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 void MothurOut::printCurrentFiles()  {
  22         try {
  23                 if (accnosfile != "")           {  mothurOut("accnos=" + accnosfile); mothurOutEndLine();                       }
  24                 if (columnfile != "")           {  mothurOut("column=" + columnfile); mothurOutEndLine();                       }
  25                 if (designfile != "")           {  mothurOut("design=" + designfile); mothurOutEndLine();                       }
  26                 if (fastafile != "")            {  mothurOut("fasta=" + fastafile); mothurOutEndLine();                         }
  27                 if (groupfile != "")            {  mothurOut("group=" + groupfile); mothurOutEndLine();                         }
  28                 if (listfile != "")                     {  mothurOut("list=" + listfile); mothurOutEndLine();                           }
  29                 if (namefile != "")                     {  mothurOut("name=" + namefile); mothurOutEndLine();                           }
  30                 if (oligosfile != "")           {  mothurOut("oligos=" + oligosfile); mothurOutEndLine();                       }
  31                 if (orderfile != "")            {  mothurOut("order=" + orderfile); mothurOutEndLine();                         }
  32                 if (ordergroupfile != "")       {  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();       }
  33                 if (phylipfile != "")           {  mothurOut("phylip=" + phylipfile); mothurOutEndLine();                       }
  34                 if (qualfile != "")                     {  mothurOut("qfile=" + qualfile); mothurOutEndLine();                          }
  35                 if (rabundfile != "")           {  mothurOut("rabund=" + rabundfile); mothurOutEndLine();                       }
  36                 if (relabundfile != "")         {  mothurOut("relabund=" + relabundfile); mothurOutEndLine();           }
  37                 if (sabundfile != "")           {  mothurOut("sabund=" + sabundfile); mothurOutEndLine();                       }
  38                 if (sfffile != "")                      {  mothurOut("sff=" + sfffile); mothurOutEndLine();                                     }
  39                 if (sharedfile != "")           {  mothurOut("shared=" + sharedfile); mothurOutEndLine();                       }
  40                 if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
  41                 if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
  42                 if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
  43                 if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
  44
  45         }
  46         catch(exception& e) {
  47                 errorOut(e, "MothurOut", "printCurrentFiles");
  48                 exit(1);
  49         }
  50 }
  51 /*********************************************************************************************/
  52 bool MothurOut::hasCurrentFiles()  {
  53         try {
  54                 bool hasCurrent = false;
  55
  56                 if (accnosfile != "")           {  return true;                 }
  57                 if (columnfile != "")           {  return true;                 }
  58                 if (designfile != "")           {  return true;                 }
  59                 if (fastafile != "")            {  return true;                 }
  60                 if (groupfile != "")            {  return true;                 }
  61                 if (listfile != "")                     {  return true;                 }
  62                 if (namefile != "")                     {  return true;                 }
  63                 if (oligosfile != "")           {  return true;                 }
  64                 if (orderfile != "")            {  return true;                 }
  65                 if (ordergroupfile != "")       {  return true;                 }
  66                 if (phylipfile != "")           {  return true;                 }
  67                 if (qualfile != "")                     {  return true;                 }
  68                 if (rabundfile != "")           {  return true;                 }
  69                 if (relabundfile != "")         {  return true;                 }
  70                 if (sabundfile != "")           {  return true;                 }
  71                 if (sfffile != "")                      {  return true;                 }
  72                 if (sharedfile != "")           {  return true;                 }
  73                 if (taxonomyfile != "")         {  return true;                 }
  74                 if (treefile != "")                     {  return true;                 }
  75                 if (flowfile != "")                     {  return true;                 }
  76                 if (processors != "1")          {  return true;                 }
  77
  78                 return hasCurrent;
  79
  80         }
  81         catch(exception& e) {
  82                 errorOut(e, "MothurOut", "hasCurrentFiles");
  83                 exit(1);
  84         }
  85 }
  86
  87 /*********************************************************************************************/
  88 void MothurOut::clearCurrentFiles()  {
  89         try {
  90                 phylipfile = "";
  91                 columnfile = "";
