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