mothurout.cpp

   1 /*
   2  *  mothurOut.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 2/25/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mothurout.h"
  11
  12
  13 /******************************************************/
  14 MothurOut* MothurOut::getInstance() {
  15         if( _uniqueInstance == 0) {
  16                 _uniqueInstance = new MothurOut();
  17         }
  18         return _uniqueInstance;
  19 }
  20 /*********************************************************************************************/
  21 set<string> MothurOut::getCurrentTypes()  {
  22         try {
  23
  24         set<string> types;
  25         types.insert("fasta");
  26         types.insert("accnos");
  27         types.insert("column");
  28         types.insert("design");
  29         types.insert("group");
  30         types.insert("list");
  31         types.insert("name");
  32         types.insert("oligos");
  33         types.insert("order");
  34         types.insert("ordergroup");
  35         types.insert("phylip");
  36         types.insert("qfile");
  37         types.insert("relabund");
  38         types.insert("sabund");
  39         types.insert("rabund");
  40         types.insert("sff");
  41         types.insert("shared");
  42         types.insert("taxonomy");
  43         types.insert("tree");
  44         types.insert("flow");
  45         types.insert("biom");
  46         types.insert("count");
  47         types.insert("processors");
  48
  49                 return types;
  50         }
  51         catch(exception& e) {
  52                 errorOut(e, "MothurOut", "getCurrentTypes");
  53                 exit(1);
  54         }
  55 }
  56 /*********************************************************************************************/
  57 void MothurOut::printCurrentFiles()  {
  58         try {
  59
  60
  61                 if (accnosfile != "")           {  mothurOut("accnos=" + accnosfile); mothurOutEndLine();                       }
  62                 if (columnfile != "")           {  mothurOut("column=" + columnfile); mothurOutEndLine();                       }
  63                 if (designfile != "")           {  mothurOut("design=" + designfile); mothurOutEndLine();                       }
  64                 if (fastafile != "")            {  mothurOut("fasta=" + fastafile); mothurOutEndLine();                         }
  65                 if (groupfile != "")            {  mothurOut("group=" + groupfile); mothurOutEndLine();                         }
  66                 if (listfile != "")                     {  mothurOut("list=" + listfile); mothurOutEndLine();                           }
  67                 if (namefile != "")                     {  mothurOut("name=" + namefile); mothurOutEndLine();                           }
  68                 if (oligosfile != "")           {  mothurOut("oligos=" + oligosfile); mothurOutEndLine();                       }
  69                 if (orderfile != "")            {  mothurOut("order=" + orderfile); mothurOutEndLine();                         }
  70                 if (ordergroupfile != "")       {  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();       }
  71                 if (phylipfile != "")           {  mothurOut("phylip=" + phylipfile); mothurOutEndLine();                       }
  72                 if (qualfile != "")                     {  mothurOut("qfile=" + qualfile); mothurOutEndLine();                          }
  73                 if (rabundfile != "")           {  mothurOut("rabund=" + rabundfile); mothurOutEndLine();                       }
  74                 if (relabundfile != "")         {  mothurOut("relabund=" + relabundfile); mothurOutEndLine();           }
  75                 if (sabundfile != "")           {  mothurOut("sabund=" + sabundfile); mothurOutEndLine();                       }
  76                 if (sfffile != "")                      {  mothurOut("sff=" + sfffile); mothurOutEndLine();                                     }
  77                 if (sharedfile != "")           {  mothurOut("shared=" + sharedfile); mothurOutEndLine();                       }
  78                 if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
  79                 if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
  80                 if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
  81         if (biomfile != "")                     {  mothurOut("biom=" + biomfile); mothurOutEndLine();                           }
  82         if (counttablefile != "")       {  mothurOut("count=" + counttablefile); mothurOutEndLine();    }
  83                 if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
  84
  85         }
  86         catch(exception& e) {
  87                 errorOut(e, "MothurOut", "printCurrentFiles");
  88                 exit(1);
  89         }
  90 }
  91 /*********************************************************************************************/
  92 bool MothurOut::hasCurrentFiles()  {
  93         try {
  94                 bool hasCurrent = false;
  95
  96                 if (accnosfile != "")           {  return true;                 }
  97                 if (columnfile != "")           {  return true;                 }
  98                 if (designfile != "")           {  return true;                 }
  99                 if (fastafile != "")            {  return true;                 }
 100                 if (groupfile != "")            {  return true;                 }
 101                 if (listfile != "")                     {  return true;                 }
 102                 if (namefile != "")                     {  return true;                 }
 103                 if (oligosfile != "")           {  return true;                 }
 104                 if (orderfile != "")            {  return true;                 }
 105                 if (ordergroupfile != "")       {  return true;                 }
 106                 if (phylipfile != "")           {  return true;                 }
 107                 if (qualfile != "")                     {  return true;                 }
 108                 if (rabundfile != "")           {  return true;                 }
 109                 if (relabundfile != "")         {  return true;                 }
 110                 if (sabundfile != "")           {  return true;                 }
 111                 if (sfffile != "")                      {  return true;                 }
 112                 if (sharedfile != "")           {  return true;                 }
 113                 if (taxonomyfile != "")         {  return true;                 }
 114                 if (treefile != "")                     {  return true;                 }
 115                 if (flowfile != "")                     {  return true;                 }
 116         if (biomfile != "")                     {  return true;                 }
 117         if (counttablefile != "")       {  return true;                 }
 118                 if (processors != "1")          {  return true;                 }
 119
 120                 return hasCurrent;
 121
 122         }
 123         catch(exception& e) {
 124                 errorOut(e, "MothurOut", "hasCurrentFiles");
 125                 exit(1);
 126         }
 127 }
 128
 129 /*********************************************************************************************/
 130 void MothurOut::clearCurrentFiles()  {
 131         try {
 132                 phylipfile = "";
 133                 columnfile = "";
 134                 listfile = "";
 135                 rabundfile = "";
 136                 sabundfile = "";
 137                 namefile = "";
 138                 groupfile = "";
 139                 designfile = "";
 140                 orderfile = "";
 141                 treefile = "";
 142                 sharedfile = "";
 143                 ordergroupfile = "";
 144                 relabundfile = "";
 145                 fastafile = "";
 146                 qualfile = "";
 147                 sfffile = "";
 148                 oligosfile = "";
 149                 accnosfile = "";
 150                 taxonomyfile = "";
 151                 flowfile = "";
 152         biomfile = "";
 153         counttablefile = "";
 154                 processors = "1";
 155         }
 156         catch(exception& e) {
 157                 errorOut(e, "MothurOut", "clearCurrentFiles");
 158                 exit(1);
 159         }
 160 }
 161 /***********************************************************************/
 162 string MothurOut::findProgramPath(string programName){
 163         try {
 164
 165                 string envPath = getenv("PATH");
 166                 string pPath = "";
 167
 168                 //delimiting path char
 169                 char delim;
 170 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 171         delim = ':';
 172 #else
 173         delim = ';';
 174 #endif
 175
 176                 //break apart path variable by ':'
 177                 vector<string> dirs;
 178                 splitAtChar(envPath, dirs, delim);
 179
 180         if (debug) { mothurOut("[DEBUG]: dir's in path: \n"); }
 181
 182                 //get path related to mothur
 183                 for (int i = 0; i < dirs.size(); i++) {
 184
 185             if (debug) { mothurOut("[DEBUG]: " + dirs[i] + "\n"); }
 186
 187                         //to lower so we can find it
 188                         string tempLower = "";
 189                         for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
 190
 191                         //is this mothurs path?
 192                         if (tempLower.find(programName) != -1) {  pPath = dirs[i]; break;  }
 193                 }
 194
 195                 if (debug) { mothurOut("[DEBUG]: programPath = " + pPath + "\n"); }
 196
 197                 if (pPath != "") {
 198                         //add programName so it looks like what argv would look like
 199 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 200             pPath += "/" + programName;
 201 #else
 202             pPath += "\\" + programName;
 203 #endif
 204                 }else {
 205                         //okay programName is not in the path, so the folder programName is in must be in the path
 206                         //lets find out which one
 207
 208                         //get path related to the program
 209                         for (int i = 0; i < dirs.size(); i++) {
 210
 211                 if (debug) { mothurOut("[DEBUG]: looking in " + dirs[i] + " for " + programName + " \n"); }
 212
 213                                 //is this the programs path?