  92                 listfile = "";
  93                 rabundfile = "";
  94                 sabundfile = "";
  95                 namefile = "";
  96                 groupfile = "";
  97                 designfile = "";
  98                 orderfile = "";
  99                 treefile = "";
 100                 sharedfile = "";
 101                 ordergroupfile = "";
 102                 relabundfile = "";
 103                 fastafile = "";
 104                 qualfile = "";
 105                 sfffile = "";
 106                 oligosfile = "";
 107                 accnosfile = "";
 108                 taxonomyfile = "";
 109                 flowfile = "";
 110                 processors = "1";
 111         }
 112         catch(exception& e) {
 113                 errorOut(e, "MothurOut", "clearCurrentFiles");
 114                 exit(1);
 115         }
 116 }
 117 /*********************************************************************************************/
 118 void MothurOut::setFileName(string filename)  {
 119         try {
 120                 logFileName = filename;
 121
 122                 #ifdef USE_MPI
 123                         int pid;
 124                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 125
 126                         if (pid == 0) { //only one process should output to screen
 127                 #endif
 128
 129                 openOutputFile(filename, out);
 130
 131                 #ifdef USE_MPI
 132                         }
 133                 #endif
 134         }
 135         catch(exception& e) {
 136                 errorOut(e, "MothurOut", "setFileName");
 137                 exit(1);
 138         }
 139 }
 140 /*********************************************************************************************/
 141 void MothurOut::setDefaultPath(string pathname)  {
 142         try {
 143
 144                 //add / to name if needed
 145                 string lastChar = pathname.substr(pathname.length()-1);
 146                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 147                         if (lastChar != "/") { pathname += "/"; }
 148                 #else
 149                         if (lastChar != "\\") { pathname += "\\"; }
 150                 #endif
 151
 152                 defaultPath = pathname;
 153
 154         }
 155         catch(exception& e) {
 156                 errorOut(e, "MothurOut", "setDefaultPath");
 157                 exit(1);
 158         }
 159 }
 160 /*********************************************************************************************/
 161 void MothurOut::setOutputDir(string pathname)  {
 162         try {
 163                 outputDir = pathname;
 164         }
 165         catch(exception& e) {
 166                 errorOut(e, "MothurOut", "setOutputDir");
 167                 exit(1);
 168         }
 169 }
 170 /*********************************************************************************************/
 171 void MothurOut::closeLog()  {
 172         try {
 173
 174                 #ifdef USE_MPI
 175                         int pid;
 176                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 177
 178                         if (pid == 0) { //only one process should output to screen
 179                 #endif
 180
 181                 out.close();
 182
 183                 #ifdef USE_MPI
 184                         }
 185                 #endif
 186         }
 187         catch(exception& e) {
 188                 errorOut(e, "MothurOut", "closeLog");
 189                 exit(1);
 190         }
 191 }
 192
 193 /*********************************************************************************************/
 194 MothurOut::~MothurOut() {
 195         try {
 196                 _uniqueInstance = 0;
 197
 198         }
 199         catch(exception& e) {
 200                 errorOut(e, "MothurOut", "MothurOut");
 201                 exit(1);
 202         }
 203 }
 204 /*********************************************************************************************/
 205 void MothurOut::mothurOut(string output) {
 206         try {
 207
 208                 #ifdef USE_MPI
 209                         int pid;
 210                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 211
 212                         if (pid == 0) { //only one process should output to screen
 213                 #endif
 214
 215                 out << output;
 216         logger() << output;
 217
 218                 #ifdef USE_MPI
 219                         }
 220                 #endif
 221         }
 222         catch(exception& e) {
 223                 errorOut(e, "MothurOut", "MothurOut");
 224                 exit(1);
 225         }
 226 }
 227 /*********************************************************************************************/
 228 void MothurOut::mothurOutEndLine() {
 229         try {
 230                 #ifdef USE_MPI
 231                         int pid;
 232                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 233
 234                         if (pid == 0) { //only one process should output to screen
 235                 #endif
 236
 237                 out << endl;
 238         logger() << endl;
 239
 240                 #ifdef USE_MPI
 241                         }
 242                 #endif
 243         }
 244         catch(exception& e) {
 245                 errorOut(e, "MothurOut", "MothurOutEndLine");
