clustersplitcommand.cpp

   1 /*
   2  *  clustersplitcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/19/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "clustersplitcommand.h"
  11 #include "readcluster.h"
  12 #include "splitmatrix.h"
  13 #include "readphylip.h"
  14 #include "readcolumn.h"
  15 #include "readmatrix.hpp"
  16 #include "inputdata.h"
  17
  18 //**********************************************************************************************************************
  19 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
  20 ClusterSplitCommand::ClusterSplitCommand(string option)  {
  21         try{
  22                 globaldata = GlobalData::getInstance();
  23                 abort = false;
  24
  25                 //allow user to run help
  26                 if(option == "help") { help(); abort = true; }
  27
  28                 else {
  29                         //valid paramters for this command
  30                         string Array[] =  {"phylip","column","name","cutoff","precision","method","showabund","timing","hard","processors","splitcutoff","outputdir","inputdir"};
  31                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  32
  33                         OptionParser parser(option);
  34                         map<string,string> parameters = parser.getParameters();
  35
  36                         ValidParameters validParameter;
  37
  38                         //check to make sure all parameters are valid for command
  39                         map<string,string>::iterator it;
  40                         for (it = parameters.begin(); it != parameters.end(); it++) {
  41                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {
  42                                         abort = true;
  43                                 }
  44                         }
  45
  46                         globaldata->newRead();
  47
  48                         //if the user changes the output directory command factory will send this info to us in the output parameter
  49                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  50
  51                                 //if the user changes the input directory command factory will send this info to us in the output parameter
  52                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  53                         if (inputDir == "not found"){   inputDir = "";          }
  54                         else {
  55                                 string path;
  56                                 it = parameters.find("phylip");
  57                                 //user has given a template file
  58                                 if(it != parameters.end()){
  59                                         path = hasPath(it->second);
  60                                         //if the user has not given a path then, add inputdir. else leave path alone.
  61                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  62                                 }
  63
  64                                 it = parameters.find("column");
  65                                 //user has given a template file
  66                                 if(it != parameters.end()){
  67                                         path = hasPath(it->second);
  68                                         //if the user has not given a path then, add inputdir. else leave path alone.
  69                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
  70                                 }
  71
  72                                 it = parameters.find("name");
  73                                 //user has given a template file
  74                                 if(it != parameters.end()){
  75                                         path = hasPath(it->second);
  76                                         //if the user has not given a path then, add inputdir. else leave path alone.
  77                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  78                                 }
  79                         }
  80
  81                         //check for required parameters
  82                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  83                         if (phylipfile == "not open") { abort = true; }
  84                         else if (phylipfile == "not found") { phylipfile = ""; }
  85                         else {  distfile = phylipfile;  format = "phylip";      }
  86
  87                         columnfile = validParameter.validFile(parameters, "column", true);
  88                         if (columnfile == "not open") { abort = true; }
  89                         else if (columnfile == "not found") { columnfile = ""; }
  90                         else {  distfile = columnfile; format = "column";       }
  91
  92                         namefile = validParameter.validFile(parameters, "name", true);
  93                         if (namefile == "not open") { abort = true; }
  94                         else if (namefile == "not found") { namefile = ""; }
  95
  96                         if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a hcluster command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
  97                         else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
  98
  99                         if (columnfile != "") {
 100                                 if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
 101                         }
 102
 103                         //check for optional parameter and set defaults
 104                         // ...at some point should added some additional type checking...
