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","taxlevel","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                         splitmethod = validParameter.validFile(parameters, "splitmethod", false);               if (splitmethod == "not found") { splitmethod = "distance"; }
 132
 133                         temp = validParameter.validFile(parameters, "cutoff", false);           if (temp == "not found")  { temp = "10"; }
 134                         convert(temp, cutoff);
 135                         cutoff += (5 / (precision * 10.0));
 136
 137                         temp = validParameter.validFile(parameters, "taxlevel", false);         if (temp == "not found")  { temp = "1"; }
 138                         convert(temp, taxLevelCutoff);
 139
 140                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found") { method = "furthest"; }
 141
 142                         if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
 143                         else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
 144
 145                         if ((splitmethod == "distance") || (splitmethod == "classify")) { }
 146                         else { m->mothurOut("Not a valid splitting method.  Valid splitting algorithms are distance or classify."); m->mothurOutEndLine(); abort = true; }
 147
 148                         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;  }
 149
 150                         showabund = validParameter.validFile(parameters, "showabund", false);
 151                         if (showabund == "not found") { showabund = "T"; }
 152
 153                         timing = validParameter.validFile(parameters, "timing", false);
 154                         if (timing == "not found") { timing = "F"; }
 155
 156                 }
 157         }
 158         catch(exception& e) {
 159                 m->errorOut(e, "ClusterSplitCommand", "ClusterSplitCommand");
 160                 exit(1);
 161         }
 162 }
 163
 164 //**********************************************************************************************************************
 165
 166 void ClusterSplitCommand::help(){
 167         try {
 168                 m->mothurOut("The cluster.split command parameter options are phylip, column, name, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, hard, processors. Phylip or column and name are required.\n");
 169                 m->mothurOut("The phylip and column parameter allow you to enter your distance file. \n");
 170                 m->mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
 171                 m->mothurOut("The cutoff parameter allow you to set the distance you want to cluster to, default is 10.0. \n");
 172                 m->mothurOut("The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n");
 173                 m->mothurOut("The method allows you to specify what clustering algorythm you want to use, default=furthest, option furthest, nearest, or average. \n");
 174                 m->mothurOut("The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance or classify. \n");
 175                 m->mothurOut("The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n");
 176                 m->mothurOut("The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=1. \n");
 177                 m->mothurOut("The cluster.split command should be in the following format: \n");
 178                 m->mothurOut("cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision, splitmethod=yourSplitmethod, taxonomy=yourTaxonomyfile, taxlevel=yourtaxlevel) \n");
 179                 m->mothurOut("Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify, taxonomy=abrecovery.silva.slv.taxonomy, taxlevel=5) \n");
 180
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "ClusterSplitCommand", "help");
 184                 exit(1);
 185         }
 186 }
 187
 188 //**********************************************************************************************************************
 189
 190 ClusterSplitCommand::~ClusterSplitCommand(){}
 191
 192 //**********************************************************************************************************************
 193
 194 int ClusterSplitCommand::execute(){
 195         try {
 196
 197                 if (abort == true) {    return 0;       }
 198
 199                 //****************** file prep work ******************************//
 200
 201                 //if user gave a phylip file convert to column file
 202                 if (format == "phylip") {
 203
 204                         ReadCluster* convert = new ReadCluster(distfile, cutoff, outputDir, false);
 205
 206                         NameAssignment* nameMap = NULL;
 207                         convert->setFormat("phylip");
 208                         convert->read(nameMap);
 209
 210                         if (m->control_pressed) {  delete convert;  return 0;  }
 211
 212                         distfile = convert->getOutputFile();
 213
 214                         //if no names file given with phylip file, create it
 215                         ListVector* listToMakeNameFile =  convert->getListVector();
 216                         if (namefile == "") {  //you need to make a namefile for split matrix
 217                                 ofstream out;
 218                                 namefile = phylipfile + ".names";
 219                                 openOutputFile(namefile, out);
 220                                 for (int i = 0; i < listToMakeNameFile->getNumBins(); i++) {
 221                                         string bin = listToMakeNameFile->get(i);
 222                                         out << bin << '\t' << bin << endl;
 223                                 }
 224                                 out.close();
 225                         }
 226                         delete listToMakeNameFile;