 246                 exit(1);
 247         }
 248 }
 249 /*********************************************************************************************/
 250 void MothurOut::mothurOut(string output, ofstream& outputFile) {
 251         try {
 252
 253 #ifdef USE_MPI
 254                 int pid;
 255                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 256
 257                 if (pid == 0) { //only one process should output to screen
 258 #endif
 259
 260
 261                         out << output;
 262                         outputFile << output;
 263             logger() << output;
 264
 265 #ifdef USE_MPI
 266                 }
 267 #endif
 268
 269         }
 270         catch(exception& e) {
 271                 errorOut(e, "MothurOut", "MothurOut");
 272                 exit(1);
 273         }
 274 }
 275 /*********************************************************************************************/
 276 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 277         try {
 278 #ifdef USE_MPI
 279                 int pid;
 280                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 281
 282                 if (pid == 0) { //only one process should output to screen
 283 #endif
 284
 285                         out << endl;
 286                         outputFile << endl;
 287             logger() << endl;
 288
 289 #ifdef USE_MPI
 290                 }
 291 #endif
 292         }
 293         catch(exception& e) {
 294                 errorOut(e, "MothurOut", "MothurOutEndLine");
 295                 exit(1);
 296         }
 297 }
 298 /*********************************************************************************************/
 299 void MothurOut::mothurOutJustToLog(string output) {
 300         try {
 301                 #ifdef USE_MPI
 302                         int pid;
 303                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 304
 305                         if (pid == 0) { //only one process should output to screen
 306                 #endif
 307
 308                 out << output;
 309
 310                 #ifdef USE_MPI
 311                         }
 312                 #endif
 313         }
 314         catch(exception& e) {
 315                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 316                 exit(1);
 317         }
 318 }
 319 /*********************************************************************************************/
 320 void MothurOut::errorOut(exception& e, string object, string function) {
 321         //double vm, rss;
 322         //mem_usage(vm, rss);
 323
 324         mothurOut("[ERROR]: ");
 325         mothurOut(toString(e.what()));
 326         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.");
 327         mothurOutEndLine();
 328 }
 329 /*********************************************************************************************/
 330 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 331 // process_mem_usage(double &, double &) - takes two doubles by reference,
 332 // attempts to read the system-dependent data for a process' virtual memory
 333 // size and resident set size, and return the results in KB.
 334 //
 335 // On failure, returns 0.0, 0.0
 336 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 337   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 338
 339            vm_usage     = 0.0;
 340            resident_set = 0.0;
 341
 342            // 'file' stat seems to give the most reliable results
 343            //
 344            ifstream stat_stream("/proc/self/stat",ios_base::in);
 345
 346            // dummy vars for leading entries in stat that we don't care about
 347            //
 348            string pid, comm, state, ppid, pgrp, session, tty_nr;
 349            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 350            string utime, stime, cutime, cstime, priority, nice;
 351            string O, itrealvalue, starttime;
 352
 353            // the two fields we want
 354            //
 355            unsigned long vsize;
 356            long rss;
 357
 358            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 359                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 360                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 361                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 362
 363            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 364            vm_usage     = vsize / 1024.0;
 365            resident_set = rss * page_size_kb;
 366
 367            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 368                 return 0;
 369
 370         #else
 371 /*              //windows memory usage
 372                 // Get the list of process identifiers.
 373                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 374
 375                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 376
 377                 // Calculate how many process identifiers were returned.
 378                 cProcesses = cbNeeded / sizeof(DWORD);
 379
 380                 // Print the memory usage for each process
 381                 for (int i = 0; i < cProcesses; i++ ) {
 382                         DWORD processID = aProcesses[i];
 383
 384                         PROCESS_MEMORY_COUNTERS pmc;
 385
 386                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 387
 388                         // Print the process identifier.