 105                         //get user cutoff and precision or use defaults
 106                         string temp;
 107                         temp = validParameter.validFile(parameters, "precision", false);
 108                         if (temp == "not found") { temp = "100"; }
 109                         //saves precision legnth for formatting below
 110                         length = temp.length();
 111                         convert(temp, precision);
 112
 113                         temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
 114                         hard = isTrue(temp);
 115
 116                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 117                         convert(temp, processors);
 118
 119                         temp = validParameter.validFile(parameters, "cutoff", false);
 120                         if (temp == "not found") { temp = "10"; }
 121                         convert(temp, cutoff);
 122                         if (!hard) {    cutoff += (5 / (precision * 10.0));  }
 123
 124                         temp = validParameter.validFile(parameters, "splitcutoff", false);
 125                         if (temp == "not found") { temp = "0.10"; }
 126                         convert(temp, splitcutoff);
 127                         if (!hard) {    splitcutoff += (5 / (precision * 10.0));  }
 128
 129                         method = validParameter.validFile(parameters, "method", false);
 130                         if (method == "not found") { method = "furthest"; }
 131
 132                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 133                         else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 134
 135                         showabund = validParameter.validFile(parameters, "showabund", false);
 136                         if (showabund == "not found") { showabund = "T"; }
 137
 138                         timing = validParameter.validFile(parameters, "timing", false);
 139                         if (timing == "not found") { timing = "F"; }
 140
 141                 }
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "ClusterSplitCommand", "ClusterSplitCommand");
 145                 exit(1);
 146         }
 147 }
 148
 149 //**********************************************************************************************************************
 150
 151 void ClusterSplitCommand::help(){
 152         try {
 153                 m->mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
 154                 m->mothurOut("The cluster command parameter options are method, cuttoff, hard, precision, showabund and timing. No parameters are required.\n");
 155                 m->mothurOut("The cluster command should be in the following format: \n");
 156                 m->mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
 157                 m->mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");
 158         }
 159         catch(exception& e) {
 160                 m->errorOut(e, "ClusterSplitCommand", "help");
 161                 exit(1);
 162         }
 163 }
 164
 165 //**********************************************************************************************************************
 166
 167 ClusterSplitCommand::~ClusterSplitCommand(){}
 168
 169 //**********************************************************************************************************************
 170
 171 int ClusterSplitCommand::execute(){
 172         try {
 173
 174                 if (abort == true) {    return 0;       }
 175
 176                 //****************** file prep work ******************************//
 177
 178                 //if user gave a phylip file convert to column file
 179                 if (format == "phylip") {
 180
 181                         ReadCluster* convert = new ReadCluster(distfile, cutoff, outputDir, false);
 182
 183                         NameAssignment* nameMap = NULL;
 184                         convert->setFormat("phylip");
 185                         convert->read(nameMap);
 186
 187                         if (m->control_pressed) {  delete convert;  return 0;  }
 188
 189                         distfile = convert->getOutputFile();
 190
 191                         //if no names file given with phylip file, create it
 192                         ListVector* listToMakeNameFile =  convert->getListVector();
 193                         if (namefile == "") {  //you need to make a namefile for split matrix
 194                                 ofstream out;
 195                                 namefile = phylipfile + ".names";
 196                                 openOutputFile(namefile, out);
 197                                 for (int i = 0; i < listToMakeNameFile->getNumBins(); i++) {
 198                                         string bin = listToMakeNameFile->get(i);
 199                                         out << bin << '\t' << bin << endl;
 200                                 }
 201                                 out.close();
 202                         }
 203                         delete listToMakeNameFile;
 204                         delete convert;
 205                 }
 206                 if (m->control_pressed) { return 0; }
 207
 208                 time_t estart = time(NULL);
 209
 210                 //split matrix into non-overlapping groups
 211                 SplitMatrix* split = new SplitMatrix(distfile, namefile, splitcutoff);
 212                 split->split();
 213
 214                 if (m->control_pressed) { delete split; return 0; }
 215
 216                 string singletonName = split->getSingletonNames();
 217                 vector< map<string, string> > distName = split->getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
 218                 delete split;
 219
 220                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to split the distance file."); m->mothurOutEndLine();
 221                 estart = time(NULL);
 222
 223                 if (m->control_pressed) { return 0; }
 224
 225                 //****************** break up files between processes and cluster each file set ******************************//
 226                 vector<string> listFileNames;
 227                 set<string> labels;
 228                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 229                                 if(processors == 1){
 230                                         listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 231                                 }else{
 232                                         vector < vector < map<string, string> > > dividedNames; //distNames[1] = vector of filenames for process 1...
