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","splitmethod","taxonomy","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                                 it = parameters.find("taxonomy");
  81                                 //user has given a template file
  82                                 if(it != parameters.end()){
  83                                         path = hasPath(it->second);
  84                                         //if the user has not given a path then, add inputdir. else leave path alone.
  85                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
  86                                 }
  87                         }
  88
  89                         //check for required parameters
  90                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  91                         if (phylipfile == "not open") { abort = true; }
  92                         else if (phylipfile == "not found") { phylipfile = ""; }
  93                         else {  distfile = phylipfile;  format = "phylip";      }
  94
  95                         columnfile = validParameter.validFile(parameters, "column", true);
  96                         if (columnfile == "not open") { abort = true; }
  97                         else if (columnfile == "not found") { columnfile = ""; }
  98                         else {  distfile = columnfile; format = "column";       }
  99
 100                         namefile = validParameter.validFile(parameters, "name", true);
 101                         if (namefile == "not open") { abort = true; }
 102                         else if (namefile == "not found") { namefile = ""; }
 103
 104                         taxFile = validParameter.validFile(parameters, "taxonomy", true);
 105                         if (taxFile == "not open") { abort = true; }
 106                         else if (taxFile == "not found") { taxFile = ""; }
 107
 108                         if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a cluster.split command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
 109                         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; }
 110
 111                         if (columnfile != "") {
 112                                 if (namefile == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; }
 113                         }
 114
 115                         //check for optional parameter and set defaults
 116                         // ...at some point should added some additional type checking...
 117                         //get user cutoff and precision or use defaults
 118                         string temp;
 119                         temp = validParameter.validFile(parameters, "precision", false);
 120                         if (temp == "not found") { temp = "100"; }
 121                         //saves precision legnth for formatting below
 122                         length = temp.length();
 123                         convert(temp, precision);
 124
 125                         temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
 126                         hard = isTrue(temp);
 127
 128                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 129                         convert(temp, processors);
 130
 131                         temp = validParameter.validFile(parameters, "cutoff", false);
 132                         if (temp == "not found") { temp = "10"; }
 133                         convert(temp, cutoff);
 134                         cutoff += (5 / (precision * 10.0));
 135
 136                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "furthest"; }
 137
 138                         splitmethod = validParameter.validFile(parameters, "splitmethod", false);               if (splitmethod == "not found") { method = "distance"; }
 139
 140                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 141                         else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 142
 143                         if ((splitmethod == "distance") || (splitmethod == "classify")) { }
 144                         else { m->mothurOut("Not a valid splitting method.  Valid splitting algorithms are distance or classify."); m->mothurOutEndLine(); abort = true; }
 145
 146                         if ((splitmethod == "classify") && (taxFile == "")) {  m->mothurOut("You need to provide a taxonomy file if you are going to use the classify splitmethod."); m->mothurOutEndLine(); abort = true;  }
 147
 148                         showabund = validParameter.validFile(parameters, "showabund", false);
 149                         if (showabund == "not found") { showabund = "T"; }
 150
 151                         timing = validParameter.validFile(parameters, "timing", false);
 152                         if (timing == "not found") { timing = "F"; }
 153
 154                 }
 155         }
 156         catch(exception& e) {
 157                 m->errorOut(e, "ClusterSplitCommand", "ClusterSplitCommand");
 158                 exit(1);
 159         }
 160 }
 161
 162 //**********************************************************************************************************************
 163
 164 void ClusterSplitCommand::help(){
 165         try {
 166                 m->mothurOut("The cluster.split command parameter options are cutoff, splitcutoff, precision, method, splitmethod, phylip, column, name, showabund, timing. Phylip or column and name are required.\n");
 167                 m->mothurOut("The phylip and column parameter allow you to enter your distance file. \n");
 168                 m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
 169                 m->mothurOut("The cluster.split command should be in the following format: \n");
 170                 m->mothurOut("cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
 171                 m->mothurOut("Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify) \n");
 172
 173         }
 174         catch(exception& e) {
 175                 m->errorOut(e, "ClusterSplitCommand", "help");
 176                 exit(1);
 177         }
 178 }
 179