 214                                 ifstream in;
 215                                 string tempIn = dirs[i];
 216 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 217                 tempIn += "/" + programName;
 218 #else
 219                 tempIn += "\\" + programName;
 220 #endif
 221                                 openInputFile(tempIn, in, "");
 222
 223                                 //if this file exists
 224                                 if (in) { in.close(); pPath = tempIn; if (debug) { mothurOut("[DEBUG]: found it, programPath = " + pPath + "\n"); } break;   }
 225                         }
 226                 }
 227
 228                 return pPath;
 229
 230         }
 231         catch(exception& e) {
 232                 errorOut(e, "MothurOut", "findProgramPath");
 233                 exit(1);
 234         }
 235 }
 236 /*********************************************************************************************/
 237 void MothurOut::setFileName(string filename)  {
 238         try {
 239                 logFileName = filename;
 240
 241                 #ifdef USE_MPI
 242                         int pid;
 243                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 244
 245                         if (pid == 0) { //only one process should output to screen
 246                 #endif
 247
 248                 openOutputFile(filename, out);
 249
 250                 #ifdef USE_MPI
 251                         }
 252                 #endif
 253         }
 254         catch(exception& e) {
 255                 errorOut(e, "MothurOut", "setFileName");
 256                 exit(1);
 257         }
 258 }
 259 /*********************************************************************************************/
 260 void MothurOut::setDefaultPath(string pathname)  {
 261         try {
 262
 263                 //add / to name if needed
 264                 string lastChar = pathname.substr(pathname.length()-1);
 265                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 266                         if (lastChar != "/") { pathname += "/"; }
 267                 #else
 268                         if (lastChar != "\\") { pathname += "\\"; }
 269                 #endif
 270
 271                 defaultPath = pathname;
 272
 273         }
 274         catch(exception& e) {
 275                 errorOut(e, "MothurOut", "setDefaultPath");
 276                 exit(1);
 277         }
 278 }
 279 /*********************************************************************************************/
 280 void MothurOut::setOutputDir(string pathname)  {
 281         try {
 282                 outputDir = pathname;
 283         }
 284         catch(exception& e) {
 285                 errorOut(e, "MothurOut", "setOutputDir");
 286                 exit(1);
 287         }
 288 }
 289 /*********************************************************************************************/
 290 void MothurOut::closeLog()  {
 291         try {
 292
 293                 #ifdef USE_MPI
 294                         int pid;
 295                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 296
 297                         if (pid == 0) { //only one process should output to screen
 298                 #endif
 299
 300                 out.close();
 301
 302                 #ifdef USE_MPI
 303                         }
 304                 #endif
 305         }
 306         catch(exception& e) {
 307                 errorOut(e, "MothurOut", "closeLog");
 308                 exit(1);
 309         }
 310 }
 311
 312 /*********************************************************************************************/
 313 MothurOut::~MothurOut() {
 314         try {
 315                 _uniqueInstance = 0;
 316
 317         }
 318         catch(exception& e) {
 319                 errorOut(e, "MothurOut", "MothurOut");
 320                 exit(1);
 321         }
 322 }
 323 /*********************************************************************************************/
 324 void MothurOut::mothurOut(string output) {
 325         try {
 326
 327                 #ifdef USE_MPI
 328                         int pid;
 329                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 330
 331                         if (pid == 0) { //only one process should output to screen
 332                 #endif
 333
 334                 out << output;
 335         logger() << output;
 336
 337                 #ifdef USE_MPI
 338                         }
 339                 #endif
 340         }
 341         catch(exception& e) {
 342                 errorOut(e, "MothurOut", "MothurOut");
 343                 exit(1);
 344         }
 345 }
 346 /*********************************************************************************************/
 347 void MothurOut::mothurOutEndLine() {
 348         try {
 349                 #ifdef USE_MPI
 350                         int pid;
 351                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 352
 353                         if (pid == 0) { //only one process should output to screen
 354                 #endif
 355
 356                 out << endl;
 357         logger() << endl;
 358
 359                 #ifdef USE_MPI
 360                         }
 361                 #endif
 362         }
 363         catch(exception& e) {
 364                 errorOut(e, "MothurOut", "MothurOutEndLine");
 365                 exit(1);
 366         }
 367 }
 368 /*********************************************************************************************/
 369 void MothurOut::mothurOut(string output, ofstream& outputFile) {
 370         try {
 371
 372 #ifdef USE_MPI
 373                 int pid;
 374                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 375
 376                 if (pid == 0) { //only one process should output to screen
 377 #endif
 378
 379
 380                         out << output;
 381                         outputFile << output;
 382             logger() << output;
 383
 384 #ifdef USE_MPI
 385                 }
 386 #endif
 387
 388         }
 389         catch(exception& e) {
 390                 errorOut(e, "MothurOut", "MothurOut");
 391                 exit(1);
 392         }
 393 }
 394 /*********************************************************************************************/
 395 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 396         try {
 397 #ifdef USE_MPI
 398                 int pid;
 399                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 400
 401                 if (pid == 0) { //only one process should output to screen
 402 #endif
 403
 404                         out << endl;
 405                         outputFile << endl;
 406             logger() << endl;
 407
 408 #ifdef USE_MPI
 409                 }
 410 #endif
 411         }
 412         catch(exception& e) {
 413                 errorOut(e, "MothurOut", "MothurOutEndLine");
 414                 exit(1);
 415         }
 416 }
 417 /*********************************************************************************************/
 418 void MothurOut::mothurOutJustToLog(string output) {
 419         try {
 420                 #ifdef USE_MPI
 421                         int pid;
 422                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 423
 424                         if (pid == 0) { //only one process should output to screen
 425                 #endif
 426
 427                 out << output;
 428
 429                 #ifdef USE_MPI
 430                         }
 431                 #endif
 432         }
 433         catch(exception& e) {
 434                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 435                 exit(1);
 436         }
 437 }
 438 /*********************************************************************************************/
 439 void MothurOut::errorOut(exception& e, string object, string function) {
 440         //double vm, rss;
 441         //mem_usage(vm, rss);
 442
 443         mothurOut("[ERROR]: ");
 444         mothurOut(toString(e.what()));
 445         mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
 446         mothurOutEndLine();
 447 }
 448 /*********************************************************************************************/
 449 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 450 // process_mem_usage(double &, double &) - takes two doubles by reference,
 451 // attempts to read the system-dependent data for a process' virtual memory
 452 // size and resident set size, and return the results in KB.
 453 //
 454 // On failure, returns 0.0, 0.0
 455 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 456   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 457
 458            vm_usage     = 0.0;
 459            resident_set = 0.0;
 460
 461            // 'file' stat seems to give the most reliable results
 462            //
 463            ifstream stat_stream("/proc/self/stat",ios_base::in);
 464
 465            // dummy vars for leading entries in stat that we don't care about
 466            //
 467            string pid, comm, state, ppid, pgrp, session, tty_nr;
 468            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 469            string utime, stime, cutime, cstime, priority, nice;
 470            string O, itrealvalue, starttime;
 471
 472            // the two fields we want
 473            //
 474            unsigned long vsize;
 475            long rss;
 476
 477            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 478                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 479                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 480                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 481
 482            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 483            vm_usage     = vsize / 1024.0;
 484            resident_set = rss * page_size_kb;
 485
 486            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 487                 return 0;
 488
 489         #else
 490 /*              //windows memory usage
 491                 // Get the list of process identifiers.
 492                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 493
 494                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 495
 496                 // Calculate how many process identifiers were returned.
 497                 cProcesses = cbNeeded / sizeof(DWORD);
 498
 499                 // Print the memory usage for each process
 500                 for (int i = 0; i < cProcesses; i++ ) {
 501                         DWORD processID = aProcesses[i];
 502
 503                         PROCESS_MEMORY_COUNTERS pmc;
 504
 505                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 506
 507                         // Print the process identifier.
 508                         printf( "\nProcess ID: %u\n", processID);
 509
 510                         if (NULL != hProcess) {
 511
 512                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 513                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 514                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 515                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 516                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 517                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 518                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 519                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 520                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 521                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 522                                 }
 523                                 CloseHandle(hProcess);
 524                         }
 525                 }
 526 */
 527                         return 0;
 528
 529         #endif
 530 }
 531
 532
 533 /***********************************************************************/
 534 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 535         try {
 536                 fileName = getFullPathName(fileName);
 537
 538                 fileHandle.open(fileName.c_str(), ios::app);
 539                 if(!fileHandle) {
 540                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 541                         return 1;
 542                 }
 543                 else {
 544                         return 0;
 545                 }
 546         }
 547         catch(exception& e) {
 548                 errorOut(e, "MothurOut", "openOutputFileAppend");
 549                 exit(1);
 550         }
 551 }
 552 /***********************************************************************/
 553 void MothurOut::gobble(istream& f){
 554         try {
 555
 556                 char d;
 557                 while(isspace(d=f.get()))               { ;}
 558                 if(!f.eof()) { f.putback(d); }
 559         }
 560         catch(exception& e) {
 561                 errorOut(e, "MothurOut", "gobble");
 562                 exit(1);
 563         }
 564 }
 565 /***********************************************************************/
 566 void MothurOut::gobble(istringstream& f){
 567         try {
 568                 char d;
 569                 while(isspace(d=f.get()))               {;}
 570                 if(!f.eof()) { f.putback(d); }
 571         }
 572         catch(exception& e) {
 573                 errorOut(e, "MothurOut", "gobble");
 574                 exit(1);
 575         }
 576 }
 577
 578 /***********************************************************************/
 579
 580 string MothurOut::getline(istringstream& fileHandle) {
 581         try {
 582
 583                 string line = "";
 584
 585                 while (!fileHandle.eof())       {
 586                         //get next character
 587                         char c = fileHandle.get();
 588
 589                         //are you at the end of the line
 590                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 591                         else {          line += c;              }
 592                 }
 593
 594                 return line;
 595
 596         }
 597         catch(exception& e) {
 598                 errorOut(e, "MothurOut", "getline");
 599                 exit(1);
 600         }
 601 }
 602 /***********************************************************************/
 603
 604 string MothurOut::getline(ifstream& fileHandle) {
 605         try {
 606
 607                 string line = "";
 608
 609                 while (fileHandle)      {
 610                         //get next character
 611                         char c = fileHandle.get();
 612
 613                         //are you at the end of the line
 614                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }
 615                         else {          line += c;              }
 616                 }
 617
 618                 return line;
 619
 620         }
 621         catch(exception& e) {
 622                 errorOut(e, "MothurOut", "getline");
 623                 exit(1);
 624         }
 625 }
 626 /***********************************************************************/
 627
 628 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 629 #ifdef USE_COMPRESSION
 630 inline bool endsWith(string s, const char * suffix){
 631   size_t suffixLength = strlen(suffix);
 632   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 633 }
 634 #endif
 635 #endif
 636
 637 string MothurOut::getRootName(string longName){
 638         try {
 639
 640                 string rootName = longName;
 641
 642 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 643 #ifdef USE_COMPRESSION
 644     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 645       int pos = rootName.find_last_of('.');
 646       rootName = rootName.substr(0, pos);
 647       cerr << "shortening " << longName << " to " << rootName << "\n";
 648     }
 649 #endif
 650 #endif
 651                 if(rootName.find_last_of(".") != rootName.npos){
 652                         int pos = rootName.find_last_of('.')+1;
 653                         rootName = rootName.substr(0, pos);
 654                 }
 655
 656                 return rootName;
 657         }
 658         catch(exception& e) {
 659                 errorOut(e, "MothurOut", "getRootName");
 660                 exit(1);
 661         }
 662 }
 663 /***********************************************************************/
 664
 665 string MothurOut::getSimpleName(string longName){
 666         try {
 667                 string simpleName = longName;
 668
 669                 size_t found;
 670                 found=longName.find_last_of("/\\");
 671
 672                 if(found != longName.npos){
 673                         simpleName = longName.substr(found+1);
 674                 }
 675
 676                 return simpleName;
 677         }
 678         catch(exception& e) {
 679                 errorOut(e, "MothurOut", "getSimpleName");
 680                 exit(1);
 681         }
 682 }
 683
 684 /***********************************************************************/
 685
 686 int MothurOut::getRandomIndex(int highest){
 687         try {
 688
 689                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 690
 691                 return random;
 692         }
 693         catch(exception& e) {
 694                 errorOut(e, "MothurOut", "getRandomIndex");
 695                 exit(1);
 696         }
 697
 698 }
 699 /**********************************************************************/
 700
 701 string MothurOut::getPathName(string longName){
 702         try {
 703                 string rootPathName = longName;
 704
 705                 if(longName.find_last_of("/\\") != longName.npos){
 706                         int pos = longName.find_last_of("/\\")+1;
 707                         rootPathName = longName.substr(0, pos);
 708                 }
 709
 710                 return rootPathName;
 711         }
 712         catch(exception& e) {
 713                 errorOut(e, "MothurOut", "getPathName");
 714                 exit(1);
 715         }
 716
 717 }
 718 /***********************************************************************/
 719
 720 bool MothurOut::dirCheck(string& dirName){
 721         try {
 722
 723         string tag = "";
 724         #ifdef USE_MPI
 725             int pid;
 726             MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 727