 233                                         dividedNames.resize(processors);
 234
 235                                         //for each file group figure out which process will complete it
 236                                         //want to divide the load intelligently so the big files are spread between processes
 237                                         int count = 1;
 238                                         for (int i = 0; i < distName.size(); i++) {
 239                                                 int processToAssign = (i+1) % processors;
 240                                                 if (processToAssign == 0) { processToAssign = processors; }
 241
 242                                                 dividedNames[(processToAssign-1)].push_back(distName[i]);
 243                                         }
 244
 245                                         //not lets reverse the order of ever other process, so we balance big files running with little ones
 246                                         for (int i = 0; i < processors; i++) {
 247                                                 int remainder = ((i+1) % processors);
 248                                                 if (remainder) {  reverse(dividedNames[i].begin(), dividedNames[i].end());  }
 249                                         }
 250
 251                                         createProcesses(dividedNames);
 252
 253                                         if (m->control_pressed) { return 0; }
 254
 255                                         //get list of list file names from each process
 256                                         for(int i=0;i<processors;i++){
 257                                                 string filename = toString(processIDS[i]) + ".temp";
 258                                                 ifstream in;
 259                                                 openInputFile(filename, in);
 260
 261                                                 while(!in.eof()) {
 262                                                         string tempName;
 263                                                         in >> tempName; gobble(in);
 264                                                         listFileNames.push_back(tempName);
 265                                                 }
 266                                                 in.close();
 267                                                 remove((toString(processIDS[i]) + ".temp").c_str());
 268
 269                                                 //get labels
 270                                                 filename = toString(processIDS[i]) + ".temp.labels";
 271                                                 ifstream in2;
 272                                                 openInputFile(filename, in2);
 273
 274                                                 while(!in2.eof()) {
 275                                                         string tempName;
 276                                                         in2 >> tempName; gobble(in);
 277                                                         if (labels.count(tempName) == 0) { labels.insert(tempName); }
 278                                                 }
 279                                                 in2.close();
 280                                                 remove((toString(processIDS[i]) + ".temp.labels").c_str());
 281                                         }
 282                                 }
 283                 #else
 284                                 listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 285                 #endif
 286
 287                 if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { remove(listFileNames[i].c_str()); } return 0; }
 288
 289                 //****************** merge list file and create rabund and sabund files ******************************//
 290
 291                 mergeLists(listFileNames, singletonName, labels);
 292
 293                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 294
 295                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
 296
 297                 m->mothurOutEndLine();
 298                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 299                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 300                 m->mothurOutEndLine();
 301
 302                 return 0;
 303         }
 304         catch(exception& e) {
 305                 m->errorOut(e, "ClusterSplitCommand", "execute");
 306                 exit(1);
 307         }
 308 }
 309 //**********************************************************************************************************************
 310 int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton, set<string> userLabels){
 311         try {
 312                 if (outputDir == "") { outputDir += hasPath(distfile); }
 313                 fileroot = outputDir + getRootName(getSimpleName(distfile));
 314
 315                 openOutputFile(fileroot+ tag + ".sabund",       outSabund);
 316                 openOutputFile(fileroot+ tag + ".rabund",       outRabund);
 317                 openOutputFile(fileroot+ tag + ".list",         outList);
 318
 319                 outputNames.push_back(fileroot+ tag + ".sabund");
 320                 outputNames.push_back(fileroot+ tag + ".rabund");
 321                 outputNames.push_back(fileroot+ tag + ".list");
 322
 323                 //read in singletons
 324                 ListVector* listSingle = NULL;
 325                 if (singleton != "none") {
 326                         ifstream in;
 327                         openInputFile(singleton, in);
 328
 329                         string firstCol, secondCol;
 330                         listSingle = new ListVector();
 331                         while (!in.eof()) {
 332                                 in >> firstCol >> secondCol; gobble(in);
 333                                 listSingle->push_back(secondCol);
 334                         }
 335                         in.close();
 336                 }
 337
 338                 vector<float> orderFloat;
 339
 340                 //go through users set and make them floats so we can sort them
 341                 for(set<string>::iterator it = userLabels.begin(); it != userLabels.end(); ++it) {
 342                         float temp;
 343
 344                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
 345                                 convert(*it, temp);
 346                                 orderFloat.push_back(temp);
 347                         }else if (*it == "unique") { orderFloat.push_back(-1.0); }
 348                         else {
 349                                 userLabels.erase(*it);
 350                                 it--;
 351                         }
 352                 }
 353
 354                 //sort order
 355                 sort(orderFloat.begin(), orderFloat.end());
 356