 389                         printf( "\nProcess ID: %u\n", processID);
 390
 391                         if (NULL != hProcess) {
 392
 393                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 394                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 395                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 396                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 397                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 398                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 399                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 400                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 401                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 402                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 403                                 }
 404                                 CloseHandle(hProcess);
 405                         }
 406                 }
 407 */
 408                         return 0;
 409
 410         #endif
 411 }
 412
 413
 414 /***********************************************************************/
 415 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 416         try {
 417                 fileName = getFullPathName(fileName);
 418
 419                 fileHandle.open(fileName.c_str(), ios::app);
 420                 if(!fileHandle) {
 421                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 422                         return 1;
 423                 }
 424                 else {
 425                         return 0;
 426                 }
 427         }
 428         catch(exception& e) {
 429                 errorOut(e, "MothurOut", "openOutputFileAppend");
 430                 exit(1);
 431         }
 432 }
 433 /***********************************************************************/
 434 void MothurOut::gobble(istream& f){
 435         try {
 436
 437                 char d;
 438                 while(isspace(d=f.get()))               { ;}
 439                 if(!f.eof()) { f.putback(d); }
 440         }
 441         catch(exception& e) {
 442                 errorOut(e, "MothurOut", "gobble");
 443                 exit(1);
 444         }
 445 }
 446 /***********************************************************************/
 447 void MothurOut::gobble(istringstream& f){
 448         try {
 449                 char d;
 450                 while(isspace(d=f.get()))               {;}
 451                 if(!f.eof()) { f.putback(d); }
 452         }
 453         catch(exception& e) {
 454                 errorOut(e, "MothurOut", "gobble");
 455                 exit(1);
 456         }
 457 }
 458
 459 /***********************************************************************/
 460
 461 string MothurOut::getline(istringstream& fileHandle) {
 462         try {
 463
 464                 string line = "";
 465
 466                 while (!fileHandle.eof())       {
 467                         //get next character
 468                         char c = fileHandle.get();
 469
 470                         //are you at the end of the line
 471                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 472                         else {          line += c;              }
 473                 }
 474
 475                 return line;
 476
 477         }
 478         catch(exception& e) {
 479                 errorOut(e, "MothurOut", "getline");
 480                 exit(1);
 481         }
 482 }
 483 /***********************************************************************/
 484
 485 string MothurOut::getline(ifstream& fileHandle) {
 486         try {
 487
 488                 string line = "";
 489
 490                 while (fileHandle)      {
 491                         //get next character
 492                         char c = fileHandle.get();
 493
 494                         //are you at the end of the line
 495                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }
 496                         else {          line += c;              }
 497                 }
 498
 499                 return line;
 500
 501         }
 502         catch(exception& e) {
 503                 errorOut(e, "MothurOut", "getline");
 504                 exit(1);
 505         }
 506 }
 507 /***********************************************************************/
 508
 509 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 510 #ifdef USE_COMPRESSION
 511 inline bool endsWith(string s, const char * suffix){
 512   size_t suffixLength = strlen(suffix);
 513   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 514 }
 515 #endif
 516 #endif
 517
 518 string MothurOut::getRootName(string longName){
 519         try {
 520
 521                 string rootName = longName;
 522
 523 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 524 #ifdef USE_COMPRESSION
 525     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 526       int pos = rootName.find_last_of('.');
 527       rootName = rootName.substr(0, pos);
 528       cerr << "shortening " << longName << " to " << rootName << "\n";
 529     }
 530 #endif
 531 #endif
 532                 if(rootName.find_last_of(".") != rootName.npos){
 533                         int pos = rootName.find_last_of('.')+1;
 534                         rootName = rootName.substr(0, pos);
 535                 }
 536
 537                 return rootName;
 538         }
 539         catch(exception& e) {
 540                 errorOut(e, "MothurOut", "getRootName");
 541                 exit(1);
 542         }
 543 }
 544 /***********************************************************************/
 545
 546 string MothurOut::getSimpleName(string longName){
 547         try {
 548                 string simpleName = longName;
 549
 550                 size_t found;
 551                 found=longName.find_last_of("/\\");
 552
 553                 if(found != longName.npos){
 554                         simpleName = longName.substr(found+1);
 555                 }
 556
 557                 return simpleName;
 558         }
 559         catch(exception& e) {
 560                 errorOut(e, "MothurOut", "getSimpleName");
 561                 exit(1);
 562         }
 563 }
 564
 565 /***********************************************************************/
 566
 567 int MothurOut::getRandomIndex(int highest){
 568         try {
 569
 570                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 571
 572                 return random;
 573         }