 728             tag = toString(pid);
 729         #endif
 730
 731         //add / to name if needed
 732         string lastChar = dirName.substr(dirName.length()-1);
 733         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 734         if (lastChar != "/") { dirName += "/"; }
 735         #else
 736         if (lastChar != "\\") { dirName += "\\"; }
 737         #endif
 738
 739         //test to make sure directory exists
 740         dirName = getFullPathName(dirName);
 741         string outTemp = dirName + tag + "temp";
 742         ofstream out;
 743         out.open(outTemp.c_str(), ios::trunc);
 744         if(!out) {
 745             mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine();
 746         }else{
 747             out.close();
 748             mothurRemove(outTemp);
 749             return true;
 750         }
 751
 752         return false;
 753     }
 754         catch(exception& e) {
 755                 errorOut(e, "MothurOut", "dirCheck");
 756                 exit(1);
 757         }
 758
 759 }
 760 /***********************************************************************/
 761
 762 string MothurOut::hasPath(string longName){
 763         try {
 764                 string path = "";
 765
 766                 size_t found;
 767                 found=longName.find_last_of("~/\\");
 768
 769                 if(found != longName.npos){
 770                         path = longName.substr(0, found+1);
 771                 }
 772
 773                 return path;
 774         }
 775         catch(exception& e) {
 776                 errorOut(e, "MothurOut", "hasPath");
 777                 exit(1);
 778         }
 779 }
 780
 781 /***********************************************************************/
 782
 783 string MothurOut::getExtension(string longName){
 784         try {
 785                 string extension = "";
 786
 787                 if(longName.find_last_of('.') != longName.npos){
 788                         int pos = longName.find_last_of('.');
 789                         extension = longName.substr(pos, longName.length());
 790                 }
 791
 792                 return extension;
 793         }
 794         catch(exception& e) {
 795                 errorOut(e, "MothurOut", "getExtension");
 796                 exit(1);
 797         }
 798 }
 799 /***********************************************************************/
 800 bool MothurOut::isBlank(string fileName){
 801         try {
 802
 803                 fileName = getFullPathName(fileName);
 804
 805                 ifstream fileHandle;
 806                 fileHandle.open(fileName.c_str());
 807                 if(!fileHandle) {
 808                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 809                         return false;
 810                 }else {
 811                         //check for blank file
 812                         gobble(fileHandle);
 813                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 814                         fileHandle.close();
 815                 }
 816                 return false;
 817         }
 818         catch(exception& e) {
 819                 errorOut(e, "MothurOut", "isBlank");
 820                 exit(1);
 821         }
 822 }
 823 /***********************************************************************/
 824
 825 string MothurOut::getFullPathName(string fileName){
 826         try{
 827
 828         string path = hasPath(fileName);
 829         string newFileName;
 830         int pos;
 831
 832         if (path == "") { return fileName; } //its a simple name
 833         else { //we need to complete the pathname
 834                 // ex. ../../../filename
 835                 // cwd = /user/work/desktop
 836
 837                 string cwd;
 838                 //get current working directory
 839                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 840
 841                         if (path.find("~") != -1) { //go to home directory
 842                                 string homeDir;
 843
 844                                 char *homepath = NULL;
 845                                 homepath = getenv ("HOME");
 846                                 if ( homepath != NULL) { homeDir = homepath; }
 847                                 else { homeDir = "";  }
 848
 849                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 850                                 return newFileName;
 851                         }else { //find path
 852                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 853                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 854
 855                                 //char* cwdpath = new char[1024];
 856                                 //size_t size;
 857                                 //cwdpath=getcwd(cwdpath,size);
 858                                 //cwd = cwdpath;
 859
 860                                 char *cwdpath = NULL;
 861                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 862                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 863                                 else { cwd = "";  }
 864
 865
 866                                 //rip off first '/'
 867                                 string simpleCWD;
 868                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 869
 870                                 //break apart the current working directory
 871                                 vector<string> dirs;
 872                                 while (simpleCWD.find_first_of('/') != string::npos) {
 873                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 874                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 875                                         dirs.push_back(dir);
 876                                 }
 877                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 878                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 879
 880
 881                                 int index = dirs.size()-1;
 882
 883                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 884                                         if (pos == 0) { break;  //you are at the end
 885                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 886                                                 path = path.substr(0, pos-1);
 887                                                 index--;
 888                                                 if (index == 0) {  break; }
 889                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 890                                                 path = path.substr(0, pos);
 891                                         }else if (pos == 1) { break;  //you are at the end
 892                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 893                                 }
 894
 895                                 for (int i = index; i >= 0; i--) {
 896                                         newFileName = dirs[i] +  "/" + newFileName;
 897                                 }
 898
 899                                 newFileName =  "/" +  newFileName;
 900                                 return newFileName;
 901                         }
 902                 #else
 903                         if (path.find("~") != string::npos) { //go to home directory
 904                                 string homeDir = getenv ("HOMEPATH");
 905                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 906                                 return newFileName;
 907                         }else { //find path
 908                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 909                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 910
 911                                 char *cwdpath = NULL;
 912                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 913                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 914                                 else { cwd = "";  }
 915
 916                                 //break apart the current working directory
 917                                 vector<string> dirs;
 918                                 while (cwd.find_first_of('\\') != -1) {
 919                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 920                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 921                                         dirs.push_back(dir);
 922
 923                                 }
 924                                 //get last one
 925                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 926
 927                                 int index = dirs.size()-1;
 928
 929                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 930                                         if (pos == 0) { break;  //you are at the end
 931                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 932                                                 path = path.substr(0, pos-1);
 933                                                 index--;
 934                                                 if (index == 0) {  break; }
 935                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 936                                                 path = path.substr(0, pos);
 937                                         }else if (pos == 1) { break;  //you are at the end
 938                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 939                                 }
 940
 941                                 for (int i = index; i >= 0; i--) {
 942                                         newFileName = dirs[i] +  "\\\\" + newFileName;
 943                                 }
 944
 945                                 return newFileName;
 946                         }
 947
 948                 #endif
 949         }
 950         }
 951         catch(exception& e) {
 952                 errorOut(e, "MothurOut", "getFullPathName");
 953                 exit(1);
 954         }
 955 }
 956 /***********************************************************************/
 957
 958 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 959         try {
 960                         //get full path name
 961                         string completeFileName = getFullPathName(fileName);
 962 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 963 #ifdef USE_COMPRESSION
 964       // check for gzipped or bzipped file
 965       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 966         string tempName = string(tmpnam(0));
 967         mkfifo(tempName.c_str(), 0666);
 968         int fork_result = fork();
 969         if (fork_result < 0) {
 970           cerr << "Error forking.\n";
 971           exit(1);
 972         } else if (fork_result == 0) {
 973           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 974           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 975           system(command.c_str());
 976           cerr << "Done decompressing " << completeFileName << "\n";
 977           mothurRemove(tempName);
 978           exit(EXIT_SUCCESS);
 979         } else {
 980           cerr << "waiting on child process " << fork_result << "\n";
 981           completeFileName = tempName;
 982         }
 983       }
 984 #endif
 985 #endif
 986                         fileHandle.open(completeFileName.c_str());
 987                         if(!fileHandle) {
 988                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 989                                 return 1;
 990                         }else {
 991                                 //check for blank file
 992                                 gobble(fileHandle);
 993                                 return 0;
 994                         }
 995         }
 996         catch(exception& e) {
 997                 errorOut(e, "MothurOut", "openInputFile - no Error");
 998                 exit(1);
 999         }
1000 }
1001 /***********************************************************************/
1002
1003 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
1004         try {
1005
1006                 //get full path name
1007                 string completeFileName = getFullPathName(fileName);
1008 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1009 #ifdef USE_COMPRESSION
1010   // check for gzipped or bzipped file
1011   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
1012     string tempName = string(tmpnam(0));
1013     mkfifo(tempName.c_str(), 0666);
1014     int fork_result = fork();
1015     if (fork_result < 0) {
1016       cerr << "Error forking.\n";
1017       exit(1);
1018     } else if (fork_result == 0) {
1019       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
1020       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
1021       system(command.c_str());
1022       cerr << "Done decompressing " << completeFileName << "\n";
1023       mothurRemove(tempName);
1024       exit(EXIT_SUCCESS);
1025     } else {
1026       cerr << "waiting on child process " << fork_result << "\n";
1027       completeFileName = tempName;
1028     }
1029   }
1030 #endif
1031 #endif
1032
1033                 fileHandle.open(completeFileName.c_str());
1034                 if(!fileHandle) {
1035                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
1036                         return 1;
1037                 }
1038                 else {
1039                         //check for blank file
1040                         gobble(fileHandle);
1041                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
1042
1043                         return 0;
1044                 }
1045         }
1046         catch(exception& e) {
1047                 errorOut(e, "MothurOut", "openInputFile");
1048                 exit(1);
1049         }
1050 }
1051 /***********************************************************************/
1052
1053 int MothurOut::renameFile(string oldName, string newName){
1054         try {
1055
1056         if (oldName == newName) { return 0; }
1057
1058                 ifstream inTest;
1059                 int exist = openInputFile(newName, inTest, "");
1060                 inTest.close();
1061
1062         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1063                 if (exist == 0) { //you could open it so you want to delete it
1064                         string command = "rm " + newName;
1065                         system(command.c_str());
1066                 }
1067
1068                 string command = "mv " + oldName + " " + newName;
1069                 system(command.c_str());
1070         #else
1071                 mothurRemove(newName);
1072                 int renameOk = rename(oldName.c_str(), newName.c_str());
1073         #endif
1074                 return 0;
1075
1076         }
1077         catch(exception& e) {
1078                 errorOut(e, "MothurOut", "renameFile");
1079                 exit(1);
1080         }
1081 }
1082
1083 /***********************************************************************/
1084
1085 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
1086         try {
1087
1088                 string completeFileName = getFullPathName(fileName);
1089 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1090 #ifdef USE_COMPRESSION
1091     // check for gzipped file
1092     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
1093       string tempName = string(tmpnam(0));
1094       mkfifo(tempName.c_str(), 0666);
1095       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
1096       int fork_result = fork();
1097       if (fork_result < 0) {
1098         cerr << "Error forking.\n";
1099         exit(1);
1100       } else if (fork_result == 0) {
1101         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
1102         system(command.c_str());
1103         exit(0);
1104       } else {
1105         completeFileName = tempName;
1106       }
1107     }
1108 #endif
1109 #endif
1110                 fileHandle.open(completeFileName.c_str(), ios::trunc);
1111                 if(!fileHandle) {
1112                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
1113                         return 1;
1114                 }
1115                 else {
1116                         return 0;
1117                 }
1118         }
1119         catch(exception& e) {
1120                 errorOut(e, "MothurOut", "openOutputFile");
1121                 exit(1);
1122         }
1123
1124 }
1125
1126 /**************************************************************************************************/
1127 int MothurOut::appendFiles(string temp, string filename) {
1128         try{
1129                 ofstream output;
1130                 ifstream input;
1131
1132                 //open output file in append mode
1133                 openOutputFileAppend(filename, output);
1134                 int ableToOpen = openInputFile(temp, input, "no error");
1135                 //int ableToOpen = openInputFile(temp, input);
1136
1137                 int numLines = 0;
1138                 if (ableToOpen == 0) { //you opened it
1139
1140             char buffer[4096];
1141             while (!input.eof()) {
1142                 input.read(buffer, 4096);
1143                 output.write(buffer, input.gcount());
1144                 //count number of lines
1145                 for (int i = 0; i < input.gcount(); i++) {  if (buffer[i] == '\n') {numLines++;} }
1146             }
1147                         input.close();
1148                 }
1149
1150                 output.close();
1151
1152                 return numLines;
1153         }
1154         catch(exception& e) {
1155                 errorOut(e, "MothurOut", "appendFiles");
1156                 exit(1);
1157         }
1158 }
1159
1160 /**************************************************************************************************/
1161 string MothurOut::sortFile(string distFile, string outputDir){
1162         try {
1163
1164                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
1165                 string outfile = getRootName(distFile) + "sorted.dist";
1166
1167
1168                 //if you can, use the unix sort since its been optimized for years
1169                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1170                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
1171                         system(command.c_str());
1172                 #else //you are stuck with my best attempt...