 227                         delete convert;
 228                 }
 229                 if (m->control_pressed) { return 0; }
 230
 231                 time_t estart = time(NULL);
 232
 233                 //split matrix into non-overlapping groups
 234                 SplitMatrix* split;
 235                 if (splitmethod == "distance")  {       split = new SplitMatrix(distfile, namefile, taxFile, cutoff, splitmethod);                      }
 236                 else                                                    {       split = new SplitMatrix(distfile, namefile, taxFile, taxLevelCutoff, splitmethod);  }
 237
 238                 split->split();
 239
 240                 if (m->control_pressed) { delete split; return 0; }
 241
 242                 string singletonName = split->getSingletonNames();
 243                 vector< map<string, string> > distName = split->getDistanceFiles();  //returns map of distance files -> namefile sorted by distance file size
 244                 delete split;
 245
 246                 if (m->control_pressed) { return 0; }
 247
 248                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to split the distance file."); m->mothurOutEndLine();
 249                 estart = time(NULL);
 250
 251                 //****************** break up files between processes and cluster each file set ******************************//
 252                 vector<string> listFileNames;
 253                 set<string> labels;
 254                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 255                                 if(processors == 1){
 256                                         listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 257                                 }else{
 258                                         vector < vector < map<string, string> > > dividedNames; //distNames[1] = vector of filenames for process 1...
 259                                         dividedNames.resize(processors);
 260
 261                                         //for each file group figure out which process will complete it
 262                                         //want to divide the load intelligently so the big files are spread between processes
 263                                         int count = 1;
 264                                         for (int i = 0; i < distName.size(); i++) {
 265                                                 int processToAssign = (i+1) % processors;
 266                                                 if (processToAssign == 0) { processToAssign = processors; }
 267
 268                                                 dividedNames[(processToAssign-1)].push_back(distName[i]);
 269                                         }
 270
 271                                         //not lets reverse the order of ever other process, so we balance big files running with little ones
 272                                         for (int i = 0; i < processors; i++) {
 273                                                 int remainder = ((i+1) % processors);
 274                                                 if (remainder) {  reverse(dividedNames[i].begin(), dividedNames[i].end());  }
 275                                         }
 276
 277                                         createProcesses(dividedNames);
 278
 279                                         if (m->control_pressed) { return 0; }
 280
 281                                         //get list of list file names from each process
 282                                         for(int i=0;i<processors;i++){
 283                                                 string filename = toString(processIDS[i]) + ".temp";
 284                                                 ifstream in;
 285                                                 openInputFile(filename, in);
 286
 287                                                 while(!in.eof()) {
 288                                                         string tempName;
 289                                                         in >> tempName; gobble(in);
 290                                                         listFileNames.push_back(tempName);
 291                                                 }
 292                                                 in.close();
 293                                                 remove((toString(processIDS[i]) + ".temp").c_str());
 294
 295                                                 //get labels
 296                                                 filename = toString(processIDS[i]) + ".temp.labels";
 297                                                 ifstream in2;
 298                                                 openInputFile(filename, in2);
 299
 300                                                 while(!in2.eof()) {
 301                                                         string tempName;
 302                                                         in2 >> tempName; gobble(in);
 303                                                         if (labels.count(tempName) == 0) { labels.insert(tempName); }
 304                                                 }
 305                                                 in2.close();
 306                                                 remove((toString(processIDS[i]) + ".temp.labels").c_str());
 307                                         }
 308                                 }
 309                 #else
 310                                 listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 311                 #endif
 312
 313                 if (m->control_pressed) { for (int i = 0; i < listFileNames.size(); i++) { remove(listFileNames[i].c_str()); } return 0; }
 314
 315                 //****************** merge list file and create rabund and sabund files ******************************//