 180 //**********************************************************************************************************************
 181
 182 ClusterSplitCommand::~ClusterSplitCommand(){}
 183
 184 //**********************************************************************************************************************
 185
 186 int ClusterSplitCommand::execute(){
 187         try {
 188
 189                 if (abort == true) {    return 0;       }
 190
 191                 //****************** file prep work ******************************//
 192
 193                 //if user gave a phylip file convert to column file
 194                 if (format == "phylip") {
 195
 196                         ReadCluster* convert = new ReadCluster(distfile, cutoff, outputDir, false);
 197
 198                         NameAssignment* nameMap = NULL;
 199                         convert->setFormat("phylip");
 200                         convert->read(nameMap);
 201
 202                         if (m->control_pressed) {  delete convert;  return 0;  }
 203
 204                         distfile = convert->getOutputFile();
 205
 206                         //if no names file given with phylip file, create it
 207                         ListVector* listToMakeNameFile =  convert->getListVector();
 208                         if (namefile == "") {  //you need to make a namefile for split matrix
 209                                 ofstream out;
 210                                 namefile = phylipfile + ".names";
 211                                 openOutputFile(namefile, out);
 212                                 for (int i = 0; i < listToMakeNameFile->getNumBins(); i++) {
 213                                         string bin = listToMakeNameFile->get(i);
 214                                         out << bin << '\t' << bin << endl;
 215                                 }
 216                                 out.close();
 217                         }
 218                         delete listToMakeNameFile;
 219                         delete convert;
 220                 }
 221                 if (m->control_pressed) { return 0; }
 222
 223                 time_t estart = time(NULL);
 224
 225                 //split matrix into non-overlapping groups
 226                 SplitMatrix* split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod);
 227                 split->split();
 228
 229                 if (m->control_pressed) { delete split; return 0; }
 230
 231                 string singletonName = split->getSingletonNames();
 232                 vector< map<string, string> > distName = split->getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
 233                 delete split;
 234
 235                 if (m->control_pressed) { return 0; }
 236
 237                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to split the distance file."); m->mothurOutEndLine();
 238                 estart = time(NULL);
 239
 240                 //****************** break up files between processes and cluster each file set ******************************//
 241                 vector<string> listFileNames;
 242                 set<string> labels;
 243                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 244                                 if(processors == 1){
 245                                         listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 246                                 }else{
 247                                         vector < vector < map<string, string> > > dividedNames; //distNames[1] = vector of filenames for process 1...
 248                                         dividedNames.resize(processors);
 249
 250                                         //for each file group figure out which process will complete it
 251                                         //want to divide the load intelligently so the big files are spread between processes
 252                                         int count = 1;
 253                                         for (int i = 0; i < distName.size(); i++) {
 254                                                 int processToAssign = (i+1) % processors;
 255                                                 if (processToAssign == 0) { processToAssign = processors; }
 256
 257                                                 dividedNames[(processToAssign-1)].push_back(distName[i]);
 258                                         }
 259
 260                                         //not lets reverse the order of ever other process, so we balance big files running with little ones
 261                                         for (int i = 0; i < processors; i++) {
 262                                                 int remainder = ((i+1) % processors);
 263                                                 if (remainder) {  reverse(dividedNames[i].begin(), dividedNames[i].end());  }
 264                                         }
 265
 266                                         createProcesses(dividedNames);
 267
 268                                         if (m->control_pressed) { return 0; }
 269
 270                                         //get list of list file names from each process
 271                                         for(int i=0;i<processors;i++){
 272                                                 string filename = toString(processIDS[i]) + ".temp";
 273                                                 ifstream in;
 274                                                 openInputFile(filename, in);
 275
 276                                                 while(!in.eof()) {
 277                                                         string tempName;
 278                                                         in >> tempName; gobble(in);
 279                                                         listFileNames.push_back(tempName);
 280                                                 }
 281                                                 in.close();
 282                                                 remove((toString(processIDS[i]) + ".temp").c_str());
 283
 284                                                 //get labels
 285                                                 filename = toString(processIDS[i]) + ".temp.labels";