1173                         //windows sort does not have a way to specify a column, only a character in the line
1174                         //since we cannot assume that the distance will always be at the the same character location on each line
1175                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1176
1177                         //read in file line by file and put distance first
1178                         string tempDistFile = distFile + ".temp";
1179                         ifstream input;
1180                         ofstream output;
1181                         openInputFile(distFile, input);
1182                         openOutputFile(tempDistFile, output);
1183
1184                         string firstName, secondName;
1185                         float dist;
1186                         while (input) {
1187                                 input >> firstName >> secondName >> dist;
1188                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1189                                 gobble(input);
1190                         }
1191                         input.close();
1192                         output.close();
1193
1194
1195                         //sort using windows sort
1196                         string tempOutfile = outfile + ".temp";
1197                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1198                         system(command.c_str());
1199
1200                         //read in sorted file and put distance at end again
1201                         ifstream input2;
1202                         openInputFile(tempOutfile, input2);
1203                         openOutputFile(outfile, output);
1204
1205                         while (input2) {
1206                                 input2 >> dist >> firstName >> secondName;
1207                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1208                                 gobble(input2);
1209                         }
1210                         input2.close();
1211                         output.close();
1212
1213                         //remove temp files
1214                         mothurRemove(tempDistFile);
1215                         mothurRemove(tempOutfile);
1216                 #endif
1217
1218                 return outfile;
1219         }
1220         catch(exception& e) {
1221                 errorOut(e, "MothurOut", "sortFile");
1222                 exit(1);
1223         }
1224 }
1225 /**************************************************************************************************/
1226 vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
1227         try {
1228                         vector<unsigned long long> positions;
1229                         ifstream inFASTA;
1230                         //openInputFile(filename, inFASTA);
1231                         inFASTA.open(filename.c_str(), ios::binary);
1232
1233                         string input;
1234                         unsigned long long count = 0;
1235                         while(!inFASTA.eof()){
1236                                 //input = getline(inFASTA);
1237                                 //cout << input << '\t' << inFASTA.tellg() << endl;
1238                                 //if (input.length() != 0) {
1239                                 //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
1240                                 //}
1241                                 //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1242                                 char c = inFASTA.get(); count++;
1243                                 if (c == '>') {
1244                                         positions.push_back(count-1);
1245                                         //cout << count << endl;
1246                                 }
1247                         }
1248                         inFASTA.close();
1249
1250                         num = positions.size();
1251
1252                         /*FILE * pFile;
1253                         long size;
1254
1255                         //get num bytes in file
1256                         pFile = fopen (filename.c_str(),"rb");
1257                         if (pFile==NULL) perror ("Error opening file");
1258                         else{
1259                                 fseek (pFile, 0, SEEK_END);
1260                                 size=ftell (pFile);
1261                                 fclose (pFile);
1262                         }*/
1263
1264                         unsigned long long size = positions[(positions.size()-1)];
1265                         ifstream in;
1266                         openInputFile(filename, in);
1267
1268                         in.seekg(size);
1269
1270                         while(in.get()){
1271                                 if(in.eof())            {       break;  }
1272                                 else                            {       size++; }
1273                         }
1274                         in.close();
1275
1276                         positions.push_back(size);
1277                         positions[0] = 0;
1278
1279                         return positions;
1280         }
1281         catch(exception& e) {
1282                 errorOut(e, "MothurOut", "setFilePosFasta");
1283                 exit(1);
1284         }
1285 }
1286 /**************************************************************************************************/
1287 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
1288         try {
1289                         filename = getFullPathName(filename);
1290
1291                         vector<unsigned long long> positions;
1292                         ifstream in;
1293                         //openInputFile(filename, in);
1294                         in.open(filename.c_str(), ios::binary);
1295
1296                         string input;
1297                         unsigned long long count = 0;
1298                         positions.push_back(0);
1299
1300                         while(!in.eof()){
1301                                 //getline counting reads
1302                                 char d = in.get(); count++;
1303                                 while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
1304                                         //get next character
1305                                         d = in.get();
1306                                         count++;
1307                                 }
1308
1309                                 if (!in.eof()) {
1310                                         d=in.get(); count++;
1311                                         while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
1312                                 }
1313                                 positions.push_back(count-1);
1314                                 //cout << count-1 << endl;
1315                         }
1316                         in.close();
1317
1318                         num = positions.size()-1;
1319
1320                         FILE * pFile;
1321                         unsigned long long size;
1322
1323                         //get num bytes in file
1324                         pFile = fopen (filename.c_str(),"rb");
1325                         if (pFile==NULL) perror ("Error opening file");
1326                         else{
1327                                 fseek (pFile, 0, SEEK_END);
1328                                 size=ftell (pFile);
1329                                 fclose (pFile);
1330                         }
1331
1332                         positions[(positions.size()-1)] = size;
1333
1334                         return positions;
1335         }
1336         catch(exception& e) {
1337                 errorOut(e, "MothurOut", "setFilePosEachLine");
1338                 exit(1);
1339         }
1340 }
1341 /**************************************************************************************************/
1342
1343 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
1344         try{
1345                 vector<unsigned long long> filePos;
1346                 filePos.push_back(0);
1347
1348                 FILE * pFile;
1349                 unsigned long long size;
1350
1351                 filename = getFullPathName(filename);
1352
1353                 //get num bytes in file
1354                 pFile = fopen (filename.c_str(),"rb");
1355                 if (pFile==NULL) perror ("Error opening file");
1356                 else{
1357                         fseek (pFile, 0, SEEK_END);
1358                         size=ftell (pFile);
1359                         fclose (pFile);
1360                 }
1361
1362         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1363
1364                 //estimate file breaks
1365                 unsigned long long chunkSize = 0;
1366                 chunkSize = size / proc;
1367
1368                 //file to small to divide by processors
1369                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1370
1371                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1372                 for (int i = 0; i < proc; i++) {
1373                         unsigned long long spot = (i+1) * chunkSize;
1374
1375                         ifstream in;
1376                         openInputFile(filename, in);
1377                         in.seekg(spot);
1378
1379                         //look for next '>'
1380                         unsigned long long newSpot = spot;
1381                         while (!in.eof()) {
1382                            char c = in.get();
1383
1384                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1385                            else if (int(c) == -1) { break; }
1386
1387                         }
1388
1389                         //there was not another sequence before the end of the file
1390                         unsigned long long sanityPos = in.tellg();
1391
1392                         if (sanityPos == -1) {  break;  }
1393                         else {  filePos.push_back(newSpot);  }
1394
1395                         in.close();
1396                 }
1397
1398                 //save end pos
1399                 filePos.push_back(size);
1400
1401                 //sanity check filePos
1402                 for (int i = 0; i < (filePos.size()-1); i++) {
1403                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1404                 }
1405
1406                 proc = (filePos.size() - 1);
1407 #else
1408                 mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
1409                 proc=1;
1410                 filePos.push_back(size);
1411 #endif
1412                 return filePos;
1413         }
1414         catch(exception& e) {
1415                 errorOut(e, "MothurOut", "divideFile");
1416                 exit(1);
1417         }
1418 }
1419 /**************************************************************************************************/
1420 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1421         try{
1422
1423                 vector<unsigned long long> filePos = divideFile(filename, proc);
1424
1425                 for (int i = 0; i < (filePos.size()-1); i++) {
1426
1427                         //read file chunk
1428                         ifstream in;
1429                         openInputFile(filename, in);
1430                         in.seekg(filePos[i]);
1431                         unsigned long long size = filePos[(i+1)] - filePos[i];
1432                         char* chunk = new char[size];
1433                         in.read(chunk, size);
1434                         in.close();
1435
1436                         //open new file
1437                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1438                         ofstream out;
1439                         openOutputFile(fileChunkName, out);
1440
1441                         out << chunk << endl;
1442                         out.close();
1443                         delete[] chunk;
1444
1445                         //save name
1446                         files.push_back(fileChunkName);
1447                 }
1448
1449                 return 0;
1450         }
1451         catch(exception& e) {
1452                 errorOut(e, "MothurOut", "divideFile");
1453                 exit(1);
1454         }
1455 }
1456 /***********************************************************************/
1457
1458 bool MothurOut::isTrue(string f){
1459         try {
1460
1461                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1462
1463                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1464                 else {  return false;  }
1465         }
1466         catch(exception& e) {
1467                 errorOut(e, "MothurOut", "isTrue");
1468                 exit(1);
1469         }
1470 }
1471
1472 /***********************************************************************/
1473
1474 float MothurOut::roundDist(float dist, int precision){
1475         try {
1476                 return int(dist * precision + 0.5)/float(precision);
1477         }
1478         catch(exception& e) {
1479                 errorOut(e, "MothurOut", "roundDist");
1480                 exit(1);
1481         }
1482 }
1483 /***********************************************************************/
1484
1485 float MothurOut::ceilDist(float dist, int precision){
1486         try {
1487                 return int(ceil(dist * precision))/float(precision);
1488         }
1489         catch(exception& e) {
1490                 errorOut(e, "MothurOut", "ceilDist");
1491                 exit(1);
1492         }
1493 }
1494 /***********************************************************************/
1495
1496 vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){
1497         try {
1498         vector<string> pieces;
1499
1500         for (int i = 0; i < size; i++) {
1501             if (!isspace(buffer[i]))  { rest += buffer[i];  }
1502             else {
1503                 if (rest != "") { pieces.push_back(rest);  rest = ""; }
1504                 while (i < size) {  //gobble white space
1505                     if (isspace(buffer[i])) { i++; }
1506                     else { rest = buffer[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
1507                 }
1508             }
1509         }
1510
1511         return pieces;
1512         }
1513         catch(exception& e) {
1514                 errorOut(e, "MothurOut", "splitWhiteSpace");
1515                 exit(1);
1516         }
1517 }
1518 /***********************************************************************/
1519 vector<string> MothurOut::splitWhiteSpace(string input){