 574         catch(exception& e) {
 575                 errorOut(e, "MothurOut", "getRandomIndex");
 576                 exit(1);
 577         }
 578
 579 }
 580 /**********************************************************************/
 581
 582 string MothurOut::getPathName(string longName){
 583         try {
 584                 string rootPathName = longName;
 585
 586                 if(longName.find_last_of("/\\") != longName.npos){
 587                         int pos = longName.find_last_of("/\\")+1;
 588                         rootPathName = longName.substr(0, pos);
 589                 }
 590
 591                 return rootPathName;
 592         }
 593         catch(exception& e) {
 594                 errorOut(e, "MothurOut", "getPathName");
 595                 exit(1);
 596         }
 597
 598 }
 599 /***********************************************************************/
 600
 601 string MothurOut::hasPath(string longName){
 602         try {
 603                 string path = "";
 604
 605                 size_t found;
 606                 found=longName.find_last_of("~/\\");
 607
 608                 if(found != longName.npos){
 609                         path = longName.substr(0, found+1);
 610                 }
 611
 612                 return path;
 613         }
 614         catch(exception& e) {
 615                 errorOut(e, "MothurOut", "hasPath");
 616                 exit(1);
 617         }
 618 }
 619
 620 /***********************************************************************/
 621
 622 string MothurOut::getExtension(string longName){
 623         try {
 624                 string extension = longName;
 625
 626                 if(longName.find_last_of('.') != longName.npos){
 627                         int pos = longName.find_last_of('.');
 628                         extension = longName.substr(pos, longName.length());
 629                 }
 630
 631                 return extension;
 632         }
 633         catch(exception& e) {
 634                 errorOut(e, "MothurOut", "getExtension");
 635                 exit(1);
 636         }
 637 }
 638 /***********************************************************************/
 639 bool MothurOut::isBlank(string fileName){
 640         try {
 641
 642                 fileName = getFullPathName(fileName);
 643
 644                 ifstream fileHandle;
 645                 fileHandle.open(fileName.c_str());
 646                 if(!fileHandle) {
 647                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 648                         return false;
 649                 }else {
 650                         //check for blank file
 651                         gobble(fileHandle);
 652                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 653                         fileHandle.close();
 654                 }
 655                 return false;
 656         }
 657         catch(exception& e) {
 658                 errorOut(e, "MothurOut", "isBlank");
 659                 exit(1);
 660         }
 661 }
 662 /***********************************************************************/
 663
 664 string MothurOut::getFullPathName(string fileName){
 665         try{
 666
 667         string path = hasPath(fileName);
 668         string newFileName;
 669         int pos;
 670
 671         if (path == "") { return fileName; } //its a simple name
 672         else { //we need to complete the pathname
 673                 // ex. ../../../filename
 674                 // cwd = /user/work/desktop
 675
 676                 string cwd;
 677                 //get current working directory
 678                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 679
 680                         if (path.find("~") != -1) { //go to home directory
 681                                 string homeDir;
 682
 683                                 char *homepath = NULL;
 684                                 homepath = getenv ("HOME");
 685                                 if ( homepath != NULL) { homeDir = homepath; }
 686                                 else { homeDir = "";  }
 687
 688                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 689                                 return newFileName;
 690                         }else { //find path
 691                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 692                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 693
 694                                 //char* cwdpath = new char[1024];
 695                                 //size_t size;
 696                                 //cwdpath=getcwd(cwdpath,size);
 697                                 //cwd = cwdpath;
 698
 699                                 char *cwdpath = NULL;
 700                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 701                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 702                                 else { cwd = "";  }
 703
 704
 705                                 //rip off first '/'
 706                                 string simpleCWD;
 707                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 708
 709                                 //break apart the current working directory
 710                                 vector<string> dirs;
 711                                 while (simpleCWD.find_first_of('/') != string::npos) {
 712                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 713                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 714                                         dirs.push_back(dir);
 715                                 }
 716                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 717                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 718
 719
 720                                 int index = dirs.size()-1;
 721
 722                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 723                                         if (pos == 0) { break;  //you are at the end
 724                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 725                                                 path = path.substr(0, pos-1);
 726                                                 index--;
 727                                                 if (index == 0) {  break; }
 728                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 729                                                 path = path.substr(0, pos);
 730                                         }else if (pos == 1) { break;  //you are at the end