 286                                                 ifstream in2;
 287                                                 openInputFile(filename, in2);
 288
 289                                                 while(!in2.eof()) {
 290                                                         string tempName;
 291                                                         in2 >> tempName; gobble(in);
 292                                                         if (labels.count(tempName) == 0) { labels.insert(tempName); }
 293                                                 }
 294                                                 in2.close();
 295                                                 remove((toString(processIDS[i]) + ".temp.labels").c_str());
 296                                         }
 297                                 }
 298                 #else
 299                                 listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 300                 #endif
 301
 302                 if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { remove(listFileNames[i].c_str()); } return 0; }
 303
 304                 //****************** merge list file and create rabund and sabund files ******************************//
 305
 306                 mergeLists(listFileNames, singletonName, labels);
 307
 308                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 309
 310                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
 311
 312                 m->mothurOutEndLine();
 313                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 314                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 315                 m->mothurOutEndLine();
 316
 317                 return 0;
 318         }
 319         catch(exception& e) {
 320                 m->errorOut(e, "ClusterSplitCommand", "execute");
 321                 exit(1);
 322         }
 323 }
 324 //**********************************************************************************************************************
 325 int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton, set<string> userLabels){
 326         try {
 327                 if (outputDir == "") { outputDir += hasPath(distfile); }
 328                 fileroot = outputDir + getRootName(getSimpleName(distfile));
 329
 330                 openOutputFile(fileroot+ tag + ".sabund",       outSabund);
 331                 openOutputFile(fileroot+ tag + ".rabund",       outRabund);
 332                 openOutputFile(fileroot+ tag + ".list",         outList);
 333
 334                 outputNames.push_back(fileroot+ tag + ".sabund");
 335                 outputNames.push_back(fileroot+ tag + ".rabund");
 336                 outputNames.push_back(fileroot+ tag + ".list");
 337
 338                 //read in singletons
 339                 ListVector* listSingle = NULL;
 340                 if (singleton != "none") {
 341                         ifstream in;
 342                         openInputFile(singleton, in);
 343
 344                         string firstCol, secondCol;
 345                         listSingle = new ListVector();
 346                         while (!in.eof()) {
 347                                 in >> firstCol >> secondCol; gobble(in);
 348                                 listSingle->push_back(secondCol);
 349                         }
 350                         in.close();
 351                 }
 352
 353                 vector<float> orderFloat;
 354
 355                 //go through users set and make them floats so we can sort them
 356                 for(set<string>::iterator it = userLabels.begin(); it != userLabels.end(); ++it) {
 357                         float temp;
 358
 359                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
 360                                 convert(*it, temp);
 361                                 orderFloat.push_back(temp);
 362                         }else if (*it == "unique") { orderFloat.push_back(-1.0); }
 363                         else {
 364                                 userLabels.erase(*it);
 365                                 it--;
 366                         }
 367                 }
 368
 369                 //sort order
 370                 sort(orderFloat.begin(), orderFloat.end());
 371
 372                 vector<InputData*> inputs;
 373                 vector<string> lastLabels;
 374                 for (int i = 0; i < listNames.size(); i++) {
 375                         InputData* input = new InputData(listNames[i], "list");
 376                         inputs.push_back(input);
 377
 378                         ifstream in;
 379                         openInputFile(listNames[i], in);
 380                         ListVector tempList(in);
 381                         lastLabels.push_back(tempList.getLabel());
 382                         in.close();
 383                 }
 384
 385                 ListVector* merged = NULL;
 386
 387                 //for each label needed
 388                 for(int l = 0; l < orderFloat.size(); l++){
 389
 390                         string thisLabel;
 391                         if (orderFloat[l] == -1) { thisLabel = "unique"; }
 392                         else { thisLabel = toString(orderFloat[l],  length-1);  }
 393
 394                         //get the list info from each file
 395                         for (int k = 0; k < listNames.size(); k++) {
 396
 397                                 if (m->control_pressed) {
 398                                         if (listSingle != NULL) { delete listSingle; remove(singleton.c_str());  }
 399                                         for (int i = 0; i < listNames.size(); i++) {  delete inputs[i];  remove(listNames[i].c_str());  }
 400                                         delete merged; merged = NULL;
 401                                         return 0;
 402                                 }
 403
 404                                 ListVector* list = inputs[k]->getListVector();
 405
 406                                 //this file has reached the end
 407                                 if (list == NULL) { list = inputs[k]->getListVector(lastLabels[k], true); }