 316
 317                 mergeLists(listFileNames, singletonName, labels);
 318
 319                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
 320
 321                 m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
 322
 323                 m->mothurOutEndLine();
 324                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 325                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 326                 m->mothurOutEndLine();
 327
 328                 return 0;
 329         }
 330         catch(exception& e) {
 331                 m->errorOut(e, "ClusterSplitCommand", "execute");
 332                 exit(1);
 333         }
 334 }
 335 //**********************************************************************************************************************
 336 int ClusterSplitCommand::mergeLists(vector<string> listNames, string singleton, set<string> userLabels){
 337         try {
 338                 if (outputDir == "") { outputDir += hasPath(distfile); }
 339                 fileroot = outputDir + getRootName(getSimpleName(distfile));
 340
 341                 openOutputFile(fileroot+ tag + ".sabund",       outSabund);
 342                 openOutputFile(fileroot+ tag + ".rabund",       outRabund);
 343                 openOutputFile(fileroot+ tag + ".list",         outList);
 344
 345                 outputNames.push_back(fileroot+ tag + ".sabund");
 346                 outputNames.push_back(fileroot+ tag + ".rabund");
 347                 outputNames.push_back(fileroot+ tag + ".list");
 348
 349                 //read in singletons
 350                 ListVector* listSingle = NULL;
 351                 if (singleton != "none") {
 352                         ifstream in;
 353                         openInputFile(singleton, in);
 354
 355                         string firstCol, secondCol;
 356                         listSingle = new ListVector();
 357                         while (!in.eof()) {
 358                                 in >> firstCol >> secondCol; gobble(in);
 359                                 listSingle->push_back(secondCol);
 360                         }
 361                         in.close();
 362                 }
 363
 364                 vector<float> orderFloat;
 365
 366                 //go through users set and make them floats so we can sort them
 367                 for(set<string>::iterator it = userLabels.begin(); it != userLabels.end(); ++it) {
 368                         float temp;
 369
 370                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
 371                                 convert(*it, temp);
 372                                 orderFloat.push_back(temp);
 373                         }else if (*it == "unique") { orderFloat.push_back(-1.0); }
 374                         else {
 375                                 userLabels.erase(*it);
 376                                 it--;
 377                         }
 378                 }
 379
 380                 //sort order
 381                 sort(orderFloat.begin(), orderFloat.end());
 382
 383                 vector<InputData*> inputs;
 384                 vector<string> lastLabels;
 385                 for (int i = 0; i < listNames.size(); i++) {
 386                         InputData* input = new InputData(listNames[i], "list");
 387                         inputs.push_back(input);
 388
 389                         ifstream in;
 390                         openInputFile(listNames[i], in);
 391                         ListVector tempList(in);
 392                         lastLabels.push_back(tempList.getLabel());
 393                         in.close();
 394                 }
 395
 396                 ListVector* merged = NULL;
 397
 398                 //for each label needed
 399                 for(int l = 0; l < orderFloat.size(); l++){
 400
 401                         string thisLabel;
 402                         if (orderFloat[l] == -1) { thisLabel = "unique"; }
 403                         else { thisLabel = toString(orderFloat[l],  length-1);  }
 404
 405                         //get the list info from each file
 406                         for (int k = 0; k < listNames.size(); k++) {
 407
 408                                 if (m->control_pressed) {
 409                                         if (listSingle != NULL) { delete listSingle; remove(singleton.c_str());  }
 410                                         for (int i = 0; i < listNames.size(); i++) {  delete inputs[i];  remove(listNames[i].c_str());  }
 411                                         delete merged; merged = NULL;
 412                                         return 0;
 413                                 }
 414
 415                                 ListVector* list = inputs[k]->getListVector();
 416
 417                                 //this file has reached the end
 418                                 if (list == NULL) { list = inputs[k]->getListVector(lastLabels[k], true); }
 419
 420                                 float labelFloat;
 421                                 if (list->getLabel() == "unique") {  labelFloat = -1.0;  }
 422                                 else { convert(list->getLabel(), labelFloat); }
 423
 424                                 //check for missing labels
 425                                 if (labelFloat > orderFloat[l]) { //you are missing the label, get the next smallest one
 426                                         //if its bigger get last label, otherwise keep it
 427                                         delete list;
 428                                         list = inputs[k]->getListVector(lastLabels[k], true); //get last list vector to use, you actually want to move back in the file
 429                                 }
 430                                 lastLabels[k] = list->getLabel();
 431