1520         try {
1521         vector<string> pieces;
1522         string rest = "";
1523
1524         for (int i = 0; i < input.length(); i++) {
1525             if (!isspace(input[i]))  { rest += input[i];  }
1526             else {
1527                 if (rest != "") { pieces.push_back(rest);  rest = ""; }
1528                 while (i < input.length()) {  //gobble white space
1529                     if (isspace(input[i])) { i++; }
1530                     else { rest = input[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
1531                 }
1532             }
1533         }
1534
1535         if (rest != "") { pieces.push_back(rest); }
1536
1537         return pieces;
1538         }
1539         catch(exception& e) {
1540                 errorOut(e, "MothurOut", "splitWhiteSpace");
1541                 exit(1);
1542         }
1543 }
1544 //**********************************************************************************************************************
1545 int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
1546         try {
1547         //open input file
1548                 ifstream in;
1549                 openInputFile(namefile, in);
1550
1551         string rest = "";
1552         char buffer[4096];
1553         bool pairDone = false;
1554         bool columnOne = true;
1555         string firstCol, secondCol;
1556
1557                 while (!in.eof()) {
1558                         if (control_pressed) { break; }
1559
1560             in.read(buffer, 4096);
1561             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1562
1563             for (int i = 0; i < pieces.size(); i++) {
1564                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1565                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1566
1567                 if (pairDone) {
1568                     //are there confidence scores, if so remove them
1569                     if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);    }
1570                     taxMap[firstCol] = secondCol;
1571                     if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
1572                     pairDone = false;
1573                 }
1574             }
1575                 }
1576                 in.close();
1577
1578         if (rest != "") {
1579             vector<string> pieces = splitWhiteSpace(rest);
1580
1581             for (int i = 0; i < pieces.size(); i++) {
1582                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1583                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1584
1585                 if (pairDone) {
1586                     //are there confidence scores, if so remove them
1587                     if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);    }
1588                     taxMap[firstCol] = secondCol;
1589                     if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
1590                     pairDone = false;
1591                 }
1592             }
1593         }
1594
1595                 return taxMap.size();
1596
1597         }
1598         catch(exception& e) {
1599                 errorOut(e, "MothurOut", "readTax");
1600                 exit(1);
1601         }
1602 }
1603 /**********************************************************************************************************************/
1604 int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool redund) {
1605         try {
1606                 //open input file
1607                 ifstream in;
1608                 openInputFile(namefile, in);
1609
1610         string rest = "";
1611         char buffer[4096];
1612         bool pairDone = false;
1613         bool columnOne = true;
1614         string firstCol, secondCol;
1615
1616                 while (!in.eof()) {
1617                         if (control_pressed) { break; }
1618
1619             in.read(buffer, 4096);
1620             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1621
1622             for (int i = 0; i < pieces.size(); i++) {
1623                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1624                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1625
1626                 if (pairDone) {
1627                     //parse names into vector
1628                     vector<string> theseNames;
1629                     splitAtComma(secondCol, theseNames);
1630                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1631                     pairDone = false;
1632                 }
1633             }
1634                 }
1635                 in.close();
1636
1637         if (rest != "") {
1638             vector<string> pieces = splitWhiteSpace(rest);
1639
1640             for (int i = 0; i < pieces.size(); i++) {
1641                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1642                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1643
1644                 if (pairDone) {
1645                     //parse names into vector
1646                     vector<string> theseNames;
1647                     splitAtComma(secondCol, theseNames);
1648                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1649                     pairDone = false;
1650                 }
1651             }
1652         }
1653
1654                 return nameMap.size();
1655
1656         }
1657         catch(exception& e) {
1658                 errorOut(e, "MothurOut", "readNames");
1659                 exit(1);
1660         }
1661 }
1662 /**********************************************************************************************************************/
1663 int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) {
1664         try {
1665                 //open input file
1666                 ifstream in;
1667                 openInputFile(namefile, in);
1668
1669         string rest = "";
1670         char buffer[4096];
1671         bool pairDone = false;
1672         bool columnOne = true;
1673         string firstCol, secondCol;
1674
1675                 while (!in.eof()) {
1676                         if (control_pressed) { break; }
1677
1678             in.read(buffer, 4096);
1679             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1680
1681             for (int i = 0; i < pieces.size(); i++) {
1682                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1683                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1684
1685                 if (pairDone) {
1686                     nameMap[secondCol] = firstCol;
1687                     pairDone = false;
1688                 }
1689             }
1690                 }
1691                 in.close();
1692
1693         if (rest != "") {
1694             vector<string> pieces = splitWhiteSpace(rest);
1695
1696             for (int i = 0; i < pieces.size(); i++) {
1697                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1698                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1699
1700                 if (pairDone) {
1701                     nameMap[secondCol] = firstCol;
1702                     pairDone = false;
1703                 }
1704             }
1705         }
1706
1707                 return nameMap.size();
1708
1709         }
1710         catch(exception& e) {
1711                 errorOut(e, "MothurOut", "readNames");
1712                 exit(1);
1713         }
1714 }
1715 /**********************************************************************************************************************/
1716 int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) {
1717         try {
1718                 nameMap.clear(); nameCount.clear();
1719                 //open input file
1720                 ifstream in;
1721                 openInputFile(namefile, in);
1722
1723         string rest = "";
1724         char buffer[4096];
1725         bool pairDone = false;
1726         bool columnOne = true;
1727         string firstCol, secondCol;
1728
1729                 while (!in.eof()) {
1730                         if (control_pressed) { break; }
1731
1732             in.read(buffer, 4096);
1733             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1734
1735             for (int i = 0; i < pieces.size(); i++) {
1736                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1737                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1738
1739                 if (pairDone) {
1740                     //parse names into vector
1741                     vector<string> theseNames;
1742                     splitAtComma(secondCol, theseNames);
1743                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1744                     nameCount[firstCol] = theseNames.size();
1745                     pairDone = false;
1746                 }
1747             }
1748                 }
1749                 in.close();
1750
1751         if (rest != "") {
1752             vector<string> pieces = splitWhiteSpace(rest);
1753
1754             for (int i = 0; i < pieces.size(); i++) {
1755                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1756                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1757
1758                 if (pairDone) {
1759                     //parse names into vector
1760                     vector<string> theseNames;
1761                     splitAtComma(secondCol, theseNames);
1762                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1763                     nameCount[firstCol] = theseNames.size();
1764                     pairDone = false;
1765                 }
1766             }
1767
1768         }
1769                 return nameMap.size();
1770
1771         }
1772         catch(exception& e) {
1773                 errorOut(e, "MothurOut", "readNames");
1774                 exit(1);
1775         }
1776 }
1777 /**********************************************************************************************************************/
1778 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1779         try {
1780                 //open input file
1781                 ifstream in;
1782                 openInputFile(namefile, in);
1783
1784         string rest = "";
1785         char buffer[4096];
1786         bool pairDone = false;
1787         bool columnOne = true;
1788         string firstCol, secondCol;
1789
1790                 while (!in.eof()) {
1791                         if (control_pressed) { break; }
1792
1793             in.read(buffer, 4096);
1794             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1795
1796             for (int i = 0; i < pieces.size(); i++) {
1797                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1798                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1799
1800                 if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
1801             }
1802                 }
1803                 in.close();
1804
1805         if (rest != "") {
1806             vector<string> pieces = splitWhiteSpace(rest);
1807
1808             for (int i = 0; i < pieces.size(); i++) {
1809                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1810                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1811
1812                 if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
1813             }
1814         }
1815
1816                 return nameMap.size();
1817
1818         }
1819         catch(exception& e) {
1820                 errorOut(e, "MothurOut", "readNames");
1821                 exit(1);
1822         }
1823 }
1824 /**********************************************************************************************************************/
1825 int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
1826         try {
1827                 //open input file
1828                 ifstream in;
1829                 openInputFile(namefile, in);
1830
1831         string rest = "";
1832         char buffer[4096];
1833         bool pairDone = false;
1834         bool columnOne = true;
1835         string firstCol, secondCol;
1836
1837                 while (!in.eof()) {
1838                         if (control_pressed) { break; }
1839
1840             in.read(buffer, 4096);
1841             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1842
1843             for (int i = 0; i < pieces.size(); i++) {
1844                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1845                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1846
1847                 if (pairDone) {
1848                     vector<string> temp;
1849                     splitAtComma(secondCol, temp);
1850                     nameMap[firstCol] = temp;
1851                     pairDone = false;
1852                 }
1853             }
1854                 }
1855                 in.close();
1856
1857         if (rest != "") {
1858             vector<string> pieces = splitWhiteSpace(rest);
1859
1860             for (int i = 0; i < pieces.size(); i++) {
1861                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1862                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1863
1864                 if (pairDone) {
1865                     vector<string> temp;
1866                     splitAtComma(secondCol, temp);
1867                     nameMap[firstCol] = temp;
1868                     pairDone = false;
1869                 }
1870             }
1871         }
1872
1873                 return nameMap.size();
1874         }
1875         catch(exception& e) {
1876                 errorOut(e, "MothurOut", "readNames");
1877                 exit(1);
1878         }
1879 }
1880 /**********************************************************************************************************************/
1881 map<string, int> MothurOut::readNames(string namefile) {
1882         try {
1883                 map<string, int> nameMap;
1884
1885                 //open input file
1886                 ifstream in;
1887                 openInputFile(namefile, in);
1888
1889         string rest = "";
1890         char buffer[4096];
1891         bool pairDone = false;
1892         bool columnOne = true;
1893         string firstCol, secondCol;
1894
1895                 while (!in.eof()) {
1896                         if (control_pressed) { break; }
1897
1898             in.read(buffer, 4096);
1899             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1900
1901             for (int i = 0; i < pieces.size(); i++) {
1902                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1903                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1904