 408
 409                                 float labelFloat;
 410                                 if (list->getLabel() == "unique") {  labelFloat = -1.0;  }
 411                                 else { convert(list->getLabel(), labelFloat); }
 412
 413                                 //check for missing labels
 414                                 if (labelFloat > orderFloat[l]) { //you are missing the label, get the next smallest one
 415                                         //if its bigger get last label, otherwise keep it
 416                                         delete list;
 417                                         list = inputs[k]->getListVector(lastLabels[k], true); //get last list vector to use, you actually want to move back in the file
 418                                 }
 419                                 lastLabels[k] = list->getLabel();
 420
 421                                 //is this the first file
 422                                 if (merged == NULL) {  merged = new ListVector();  merged->setLabel(thisLabel); }
 423
 424                                 for (int j = 0; j < list->getNumBins(); j++) {
 425                                         merged->push_back(list->get(j));
 426                                 }
 427
 428                                 delete list;
 429                         }
 430
 431                         //add in singletons
 432                         for (int j = 0; j < listSingle->getNumBins(); j++) {
 433                                 merged->push_back(listSingle->get(j));
 434                         }
 435
 436                         //print to files
 437                         printData(merged);
 438
 439                         delete merged; merged = NULL;
 440                 }
 441
 442                 if (listSingle != NULL) { delete listSingle; remove(singleton.c_str());  }
 443
 444                 for (int i = 0; i < listNames.size(); i++) {  delete inputs[i];  remove(listNames[i].c_str());  }
 445
 446                 return 0;
 447         }
 448         catch(exception& e) {
 449                 m->errorOut(e, "ClusterSplitCommand", "mergeLists");
 450                 exit(1);
 451         }
 452 }
 453 //**********************************************************************************************************************
 454
 455 void ClusterSplitCommand::printData(ListVector* oldList){
 456         try {
 457                 string label = oldList->getLabel();
 458                 RAbundVector oldRAbund = oldList->getRAbundVector();
 459
 460                 oldRAbund.setLabel(label);
 461                 if (isTrue(showabund)) {
 462                         oldRAbund.getSAbundVector().print(cout);
 463                 }
 464                 oldRAbund.print(outRabund);
 465                 oldRAbund.getSAbundVector().print(outSabund);
 466
 467                 oldList->print(outList);
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "ClusterSplitCommand", "printData");
 471                 exit(1);
 472         }
 473 }
 474 //**********************************************************************************************************************
 475 int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> > > dividedNames){
 476         try {
 477
 478         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 479                 int process = 0;
 480                 int exitCommand = 1;
 481                 processIDS.clear();
 482
 483                 //loop through and create all the processes you want
 484                 while (process != processors) {
 485                         int pid = fork();
 486
 487                         if (pid > 0) {
 488                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 489                                 process++;
 490                         }else if (pid == 0){
 491                                 set<string> labels;
 492                                 vector<string> listFileNames = cluster(dividedNames[process], labels);
 493
 494                                 //write out names to file
 495                                 string filename = toString(getpid()) + ".temp";
 496                                 ofstream out;
 497                                 openOutputFile(filename, out);
 498                                 for (int j = 0; j < listFileNames.size(); j++) { out << listFileNames[j] << endl;  }
 499                                 out.close();
 500
 501                                 //print out labels
 502                                 ofstream outLabels;
 503                                 filename = toString(getpid()) + ".temp.labels";
 504                                 openOutputFile(filename, outLabels);
 505
 506                                 for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {
 507                                         outLabels << (*it) << endl;
 508                                 }
 509                                 outLabels.close();
 510
 511                                 exit(0);
 512                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 513                 }
 514
 515                 //force parent to wait until all the processes are done
 516                 for (int i=0;i<processors;i++) {
 517                         int temp = processIDS[i];
 518                         wait(&temp);
 519                 }
 520
 521                 return exitCommand;
 522         #endif
 523
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "ClusterSplitCommand", "createProcesses");
 527                 exit(1);
 528         }
 529 }
 530 //**********************************************************************************************************************
 531
 532 vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNames, set<string>& labels){
 533         try {
 534                 Cluster* cluster;
 535                 SparseMatrix* matrix;
 536                 ListVector* list;
 537                 ListVector oldList;
 538                 RAbundVector* rabund;
 539
 540                 vector<string> listFileNames;
 541