 432                                 //is this the first file
 433                                 if (merged == NULL) {  merged = new ListVector();  merged->setLabel(thisLabel); }
 434
 435                                 for (int j = 0; j < list->getNumBins(); j++) {
 436                                         merged->push_back(list->get(j));
 437                                 }
 438
 439                                 delete list;
 440                         }
 441
 442                         //add in singletons
 443                         if (listSingle != NULL) {
 444                                 for (int j = 0; j < listSingle->getNumBins(); j++) {
 445                                         merged->push_back(listSingle->get(j));
 446                                 }
 447                         }
 448
 449                         //print to files
 450                         printData(merged);
 451
 452                         delete merged; merged = NULL;
 453                 }
 454
 455                 if (listSingle != NULL) { delete listSingle; remove(singleton.c_str());  }
 456
 457                 for (int i = 0; i < listNames.size(); i++) {  delete inputs[i];  remove(listNames[i].c_str());  }
 458
 459                 return 0;
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "ClusterSplitCommand", "mergeLists");
 463                 exit(1);
 464         }
 465 }
 466 //**********************************************************************************************************************
 467
 468 void ClusterSplitCommand::printData(ListVector* oldList){
 469         try {
 470                 string label = oldList->getLabel();
 471                 RAbundVector oldRAbund = oldList->getRAbundVector();
 472
 473                 oldRAbund.setLabel(label);
 474                 if (isTrue(showabund)) {
 475                         oldRAbund.getSAbundVector().print(cout);
 476                 }
 477                 oldRAbund.print(outRabund);
 478                 oldRAbund.getSAbundVector().print(outSabund);
 479
 480                 oldList->print(outList);
 481         }
 482         catch(exception& e) {
 483                 m->errorOut(e, "ClusterSplitCommand", "printData");
 484                 exit(1);
 485         }
 486 }
 487 //**********************************************************************************************************************
 488 int ClusterSplitCommand::createProcesses(vector < vector < map<string, string> > > dividedNames){
 489         try {
 490
 491         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 492                 int process = 0;
 493                 int exitCommand = 1;
 494                 processIDS.clear();
 495
 496                 //loop through and create all the processes you want
 497                 while (process != processors) {
 498                         int pid = fork();
 499
 500                         if (pid > 0) {
 501                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 502                                 process++;
 503                         }else if (pid == 0){
 504                                 set<string> labels;
 505                                 vector<string> listFileNames = cluster(dividedNames[process], labels);
 506
 507                                 //write out names to file
 508                                 string filename = toString(getpid()) + ".temp";
 509                                 ofstream out;
 510                                 openOutputFile(filename, out);
 511                                 for (int j = 0; j < listFileNames.size(); j++) { out << listFileNames[j] << endl;  }
 512                                 out.close();
 513
 514                                 //print out labels
 515                                 ofstream outLabels;
 516                                 filename = toString(getpid()) + ".temp.labels";
 517                                 openOutputFile(filename, outLabels);
 518
 519                                 for (set<string>::iterator it = labels.begin(); it != labels.end(); it++) {
 520                                         outLabels << (*it) << endl;
 521                                 }
 522                                 outLabels.close();
 523
 524                                 exit(0);
 525                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 526                 }
 527
 528                 //force parent to wait until all the processes are done
 529                 for (int i=0;i<processors;i++) {
 530                         int temp = processIDS[i];
 531                         wait(&temp);
 532                 }
 533
 534                 return exitCommand;
 535         #endif
 536
 537         }
 538         catch(exception& e) {
 539                 m->errorOut(e, "ClusterSplitCommand", "createProcesses");
 540                 exit(1);
 541         }
 542 }
 543 //**********************************************************************************************************************
 544
 545 vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNames, set<string>& labels){
 546         try {
 547                 Cluster* cluster;
 548                 SparseMatrix* matrix;
 549                 ListVector* list;
 550                 ListVector oldList;
 551                 RAbundVector* rabund;
 552
 553                 vector<string> listFileNames;
 554
 555                 //cluster each distance file
 556                 for (int i = 0; i < distNames.size(); i++) {
 557
 558                         string thisNamefile = distNames[i].begin()->second;
 559                         string thisDistFile = distNames[i].begin()->first;
 560
 561                         //read in distance file
 562                         globaldata->setNameFile(thisNamefile);