1905                 if (pairDone) {
1906                     int num = getNumNames(secondCol);
1907                     nameMap[firstCol] = num;
1908                     pairDone = false;
1909                 }
1910             }
1911                 }
1912         in.close();
1913
1914         if (rest != "") {
1915             vector<string> pieces = splitWhiteSpace(rest);
1916             for (int i = 0; i < pieces.size(); i++) {
1917                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1918                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1919
1920                 if (pairDone) {
1921                     int num = getNumNames(secondCol);
1922                     nameMap[firstCol] = num;
1923                     pairDone = false;
1924                 }
1925             }
1926         }
1927
1928                 return nameMap;
1929
1930         }
1931         catch(exception& e) {
1932                 errorOut(e, "MothurOut", "readNames");
1933                 exit(1);
1934         }
1935 }
1936 /**********************************************************************************************************************/
1937 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1938         try {
1939                 int error = 0;
1940
1941                 //open input file
1942                 ifstream in;
1943                 openInputFile(namefile, in);
1944
1945         string rest = "";
1946         char buffer[4096];
1947         bool pairDone = false;
1948         bool columnOne = true;
1949         string firstCol, secondCol;
1950
1951                 while (!in.eof()) {
1952                         if (control_pressed) { break; }
1953
1954             in.read(buffer, 4096);
1955             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1956
1957             for (int i = 0; i < pieces.size(); i++) {
1958                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1959                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1960
1961                 if (pairDone) {
1962                     int num = getNumNames(secondCol);
1963
1964                     map<string, string>::iterator it = fastamap.find(firstCol);
1965                     if (it == fastamap.end()) {
1966                         error = 1;
1967                         mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1968                     }else {
1969                         seqPriorityNode temp(num, it->second, firstCol);
1970                         nameVector.push_back(temp);
1971                     }
1972
1973                     pairDone = false;
1974                 }
1975             }
1976                 }
1977         in.close();
1978
1979         if (rest != "") {
1980             vector<string> pieces = splitWhiteSpace(rest);
1981
1982             for (int i = 0; i < pieces.size(); i++) {
1983                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1984                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1985
1986                 if (pairDone) {
1987                     int num = getNumNames(secondCol);
1988
1989                     map<string, string>::iterator it = fastamap.find(firstCol);
1990                     if (it == fastamap.end()) {
1991                         error = 1;
1992                         mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1993                     }else {
1994                         seqPriorityNode temp(num, it->second, firstCol);
1995                         nameVector.push_back(temp);
1996                     }
1997
1998                     pairDone = false;
1999                 }
2000             }
2001         }
2002                 return error;
2003         }
2004         catch(exception& e) {
2005                 errorOut(e, "MothurOut", "readNames");
2006                 exit(1);
2007         }
2008 }
2009 //**********************************************************************************************************************
2010 set<string> MothurOut::readAccnos(string accnosfile){
2011         try {
2012                 set<string> names;
2013                 ifstream in;
2014                 openInputFile(accnosfile, in);
2015                 string name;
2016
2017         string rest = "";
2018         char buffer[4096];
2019
2020                 while (!in.eof()) {
2021                         if (control_pressed) { break; }
2022
2023             in.read(buffer, 4096);
2024             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
2025
2026             for (int i = 0; i < pieces.size(); i++) {  names.insert(pieces[i]);  }
2027         }
2028                 in.close();
2029
2030         if (rest != "") {
2031             vector<string> pieces = splitWhiteSpace(rest);
2032             for (int i = 0; i < pieces.size(); i++) {  names.insert(pieces[i]);  }
2033         }
2034                 return names;
2035         }
2036         catch(exception& e) {
2037                 errorOut(e, "MothurOut", "readAccnos");
2038                 exit(1);
2039         }
2040 }
2041 //**********************************************************************************************************************
2042 int MothurOut::readAccnos(string accnosfile, vector<string>& names){
2043         try {
2044         names.clear();
2045                 ifstream in;
2046                 openInputFile(accnosfile, in);
2047                 string name;
2048
2049         string rest = "";
2050         char buffer[4096];
2051
2052                 while (!in.eof()) {
2053                         if (control_pressed) { break; }
2054
2055             in.read(buffer, 4096);
2056             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
2057
2058             for (int i = 0; i < pieces.size(); i++) {  names.push_back(pieces[i]);  }
2059         }
2060                 in.close();
2061
2062         if (rest != "") {
2063             vector<string> pieces = splitWhiteSpace(rest);
2064             for (int i = 0; i < pieces.size(); i++) {  names.push_back(pieces[i]);  }
2065         }
2066
2067                 return 0;
2068         }
2069         catch(exception& e) {
2070                 errorOut(e, "MothurOut", "readAccnos");
2071                 exit(1);
2072         }
2073 }
2074 /***********************************************************************/
2075
2076 int MothurOut::getNumNames(string names){
2077         try {
2078                 int count = 0;
2079
2080                 if(names != ""){
2081                         count = 1;
2082                         for(int i=0;i<names.size();i++){
2083                                 if(names[i] == ','){
2084                                         count++;
2085                                 }
2086                         }
2087                 }
2088
2089                 return count;
2090         }
2091         catch(exception& e) {
2092                 errorOut(e, "MothurOut", "getNumNames");
2093                 exit(1);
2094         }
2095 }
2096 /***********************************************************************/
2097
2098 int MothurOut::getNumChar(string line, char c){
2099         try {
2100                 int count = 0;
2101
2102                 if(line != ""){
2103                         for(int i=0;i<line.size();i++){
2104                                 if(line[i] == c){
2105                                         count++;
2106                                 }
2107                         }
2108                 }
2109
2110                 return count;
2111         }
2112         catch(exception& e) {
2113                 errorOut(e, "MothurOut", "getNumChar");
2114                 exit(1);
2115         }
2116 }
2117 //**********************************************************************************************************************
2118 bool MothurOut::isSubset(vector<string> bigset, vector<string> subset) {
2119         try {
2120
2121
2122                 if (subset.size() > bigset.size()) { return false;  }
2123
2124                 //check if each guy in suset is also in bigset
2125                 for (int i = 0; i < subset.size(); i++) {
2126                         bool match = false;
2127                         for (int j = 0; j < bigset.size(); j++) {
2128                                 if (subset[i] == bigset[j]) { match = true; break; }
2129                         }
2130
2131                         //you have a guy in subset that had no match in bigset
2132                         if (match == false) { return false; }
2133                 }
2134
2135                 return true;
2136
2137         }
2138         catch(exception& e) {
2139                 errorOut(e, "MothurOut", "isSubset");
2140                 exit(1);
2141         }
2142 }
2143 /***********************************************************************/
2144 int MothurOut::mothurRemove(string filename){
2145         try {
2146                 filename = getFullPathName(filename);
2147                 int error = remove(filename.c_str());
2148                 //if (error != 0) {
2149                 //      if (errno != ENOENT) { //ENOENT == file does not exist
2150                 //              string message = "Error deleting file " + filename;
2151                 //              perror(message.c_str());
2152                 //      }
2153                 //}
2154                 return error;
2155         }
2156         catch(exception& e) {
2157                 errorOut(e, "MothurOut", "mothurRemove");
2158                 exit(1);
2159         }
2160 }
2161 /***********************************************************************/
2162 bool MothurOut::mothurConvert(string item, int& num){
2163         try {
2164                 bool error = false;
2165
2166                 if (isNumeric1(item)) {
2167                         convert(item, num);
2168                 }else {
2169                         num = 0;
2170                         error = true;
2171                         mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
2172                         commandInputsConvertError = true;
2173                 }
2174
2175                 return error;
2176         }
2177         catch(exception& e) {
2178                 errorOut(e, "MothurOut", "mothurConvert");
2179                 exit(1);
2180         }
2181 }
2182 /***********************************************************************/
2183 bool MothurOut::mothurConvert(string item, intDist& num){
2184         try {
2185                 bool error = false;
2186
2187                 if (isNumeric1(item)) {
2188                         convert(item, num);
2189                 }else {
2190                         num = 0;
2191                         error = true;
2192                         mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
2193                         commandInputsConvertError = true;
2194                 }
2195
2196                 return error;
2197         }
2198         catch(exception& e) {
2199                 errorOut(e, "MothurOut", "mothurConvert");
2200                 exit(1);
2201         }
2202 }
2203
2204 /***********************************************************************/
2205 bool MothurOut::isNumeric1(string stringToCheck){
2206         try {
2207                 bool numeric = false;
2208
2209                 if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
2210
2211                 return numeric;
2212         }
2213         catch(exception& e) {
2214                 errorOut(e, "MothurOut", "isNumeric1");
2215                 exit(1);
2216         }
2217
2218 }
2219 /***********************************************************************/
2220 bool MothurOut::mothurConvert(string item, float& num){
2221         try {
2222                 bool error = false;
2223
2224                 if (isNumeric1(item)) {
2225                         convert(item, num);
2226                 }else {
2227                         num = 0;
2228                         error = true;
2229                         mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
2230                         commandInputsConvertError = true;
2231                 }
2232
2233                 return error;
2234         }
2235         catch(exception& e) {
2236                 errorOut(e, "MothurOut", "mothurConvert");
2237                 exit(1);
2238         }
2239 }
2240 /***********************************************************************/
2241 bool MothurOut::mothurConvert(string item, double& num){
2242         try {
2243                 bool error = false;
2244
2245                 if (isNumeric1(item)) {
2246                         convert(item, num);
2247                 }else {
2248                         num = 0;
2249                         error = true;
2250                         mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
2251                         commandInputsConvertError = true;
2252                 }
2253
2254                 return error;
2255         }
2256         catch(exception& e) {
2257                 errorOut(e, "MothurOut", "mothurConvert");
2258                 exit(1);
2259         }
2260 }
2261 /**************************************************************************************************/
2262
2263 vector<vector<double> > MothurOut::binomial(int maxOrder){
2264         try {
2265         vector<vector<double> > binomial(maxOrder+1);
2266
2267     for(int i=0;i<=maxOrder;i++){
2268                 binomial[i].resize(maxOrder+1);
2269                 binomial[i][0]=1;
2270                 binomial[0][i]=0;
2271     }
2272     binomial[0][0]=1;
2273
2274     binomial[1][0]=1;
2275     binomial[1][1]=1;
2276
2277     for(int i=2;i<=maxOrder;i++){
2278                 binomial[1][i]=0;
2279     }
2280
2281     for(int i=2;i<=maxOrder;i++){
2282                 for(int j=1;j<=maxOrder;j++){
2283                         if(i==j){       binomial[i][j]=1;                                                                       }
2284                         if(j>i) {       binomial[i][j]=0;                                                                       }
2285                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
2286                 }
2287     }
2288
2289         return binomial;
2290
2291         }
2292         catch(exception& e) {
2293                 errorOut(e, "MothurOut", "binomial");
2294                 exit(1);
2295         }
2296 }
2297 /**************************************************************************************************/
2298 unsigned int MothurOut::fromBase36(string base36){
2299         try {
