 string groupFileName = fileRoot + ".pn.groups";
2099                 ofstream groupFile;
2100                 m->openOutputFile(groupFileName, groupFile);
2101
2102                 for(int i=0;i<numSeqs;i++){
2103                         groupFile << seqNameVector[i] << '\t' << fileRoot << endl;
2104                 }
2105                 groupFile.close();
2106         }
2107         catch(exception& e) {
2108                 m->errorOut(e, "ShhherCommand", "writeGroups");
2109                 exit(1);
2110         }
2111 }
2112
2113 /**************************************************************************************************/
2114
2115 void ShhherCommand::writeClusters(vector<int> otuCounts){
2116         try {
2117                 string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".pn.counts";
2118                 ofstream otuCountsFile;
2119                 m->openOutputFile(otuCountsFileName, otuCountsFile);
2120
2121                 string bases = "TACG";
2122
2123                 for(int i=0;i<numOTUs;i++){
2124                         //output the translated version of the centroid sequence for the otu
2125                         if(otuCounts[i] > 0){
2126                                 int index = centroids[i];
2127
2128                                 otuCountsFile << "ideal\t";
2129                                 for(int j=8;j<numFlowCells;j++){
2130                                         char base = bases[j % 4];
2131                                         for(int s=0;s<uniqueFlowgrams[index * numFlowCells + j];s++){
2132                                                 otuCountsFile << base;
2133                                         }
2134                                 }
2135                                 otuCountsFile << endl;
2136
2137                                 for(int j=0;j<nSeqsPerOTU[i];j++){
2138                                         int sequence = aaI[i][j];
2139                                         otuCountsFile << seqNameVector[sequence] << '\t';
2140
2141                                         for(int k=8;k<lengths[sequence];k++){
2142                                                 char base = bases[k % 4];
2143                                                 int freq = int(0.01 * (double)flowDataIntI[sequence * numFlowCells + k] + 0.5);
2144
2145                                                 for(int s=0;s<freq;s++){
2146                                                         otuCountsFile << base;
2147                                                 }
2148                                         }
2149                                         otuCountsFile << endl;
2150                                 }
2151                                 otuCountsFile << endl;
2152                         }
2153                 }
2154                 otuCountsFile.close();
2155         }
2156         catch(exception& e) {
2157                 m->errorOut(e, "ShhherCommand", "writeClusters");
2158                 exit(1);
2159         }
2160 }
2161
2162 //**********************************************************************************************************************