 357                 vector<InputData*> inputs;
 358                 vector<string> lastLabels;
 359                 for (int i = 0; i < listNames.size(); i++) {
 360                         InputData* input = new InputData(listNames[i], "list");
 361                         inputs.push_back(input);
 362
 363                         ifstream in;
 364                         openInputFile(listNames[i], in);
 365                         ListVector tempList(in);
 366                         lastLabels.push_back(tempList.getLabel());
 367                         in.close();
 368                 }
 369
 370                 ListVector* merged = NULL;
 371
 372                 //for each label needed
 373                 for(int l = 0; l < orderFloat.size(); l++){
 374
 375                         string thisLabel;
 376                         if (orderFloat[l] == -1) { thisLabel = "unique"; }
 377                         else { thisLabel = toString(orderFloat[l],  length-1);  }
 378
 379                         //get the list info from each file
 380                         for (int k = 0; k < listNames.size(); k++) {
 381
 382                                 if (m->control_pressed) {
 383                                         if (listSingle != NULL) { delete listSingle; remove(singleton.c_str());  }
 384                                         for (int i = 0; i < listNames.size(); i++) {  delete inputs[i];  remove(listNames[i].c_str());  }
 385                                         delete merged; merged = NULL;
 386                                         return 0;
 387                                 }
 388
 389                                 ListVector* list = inputs[k]->getListVector();
 390
 391                                 //this file has reached the end
 392                                 if (list == NULL) { list = inputs[k]->getListVector(lastLabels[k], true); }
 393
 394                                 float labelFloat;
 395                                 if (list->getLabel() == "unique") {  labelFloat = -1.0;  }
 396                                 else { convert(list->getLabel(), labelFloat); }
 397
 398                                 //check for missing labels
 399                                 if (labelFloat > orderFloat[l]) { //you are missing the label, get the next smallest one
 400                                         //if its bigger get last label, otherwise keep it
 401                                         delete list;
 402                                         list = inputs[k]->getListVector(lastLabels[k], true); //get last list vector to use, you actually want to move back in the file
 403                                 }
 404                                 lastLabels[k] = list->getLabel();
 405
 406                                 //is this the first file
 407                                 if (merged == NULL) {  merged = new ListVector();  merged->setLabel(thisLabel); }
 408
 409                                 for (int j = 0; j < list->getNumBins(); j++) {
 410                                         merged->push_back(list->get(j));
 411                                 }
 412
 413                                 delete list;
 414                         }
 415
 416                         //add in singletons
 417                         for (int j = 0; j < listSingle->getNumBins(); j++) {
 418                                 merged->push_back(listSingle->get(j));
 419                         }
 420
 421                         //print to files
 422                         printData(merged);
 423
 424                         delete merged; merged = NULL;
 425                 }
 426
 427                 if (listSingle != NULL) { delete listSingle; remove(singleton.c_str());  }
 428
 429                 for (int i = 0; i < listNames.size(); i++) {  delete inputs[i];  remove(listNames[i].c_str());  }
 430
 431                 return 0;
 432         }
 433         catch(exception& e) {
 434                 m->errorOut(e, "ClusterSplitCommand", "mergeLists");
 435                 exit(1);
 436         }
 437 }
 438 //**********************************************************************************************************************
 439
 440 void ClusterSplitCommand::printData(ListVector* oldList){
 441         try {
 442                 string label = oldList->getLabel();
 443                 RAbundVector oldRAbund = oldList->getRAbundVector();
 444
 445                 oldRAbund.setLabel(label);
 446                 if (isTrue(showabund)) {
 447                         oldRAbund.getSAbundVector().print(cout);
 448                 }
 449                 oldRAbund.print(outRabund);
 450                 oldRAbund.getSAbundVector().print(outSabund);
 451
 452                 oldList->print(outList);
 453         }
 454         catch(exception& e) {
 455                 m->errorOut(e, "ClusterSplitCommand", "printData");
 456                 exit(1);
 457         }
 458 }
 459 //**********************************************************************************************************************
 460 int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> > > dividedNames){
 461         try {
 462
 463         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 464                 int process = 0;
 465                 int exitCommand = 1;
 466                 processIDS.clear();
 467
 468                 //loop through and create all the processes you want
 469                 while (process != processors) {
 470                         int pid = fork();
 471
 472                         if (pid > 0) {
 473                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 474                                 process++;
 475                         }else if (pid == 0){
 476                                 set<string> labels;
 477                                 vector<string> listFileNames = cluster(dividedNames[process], labels);
 478
 479                                 //write out names to file
 480                                 string filename = toString(getpid()) + ".temp";
 481                                 ofstream out;
 482                                 openOutputFile(filename, out);
 483                                 for (int j = 0; j < listFileNames.size(); j++) { out << listFileNames[j] << endl;  }
 484                                 out.close();
 485
 486                                 //print out labels
 487                                 ofstream outLabels;
 488                                 filename = toString(getpid()) + ".temp.labels";
 489                                 openOutputFile(filename, outLabels);
 490
 491                                 for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {
 492                                         outLabels << (*it) << endl;
 493                                 }
 494                                 outLabels.close();
 495
 496                                 exit(0);