2300                 unsigned int num = 0;
2301
2302                 map<char, int> converts;
2303                 converts['A'] = 0;
2304                 converts['a'] = 0;
2305                 converts['B'] = 1;
2306                 converts['b'] = 1;
2307                 converts['C'] = 2;
2308                 converts['c'] = 2;
2309                 converts['D'] = 3;
2310                 converts['d'] = 3;
2311                 converts['E'] = 4;
2312                 converts['e'] = 4;
2313                 converts['F'] = 5;
2314                 converts['f'] = 5;
2315                 converts['G'] = 6;
2316                 converts['g'] = 6;
2317                 converts['H'] = 7;
2318                 converts['h'] = 7;
2319                 converts['I'] = 8;
2320                 converts['i'] = 8;
2321                 converts['J'] = 9;
2322                 converts['j'] = 9;
2323                 converts['K'] = 10;
2324                 converts['k'] = 10;
2325                 converts['L'] = 11;
2326                 converts['l'] = 11;
2327                 converts['M'] = 12;
2328                 converts['m'] = 12;
2329                 converts['N'] = 13;
2330                 converts['n'] = 13;
2331                 converts['O'] = 14;
2332                 converts['o'] = 14;
2333                 converts['P'] = 15;
2334                 converts['p'] = 15;
2335                 converts['Q'] = 16;
2336                 converts['q'] = 16;
2337                 converts['R'] = 17;
2338                 converts['r'] = 17;
2339                 converts['S'] = 18;
2340                 converts['s'] = 18;
2341                 converts['T'] = 19;
2342                 converts['t'] = 19;
2343                 converts['U'] = 20;
2344                 converts['u'] = 20;
2345                 converts['V'] = 21;
2346                 converts['v'] = 21;
2347                 converts['W'] = 22;
2348                 converts['w'] = 22;
2349                 converts['X'] = 23;
2350                 converts['x'] = 23;
2351                 converts['Y'] = 24;
2352                 converts['y'] = 24;
2353                 converts['Z'] = 25;
2354                 converts['z'] = 25;
2355                 converts['0'] = 26;
2356                 converts['1'] = 27;
2357                 converts['2'] = 28;
2358                 converts['3'] = 29;
2359                 converts['4'] = 30;
2360                 converts['5'] = 31;
2361                 converts['6'] = 32;
2362                 converts['7'] = 33;
2363                 converts['8'] = 34;
2364                 converts['9'] = 35;
2365
2366                 int i = 0;
2367                 while (i < base36.length()) {
2368                         char c = base36[i];
2369                         num = 36 * num + converts[c];
2370                         i++;
2371                 }
2372
2373                 return num;
2374
2375         }
2376         catch(exception& e) {
2377                 errorOut(e, "MothurOut", "fromBase36");
2378                 exit(1);
2379         }
2380 }
2381 /***********************************************************************/
2382
2383 int MothurOut::factorial(int num){
2384         try {
2385                 int total = 1;
2386
2387                 for (int i = 1; i <= num; i++) {
2388                         total *= i;
2389                 }
2390
2391                 return total;
2392         }
2393         catch(exception& e) {
2394                 errorOut(e, "MothurOut", "factorial");
2395                 exit(1);
2396         }
2397 }
2398 /***********************************************************************/
2399
2400 int MothurOut::getNumSeqs(ifstream& file){
2401         try {
2402                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
2403                 file.seekg(0);
2404                 return numSeqs;
2405         }
2406         catch(exception& e) {
2407                 errorOut(e, "MothurOut", "getNumSeqs");
2408                 exit(1);
2409         }
2410 }
2411 /***********************************************************************/
2412 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
2413         try {
2414                 string input;
2415                 numSeqs = 0;
2416                 while(!file.eof()){
2417                         input = getline(file);
2418                         if (input.length() != 0) {
2419                                 if(input[0] == '>'){ numSeqs++; }
2420                         }
2421                 }
2422         }
2423         catch(exception& e) {
2424                 errorOut(e, "MothurOut", "getNumSeqs");
2425                 exit(1);
2426         }
2427 }
2428 /***********************************************************************/
2429
2430 //This function parses the estimator options and puts them in a vector
2431 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
2432         try {
2433                 string individual = "";
2434                 int estimLength = estim.size();
2435                 for(int i=0;i<estimLength;i++){
2436                         if(estim[i] == symbol){
2437                                 container.push_back(individual);
2438                                 individual = "";
2439                         }
2440                         else{
2441                                 individual += estim[i];
2442                         }
2443                 }
2444                 container.push_back(individual);
2445
2446         }
2447         catch(exception& e) {
2448                 errorOut(e, "MothurOut", "splitAtChar");
2449                 exit(1);
2450         }
2451 }
2452
2453 /***********************************************************************/
2454
2455 //This function parses the estimator options and puts them in a vector
2456 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
2457         try {
2458                 string individual = "";
2459                 int estimLength = estim.size();
2460                 bool prevEscape = false;
2461                 for(int i=0;i<estimLength;i++){
2462                         if(prevEscape){
2463                                 individual += estim[i];
2464                                 prevEscape = false;
2465                         }
2466                         else{
2467                                 if(estim[i] == '\\'){
2468                                         prevEscape = true;
2469                                 }
2470                                 else if(estim[i] == '-'){
2471                                         container.push_back(individual);
2472                                         individual = "";
2473                                         prevEscape = false;
2474                                 }
2475                                 else{
2476                                         individual += estim[i];
2477                                         prevEscape = false;
2478                                 }
2479                         }
2480                 }
2481                 container.push_back(individual);
2482         }
2483         catch(exception& e) {
2484                 errorOut(e, "MothurOut", "splitAtDash");
2485                 exit(1);
2486         }
2487 }
2488
2489 /***********************************************************************/
2490 //This function parses the label options and puts them in a set
2491 void MothurOut::splitAtDash(string& estim, set<string>& container) {
2492         try {
2493                 string individual = "";
2494                 int estimLength = estim.size();
2495                 bool prevEscape = false;
2496                 for(int i=0;i<estimLength;i++){
2497                         if(prevEscape){
2498                                 individual += estim[i];
2499                                 prevEscape = false;
2500                         }
2501                         else{
2502                                 if(estim[i] == '\\'){
2503                                         prevEscape = true;
2504                                 }
2505                                 else if(estim[i] == '-'){
2506                                         container.insert(individual);
2507                                         individual = "";
2508                                         prevEscape = false;
2509                                 }
2510                                 else{
2511                                         individual += estim[i];
2512                                         prevEscape = false;
2513                                 }
2514                         }
2515                 }
2516                 container.insert(individual);
2517
2518         }
2519         catch(exception& e) {
2520                 errorOut(e, "MothurOut", "splitAtDash");
2521                 exit(1);
2522         }
2523 }
2524 /***********************************************************************/
2525 //This function parses the line options and puts them in a set
2526 void MothurOut::splitAtDash(string& estim, set<int>& container) {
2527         try {
2528                 string individual = "";
2529                 int lineNum;
2530                 int estimLength = estim.size();
2531                 bool prevEscape = false;
2532                 for(int i=0;i<estimLength;i++){
2533                         if(prevEscape){
2534                                 individual += estim[i];
2535                                 prevEscape = false;
2536                         }
2537                         else{
2538                                 if(estim[i] == '\\'){
2539                                         prevEscape = true;
2540                                 }
2541                                 else if(estim[i] == '-'){
2542                                         convert(individual, lineNum); //convert the string to int
2543                                         container.insert(lineNum);
2544                                         individual = "";
2545                                         prevEscape = false;
2546                                 }
2547                                 else{
2548                                         individual += estim[i];
2549                                         prevEscape = false;
2550                                 }
2551                         }
2552                 }
2553                 convert(individual, lineNum); //convert the string to int
2554                 container.insert(lineNum);
2555         }
2556         catch(exception& e) {
2557                 errorOut(e, "MothurOut", "splitAtDash");
2558                 exit(1);
2559         }
2560 }
2561 /***********************************************************************/
2562 string MothurOut::makeList(vector<string>& names) {
2563         try {
2564                 string list = "";
2565
2566         if (names.size() == 0) { return list; }
2567
2568         for (int i = 0; i < names.size()-1; i++) { list += names[i] + ",";  }
2569
2570         //get last name
2571         list += names[names.size()-1];
2572
2573         return list;
2574     }
2575         catch(exception& e) {
2576                 errorOut(e, "MothurOut", "makeList");
2577                 exit(1);
2578         }
2579 }
2580
2581 /***********************************************************************/
2582 //This function parses the a string and puts peices in a vector
2583 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
2584         try {
2585                 string individual = "";
2586                 int estimLength = estim.size();
2587                 for(int i=0;i<estimLength;i++){
2588                         if(estim[i] == ','){
2589                                 container.push_back(individual);
2590                                 individual = "";
2591                         }
2592                         else{
2593                                 individual += estim[i];
2594                         }
2595                 }
2596                 container.push_back(individual);
2597
2598
2599
2600
2601 //              string individual;
2602 //
2603 //              while (estim.find_first_of(',') != -1) {
2604 //                      individual = estim.substr(0,estim.find_first_of(','));
2605 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
2606 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
2607 //                              container.push_back(individual);
2608 //                      }
2609 //              }
2610 //              //get last one
2611 //              container.push_back(estim);
2612         }
2613         catch(exception& e) {
2614                 errorOut(e, "MothurOut", "splitAtComma");
2615                 exit(1);
2616         }
2617 }
2618 /***********************************************************************/
2619 //This function splits up the various option parameters
2620 void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
2621         try {
2622                 prefix = suffix.substr(0,suffix.find_first_of(c));
2623                 if ((suffix.find_first_of(c)+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
2624                         suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
2625                         string space = " ";
2626                         while(suffix.at(0) == ' ')
2627                                 suffix = suffix.substr(1, suffix.length());
2628                 }
2629
2630         }
2631         catch(exception& e) {
2632                 errorOut(e, "MothurOut", "splitAtComma");
2633                 exit(1);
2634         }
2635 }
2636
2637 /***********************************************************************/
2638
2639 //This function splits up the various option parameters
2640 void MothurOut::splitAtComma(string& prefix, string& suffix){
2641         try {
2642                 prefix = suffix.substr(0,suffix.find_first_of(','));
2643                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
2644                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
2645                         string space = " ";
2646                         while(suffix.at(0) == ' ')
2647                                 suffix = suffix.substr(1, suffix.length());
2648                 }
2649
2650         }
2651         catch(exception& e) {
2652                 errorOut(e, "MothurOut", "splitAtComma");
2653                 exit(1);
2654         }
2655 }
2656 /***********************************************************************/
2657
2658 //This function separates the key value from the option value i.e. dist=96_...