 542                 //cluster each distance file
 543                 for (int i = 0; i < distNames.size(); i++) {
 544
 545                         string thisNamefile = distNames[i].begin()->second;
 546                         string thisDistFile = distNames[i].begin()->first;
 547
 548                         //read in distance file
 549                         globaldata->setNameFile(thisNamefile);
 550                         globaldata->setColumnFile(thisDistFile); globaldata->setFormat("column");
 551
 552                         ReadMatrix* read = new ReadColumnMatrix(thisDistFile);
 553                         read->setCutoff(cutoff);
 554
 555                         NameAssignment* nameMap = new NameAssignment(thisNamefile);
 556                         nameMap->readMap();
 557                         read->read(nameMap);
 558
 559                         if (m->control_pressed) {  delete read; delete nameMap; return listFileNames; }
 560
 561                         list = read->getListVector();
 562                         oldList = *list;
 563                         matrix = read->getMatrix();
 564
 565                         delete read;
 566                         delete nameMap;
 567
 568                         m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
 569
 570                         rabund = new RAbundVector(list->getRAbundVector());
 571
 572                         //create cluster
 573                         if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
 574                         else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
 575                         else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);     }
 576                         tag = cluster->getTag();
 577
 578                         if (outputDir == "") { outputDir += hasPath(thisDistFile); }
 579                         fileroot = outputDir + getRootName(getSimpleName(thisDistFile));
 580
 581                         ofstream listFile;
 582                         openOutputFile(fileroot+ tag + ".list", listFile);
 583
 584                         listFileNames.push_back(fileroot+ tag + ".list");
 585
 586                         time_t estart = time(NULL);
 587
 588                         float previousDist = 0.00000;
 589                         float rndPreviousDist = 0.00000;
 590
 591                         oldList = *list;
 592
 593                         print_start = true;
 594                         start = time(NULL);
 595                         double saveCutoff = cutoff;
 596
 597                         while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
 598
 599                                 if (m->control_pressed) { //clean up
 600                                         delete matrix; delete list;     delete cluster; delete rabund;
 601                                         listFile.close();
 602                                         for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
 603                                         listFileNames.clear(); return listFileNames;
 604                                 }
 605
 606                                 cluster->update(cutoff);
 607
 608                                 float dist = matrix->getSmallDist();
 609                                 float rndDist;
 610                                 if (hard) {
 611                                         rndDist = ceilDist(dist, precision);
 612                                 }else{
 613                                         rndDist = roundDist(dist, precision);
 614                                 }
 615
 616                                 if(previousDist <= 0.0000 && dist != previousDist){
 617                                         oldList.setLabel("unique");
 618                                         oldList.print(listFile);
 619                                         if (labels.count("unique") == 0) {  labels.insert("unique");  }
 620                                 }
 621                                 else if(rndDist != rndPreviousDist){
 622                                         oldList.setLabel(toString(rndPreviousDist,  length-1));
 623                                         oldList.print(listFile);
 624                                         if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
 625                                 }
 626
 627                                 previousDist = dist;
 628                                 rndPreviousDist = rndDist;
 629                                 oldList = *list;
 630                         }
 631
 632
 633                         if(previousDist <= 0.0000){
 634                                 oldList.setLabel("unique");
 635                                 oldList.print(listFile);
 636                                 if (labels.count("unique") == 0) { labels.insert("unique"); }
 637                         }
 638                         else if(rndPreviousDist<cutoff){
 639                                 oldList.setLabel(toString(rndPreviousDist,  length-1));
 640                                 oldList.print(listFile);
 641                                 if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
 642                         }
 643
 644                         delete matrix; delete list;     delete cluster; delete rabund;
 645                         listFile.close();
 646
 647                         if (m->control_pressed) { //clean up
 648                                 for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
 649                                 listFileNames.clear(); return listFileNames;
 650                         }
 651
 652                         remove(thisDistFile.c_str());
 653                         remove(thisNamefile.c_str());
 654                 }
 655
 656
 657                 return listFileNames;
 658
 659         }
 660         catch(exception& e) {
 661                 m->errorOut(e, "ClusterSplitCommand", "cluster");
 662                 exit(1);
 663         }
 664
 665
 666 }
 667
 668 //**********************************************************************************************************************