 497                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 498                 }
 499
 500                 //force parent to wait until all the processes are done
 501                 for (int i=0;i<processors;i++) {
 502                         int temp = processIDS[i];
 503                         wait(&temp);
 504                 }
 505
 506                 return exitCommand;
 507         #endif
 508
 509         }
 510         catch(exception& e) {
 511                 m->errorOut(e, "ClusterSplitCommand", "createProcesses");
 512                 exit(1);
 513         }
 514 }
 515 //**********************************************************************************************************************
 516
 517 vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNames, set<string>& labels){
 518         try {
 519                 Cluster* cluster;
 520                 SparseMatrix* matrix;
 521                 ListVector* list;
 522                 ListVector oldList;
 523                 RAbundVector* rabund;
 524
 525                 vector<string> listFileNames;
 526
 527                 //cluster each distance file
 528                 for (int i = 0; i < distNames.size(); i++) {
 529
 530                         string thisNamefile = distNames[i].begin()->second;
 531                         string thisDistFile = distNames[i].begin()->first;
 532
 533                         //read in distance file
 534                         globaldata->setNameFile(thisNamefile);
 535                         globaldata->setColumnFile(thisDistFile); globaldata->setFormat("column");
 536
 537                         ReadMatrix* read = new ReadColumnMatrix(thisDistFile);
 538                         read->setCutoff(cutoff);
 539
 540                         NameAssignment* nameMap = new NameAssignment(thisNamefile);
 541                         nameMap->readMap();
 542                         read->read(nameMap);
 543
 544                         if (m->control_pressed) {  delete read; delete nameMap; return listFileNames; }
 545
 546                         list = read->getListVector();
 547                         oldList = *list;
 548                         matrix = read->getMatrix();
 549
 550                         delete read;
 551                         delete nameMap;
 552
 553                         m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
 554
 555                         rabund = new RAbundVector(list->getRAbundVector());
 556
 557                         //create cluster
 558                         if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
 559                         else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
 560                         else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);     }
 561                         tag = cluster->getTag();
 562
 563                         if (outputDir == "") { outputDir += hasPath(thisDistFile); }
 564                         fileroot = outputDir + getRootName(getSimpleName(thisDistFile));
 565
 566                         ofstream listFile;
 567                         openOutputFile(fileroot+ tag + ".list", listFile);
 568
 569                         listFileNames.push_back(fileroot+ tag + ".list");
 570
 571                         time_t estart = time(NULL);
 572
 573                         float previousDist = 0.00000;
 574                         float rndPreviousDist = 0.00000;
 575
 576                         oldList = *list;
 577
 578                         print_start = true;
 579                         start = time(NULL);
 580                         double saveCutoff = cutoff;
 581
 582                         while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
 583
 584                                 if (m->control_pressed) { //clean up
 585                                         delete matrix; delete list;     delete cluster; delete rabund;
 586                                         listFile.close();
 587                                         for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
 588                                         listFileNames.clear(); return listFileNames;
 589                                 }
 590
 591                                 cluster->update(cutoff);
 592
 593                                 float dist = matrix->getSmallDist();
 594                                 float rndDist = roundDist(dist, precision);
 595
 596                                 if(previousDist <= 0.0000 && dist != previousDist){
 597                                         oldList.setLabel("unique");
 598                                         oldList.print(listFile);
 599                                         if (labels.count("unique") == 0) {  labels.insert("unique");  }
 600                                 }
 601                                 else if(rndDist != rndPreviousDist){
 602                                         oldList.setLabel(toString(rndPreviousDist,  length-1));
 603                                         oldList.print(listFile);
 604                                         if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
 605                                 }
 606
 607                                 previousDist = dist;
 608                                 rndPreviousDist = rndDist;
 609                                 oldList = *list;
 610                         }
 611
 612
 613                         if(previousDist <= 0.0000){
 614                                 oldList.setLabel("unique");
 615                                 oldList.print(listFile);
 616                                 if (labels.count("unique") == 0) { labels.insert("unique"); }
 617                         }
 618                         else if(rndPreviousDist<cutoff){
 619                                 oldList.setLabel(toString(rndPreviousDist,  length-1));
 620                                 oldList.print(listFile);
 621                                 if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
 622                         }
 623
 624                         delete matrix; delete list;     delete cluster; delete rabund;
 625                         listFile.close();
 626
 627                         if (m->control_pressed) { //clean up
 628                                 for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
 629                                 listFileNames.clear(); return listFileNames;
 630                         }
 631
 632                         remove(thisDistFile.c_str());
 633                         remove(thisNamefile.c_str());
 634                 }
 635
 636
 637                 return listFileNames;
 638
 639         }
 640         catch(exception& e) {
 641                 m->errorOut(e, "ClusterSplitCommand", "cluster");
 642                 exit(1);
 643         }
 644
 645
 646 }
 647
 648 //**********************************************************************************************************************