 731                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 732                                 }
 733
 734                                 for (int i = index; i >= 0; i--) {
 735                                         newFileName = dirs[i] +  "/" + newFileName;
 736                                 }
 737
 738                                 newFileName =  "/" +  newFileName;
 739                                 return newFileName;
 740                         }
 741                 #else
 742                         if (path.find("~") != string::npos) { //go to home directory
 743                                 string homeDir = getenv ("HOMEPATH");
 744                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 745                                 return newFileName;
 746                         }else { //find path
 747                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 748                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 749
 750                                 char *cwdpath = NULL;
 751                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 752                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 753                                 else { cwd = "";  }
 754
 755                                 //break apart the current working directory
 756                                 vector<string> dirs;
 757                                 while (cwd.find_first_of('\\') != -1) {
 758                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 759                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 760                                         dirs.push_back(dir);
 761
 762                                 }
 763                                 //get last one
 764                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 765
 766                                 int index = dirs.size()-1;
 767
 768                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 769                                         if (pos == 0) { break;  //you are at the end
 770                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 771                                                 path = path.substr(0, pos-1);
 772                                                 index--;
 773                                                 if (index == 0) {  break; }
 774                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 775                                                 path = path.substr(0, pos);
 776                                         }else if (pos == 1) { break;  //you are at the end
 777                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 778                                 }
 779
 780                                 for (int i = index; i >= 0; i--) {
 781                                         newFileName = dirs[i] +  "\\" + newFileName;
 782                                 }
 783
 784                                 return newFileName;
 785                         }
 786
 787                 #endif
 788         }
 789         }
 790         catch(exception& e) {
 791                 errorOut(e, "MothurOut", "getFullPathName");
 792                 exit(1);
 793         }
 794 }
 795 /***********************************************************************/
 796
 797 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 798         try {
 799                         //get full path name
 800                         string completeFileName = getFullPathName(fileName);
 801 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 802 #ifdef USE_COMPRESSION
 803       // check for gzipped or bzipped file
 804       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 805         string tempName = string(tmpnam(0));
 806         mkfifo(tempName.c_str(), 0666);
 807         int fork_result = fork();
 808         if (fork_result < 0) {
 809           cerr << "Error forking.\n";
 810           exit(1);
 811         } else if (fork_result == 0) {
 812           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 813           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 814           system(command.c_str());
 815           cerr << "Done decompressing " << completeFileName << "\n";
 816           mothurRemove(tempName);
 817           exit(EXIT_SUCCESS);
 818         } else {
 819           cerr << "waiting on child process " << fork_result << "\n";
 820           completeFileName = tempName;
 821         }
 822       }
 823 #endif
 824 #endif
 825                         fileHandle.open(completeFileName.c_str());
 826                         if(!fileHandle) {
 827                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 828                                 return 1;
 829                         }else {
 830                                 //check for blank file
 831                                 gobble(fileHandle);
 832                                 return 0;
 833                         }
 834         }
 835         catch(exception& e) {
 836                 errorOut(e, "MothurOut", "openInputFile - no Error");
 837                 exit(1);
 838         }
 839 }
 840 /***********************************************************************/
 841
 842 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 843         try {
 844
 845                 //get full path name
 846                 string completeFileName = getFullPathName(fileName);
 847 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 848 #ifdef USE_COMPRESSION
 849   // check for gzipped or bzipped file
 850   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 851     string tempName = string(tmpnam(0));
 852     mkfifo(tempName.c_str(), 0666);
 853     int fork_result = fork();
 854     if (fork_result < 0) {
 855       cerr << "Error forking.\n";
 856       exit(1);
 857     } else if (fork_result == 0) {
 858       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 859       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 860       system(command.c_str());
 861       cerr << "Done decompressing " << completeFileName << "\n";
 862       mothurRemove(tempName);
 863       exit(EXIT_SUCCESS);
 864     } else {
 865       cerr << "waiting on child process " << fork_result << "\n";
 866       completeFileName = tempName;
 867     }
 868   }
 869 #endif
 870 #endif
 871
 872                 fileHandle.open(completeFileName.c_str());
 873                 if(!fileHandle) {
 874                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 875                         return 1;