 563                         globaldata->setColumnFile(thisDistFile); globaldata->setFormat("column");
 564
 565                         ReadMatrix* read = new ReadColumnMatrix(thisDistFile);
 566                         read->setCutoff(cutoff);
 567
 568                         NameAssignment* nameMap = new NameAssignment(thisNamefile);
 569                         nameMap->readMap();
 570                         read->read(nameMap);
 571
 572                         if (m->control_pressed) {  delete read; delete nameMap; return listFileNames; }
 573
 574                         list = read->getListVector();
 575                         oldList = *list;
 576                         matrix = read->getMatrix();
 577
 578                         delete read;
 579                         delete nameMap;
 580
 581                         m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
 582
 583                         rabund = new RAbundVector(list->getRAbundVector());
 584
 585                         //create cluster
 586                         if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
 587                         else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
 588                         else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);     }
 589                         tag = cluster->getTag();
 590
 591                         if (outputDir == "") { outputDir += hasPath(thisDistFile); }
 592                         fileroot = outputDir + getRootName(getSimpleName(thisDistFile));
 593
 594                         ofstream listFile;
 595                         openOutputFile(fileroot+ tag + ".list", listFile);
 596
 597                         listFileNames.push_back(fileroot+ tag + ".list");
 598
 599                         time_t estart = time(NULL);
 600
 601                         float previousDist = 0.00000;
 602                         float rndPreviousDist = 0.00000;
 603
 604                         oldList = *list;
 605
 606                         print_start = true;
 607                         start = time(NULL);
 608                         double saveCutoff = cutoff;
 609
 610                         while (matrix->getSmallDist() < cutoff && matrix->getNNodes() > 0){
 611
 612                                 if (m->control_pressed) { //clean up
 613                                         delete matrix; delete list;     delete cluster; delete rabund;
 614                                         listFile.close();
 615                                         for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
 616                                         listFileNames.clear(); return listFileNames;
 617                                 }
 618
 619                                 cluster->update(cutoff);
 620
 621                                 float dist = matrix->getSmallDist();
 622                                 float rndDist;
 623                                 if (hard) {
 624                                         rndDist = ceilDist(dist, precision);
 625                                 }else{
 626                                         rndDist = roundDist(dist, precision);
 627                                 }
 628
 629                                 if(previousDist <= 0.0000 && dist != previousDist){
 630                                         oldList.setLabel("unique");
 631                                         oldList.print(listFile);
 632                                         if (labels.count("unique") == 0) {  labels.insert("unique");  }
 633                                 }
 634                                 else if(rndDist != rndPreviousDist){
 635                                         oldList.setLabel(toString(rndPreviousDist,  length-1));
 636                                         oldList.print(listFile);
 637                                         if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
 638                                 }
 639
 640                                 previousDist = dist;
 641                                 rndPreviousDist = rndDist;
 642                                 oldList = *list;
 643                         }
 644
 645
 646                         if(previousDist <= 0.0000){
 647                                 oldList.setLabel("unique");
 648                                 oldList.print(listFile);
 649                                 if (labels.count("unique") == 0) { labels.insert("unique"); }
 650                         }
 651                         else if(rndPreviousDist<cutoff){
 652                                 oldList.setLabel(toString(rndPreviousDist,  length-1));
 653                                 oldList.print(listFile);
 654                                 if (labels.count(toString(rndPreviousDist,  length-1)) == 0) { labels.insert(toString(rndPreviousDist,  length-1)); }
 655                         }
 656
 657                         delete matrix; delete list;     delete cluster; delete rabund;
 658                         listFile.close();
 659
 660                         if (m->control_pressed) { //clean up
 661                                 for (int i = 0; i < listFileNames.size(); i++) {        remove(listFileNames[i].c_str());       }
 662                                 listFileNames.clear(); return listFileNames;
 663                         }
 664
 665                         remove(thisDistFile.c_str());
 666                         remove(thisNamefile.c_str());
 667                 }
 668
 669
 670                 return listFileNames;
 671
 672         }
 673         catch(exception& e) {
 674                 m->errorOut(e, "ClusterSplitCommand", "cluster");
 675                 exit(1);
 676         }
 677
 678
 679 }
 680
 681 //**********************************************************************************************************************