2659 void MothurOut::splitAtEquals(string& key, string& value){
2660         try {
2661                 if(value.find_first_of('=') != -1){
2662                         key = value.substr(0,value.find_first_of('='));
2663                         if ((value.find_first_of('=')+1) <= value.length()) {
2664                                 value = value.substr(value.find_first_of('=')+1, value.length());
2665                         }
2666                 }else{
2667                         key = value;
2668                         value = 1;
2669                 }
2670         }
2671         catch(exception& e) {
2672                 errorOut(e, "MothurOut", "splitAtEquals");
2673                 exit(1);
2674         }
2675 }
2676
2677 /**************************************************************************************************/
2678
2679 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
2680         try {
2681                 for (int i = 0; i < Groups.size(); i++) {
2682                         if (groupname == Groups[i]) { return true; }
2683                 }
2684                 return false;
2685         }
2686         catch(exception& e) {
2687                 errorOut(e, "MothurOut", "inUsersGroups");
2688                 exit(1);
2689         }
2690 }
2691 /**************************************************************************************************/
2692 //returns true if any of the strings in first vector are in second vector
2693 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
2694         try {
2695
2696                 for (int i = 0; i < groupnames.size(); i++) {
2697                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
2698                 }
2699                 return false;
2700         }
2701         catch(exception& e) {
2702                 errorOut(e, "MothurOut", "inUsersGroups");
2703                 exit(1);
2704         }
2705 }
2706 /***********************************************************************/
2707 //this function determines if the user has given us labels that are smaller than the given label.
2708 //if so then it returns true so that the calling function can run the previous valid distance.
2709 //it's a "smart" distance function.  It also checks for invalid labels.
2710 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
2711         try {
2712
2713                 set<string>::iterator it;
2714                 vector<float> orderFloat;
2715                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
2716                 map<string, float>::iterator it2;
2717                 float labelFloat;
2718                 bool smaller = false;
2719
2720                 //unique is the smallest line
2721                 if (label == "unique") {  return false;  }
2722                 else {
2723                         if (convertTestFloat(label, labelFloat)) {
2724                                 convert(label, labelFloat);
2725                         }else { //cant convert
2726                                 return false;
2727                         }
2728                 }
2729
2730                 //go through users set and make them floats
2731                 for(it = userLabels.begin(); it != userLabels.end();) {
2732
2733                         float temp;
2734                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
2735                                 convert(*it, temp);
2736                                 orderFloat.push_back(temp);
2737                                 userMap[*it] = temp;
2738                                 it++;
2739                         }else if (*it == "unique") {
2740                                 orderFloat.push_back(-1.0);
2741                                 userMap["unique"] = -1.0;
2742                                 it++;
2743                         }else {
2744                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
2745                                 userLabels.erase(it++);
2746                         }
2747                 }
2748
2749                 //sort order
2750                 sort(orderFloat.begin(), orderFloat.end());
2751
2752                 /*************************************************/
2753                 //is this label bigger than any of the users labels
2754                 /*************************************************/
2755
2756                 //loop through order until you find a label greater than label
2757                 for (int i = 0; i < orderFloat.size(); i++) {
2758                         if (orderFloat[i] < labelFloat) {
2759                                 smaller = true;
2760                                 if (orderFloat[i] == -1) {
2761                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
2762                                         userLabels.erase("unique");
2763                                 }
2764                                 else {
2765                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
2766                                         string s = "";
2767                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
2768                                                 if (it2->second == orderFloat[i]) {
2769                                                         s = it2->first;
2770                                                         //remove small labels
2771                                                         userLabels.erase(s);
2772                                                         break;
2773                                                 }
2774                                         }
2775                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
2776                                 }
2777                         //since they are sorted once you find a bigger one stop looking
2778                         }else { break; }
2779                 }
2780
2781                 return smaller;
2782
2783         }
2784         catch(exception& e) {
2785                 errorOut(e, "MothurOut", "anyLabelsToProcess");
2786                 exit(1);
2787         }
2788 }
2789
2790 /**************************************************************************************************/
2791 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
2792         try {
2793
2794                 bool good = true;
2795
2796                 string line = getline(file);
2797
2798                 //before we added this check
2799                 if (line[0] != '#') {  good = false;  }
2800                 else {
2801                         //rip off #
2802                         line = line.substr(1);
2803
2804                         vector<string> versionVector;
2805                         splitAtChar(version, versionVector, '.');
2806
2807                         //check file version
2808                         vector<string> linesVector;
2809                         splitAtChar(line, linesVector, '.');
2810
2811                         if (versionVector.size() != linesVector.size()) { good = false; }
2812                         else {
2813                                 for (int j = 0; j < versionVector.size(); j++) {
2814                                         int num1, num2;
2815                                         convert(versionVector[j], num1);
2816                                         convert(linesVector[j], num2);
2817
2818                                         //if mothurs version is newer than this files version, then we want to remake it
2819                                         if (num1 > num2) {  good = false; break;  }
2820                                 }
2821                         }
2822
2823                 }
2824
2825                 if (!good) {  file.close();  }
2826                 else { file.seekg(0);  }
2827
2828                 return good;
2829         }
2830         catch(exception& e) {
2831                 errorOut(e, "MothurOut", "checkReleaseVersion");
2832                 exit(1);
2833         }
2834 }
2835 /**************************************************************************************************/
2836 bool MothurOut::isContainingOnlyDigits(string input) {
2837         try{
2838
2839                 //are you a digit in ascii code
2840                 for (int i = 0;i < input.length(); i++){
2841                         if( input[i]>47 && input[i]<58){}
2842                         else { return false; }
2843                 }
2844
2845                 return true;
2846         }
2847         catch(exception& e) {
2848                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
2849                 exit(1);
2850         }
2851 }
2852 /**************************************************************************************************/
2853 int MothurOut::removeConfidences(string& tax) {
2854         try {
2855
2856                 string taxon;
2857                 string newTax = "";
2858
2859                 while (tax.find_first_of(';') != -1) {
2860
2861                         if (control_pressed) { return 0; }
2862
2863                         //get taxon
2864                         taxon = tax.substr(0,tax.find_first_of(';'));
2865
2866                         int pos = taxon.find_last_of('(');
2867                         if (pos != -1) {
2868                                 //is it a number?
2869                                 int pos2 = taxon.find_last_of(')');
2870                                 if (pos2 != -1) {
2871                                         string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
2872                                         if (isNumeric1(confidenceScore)) {
2873                                                 taxon = taxon.substr(0, pos); //rip off confidence
2874                                         }
2875                                 }
2876                         }
2877                         taxon += ";";
2878
2879                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
2880                         newTax += taxon;
2881                 }
2882
2883                 tax = newTax;
2884
2885                 return 0;
2886         }
2887         catch(exception& e) {
2888                 errorOut(e, "MothurOut", "removeConfidences");
2889                 exit(1);
2890         }
2891 }
2892 /**************************************************************************************************/
2893 string MothurOut::removeQuotes(string tax) {
2894         try {
2895
2896                 string taxon;
2897                 string newTax = "";
2898
2899                 for (int i = 0; i < tax.length(); i++) {
2900
2901                         if (control_pressed) { return newTax; }
2902
2903             if ((tax[i] != '\'') && (tax[i] != '\"')) { newTax += tax[i]; }
2904
2905         }
2906
2907                 return newTax;
2908         }
2909         catch(exception& e) {
2910                 errorOut(e, "MothurOut", "removeQuotes");
2911                 exit(1);
2912         }
2913 }
2914 /**************************************************************************************************/
2915 // function for calculating standard deviation
2916 double MothurOut::getStandardDeviation(vector<int>& featureVector){
2917     try {
2918         //finds sum
2919         double average = 0;
2920         for (int i = 0; i < featureVector.size(); i++) { average += featureVector[i]; }
2921         average /= (double) featureVector.size();
2922
2923         //find standard deviation
2924         double stdDev = 0;
2925         for (int i = 0; i < featureVector.size(); i++) { //compute the difference of each dist from the mean, and square the result of each
2926             stdDev += ((featureVector[i] - average) * (featureVector[i] - average));
2927         }
2928
2929         stdDev /= (double) featureVector.size();
2930         stdDev = sqrt(stdDev);
2931
2932         return stdDev;
2933     }
2934         catch(exception& e) {
2935                 errorOut(e, "MothurOut", "getStandardDeviation");
2936                 exit(1);
2937         }
2938 }
2939 /**************************************************************************************************/
2940
2941
2942