 876                 }
 877                 else {
 878                         //check for blank file
 879                         gobble(fileHandle);
 880                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 881
 882                         return 0;
 883                 }
 884         }
 885         catch(exception& e) {
 886                 errorOut(e, "MothurOut", "openInputFile");
 887                 exit(1);
 888         }
 889 }
 890 /***********************************************************************/
 891
 892 int MothurOut::renameFile(string oldName, string newName){
 893         try {
 894                 ifstream inTest;
 895                 int exist = openInputFile(newName, inTest, "");
 896                 inTest.close();
 897
 898         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 899                 if (exist == 0) { //you could open it so you want to delete it
 900                         string command = "rm " + newName;
 901                         system(command.c_str());
 902                 }
 903
 904                 string command = "mv " + oldName + " " + newName;
 905                 system(command.c_str());
 906         #else
 907                 mothurRemove(newName);
 908                 int renameOk = rename(oldName.c_str(), newName.c_str());
 909         #endif
 910                 return 0;
 911
 912         }
 913         catch(exception& e) {
 914                 errorOut(e, "MothurOut", "renameFile");
 915                 exit(1);
 916         }
 917 }
 918
 919 /***********************************************************************/
 920
 921 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 922         try {
 923
 924                 string completeFileName = getFullPathName(fileName);
 925 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 926 #ifdef USE_COMPRESSION
 927     // check for gzipped file
 928     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 929       string tempName = string(tmpnam(0));
 930       mkfifo(tempName.c_str(), 0666);
 931       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 932       int fork_result = fork();
 933       if (fork_result < 0) {
 934         cerr << "Error forking.\n";
 935         exit(1);
 936       } else if (fork_result == 0) {
 937         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 938         system(command.c_str());
 939         exit(0);
 940       } else {
 941         completeFileName = tempName;
 942       }
 943     }
 944 #endif
 945 #endif
 946                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 947                 if(!fileHandle) {
 948                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 949                         return 1;
 950                 }
 951                 else {
 952                         return 0;
 953                 }
 954         }
 955         catch(exception& e) {
 956                 errorOut(e, "MothurOut", "openOutputFile");
 957                 exit(1);
 958         }
 959
 960 }
 961
 962 /**************************************************************************************************/
 963 int MothurOut::appendFiles(string temp, string filename) {
 964         try{
 965                 ofstream output;
 966                 ifstream input;
 967
 968                 //open output file in append mode
 969                 openOutputFileAppend(filename, output);
 970                 int ableToOpen = openInputFile(temp, input, "no error");
 971                 //int ableToOpen = openInputFile(temp, input);
 972
 973                 int numLines = 0;
 974                 if (ableToOpen == 0) { //you opened it
 975                         while(char c = input.get()){
 976                                 if(input.eof())         {       break;                  }
 977                                 else                            {       output << c;    if (c == '\n') {numLines++;} }
 978                         }
 979                         input.close();
 980                 }
 981
 982                 output.close();
 983
 984                 return numLines;
 985         }
 986         catch(exception& e) {
 987                 errorOut(e, "MothurOut", "appendFiles");
 988                 exit(1);
 989         }
 990 }
 991
 992 /**************************************************************************************************/
 993 string MothurOut::sortFile(string distFile, string outputDir){
 994         try {
 995
 996                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 997                 string outfile = getRootName(distFile) + "sorted.dist";
 998
 999
1000                 //if you can, use the unix sort since its been optimized for years
1001                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1002                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
1003                         system(command.c_str());
1004                 #else //you are stuck with my best attempt...
1005                         //windows sort does not have a way to specify a column, only a character in the line
1006                         //since we cannot assume that the distance will always be at the the same character location on each line
1007                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1008
1009                         //read in file line by file and put distance first
1010                         string tempDistFile = distFile + ".temp";
1011                         ifstream input;
1012                         ofstream output;
1013                         openInputFile(distFile, input);
1014                         openOutputFile(tempDistFile, output);
1015
1016                         string firstName, secondName;
1017                         float dist;
1018                         while (input) {
1019                                 input >> firstName >> secondName >> dist;
1020                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1021                                 gobble(input);
1022                         }
1023                         input.close();
1024                         output.close();
1025
1026
1027                         //sort using windows sort
1028                         string tempOutfile = outfile + ".temp";
1029                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1030                         system(command.c_str());
1031
1032                         //read in sorted file and put distance at end again
1033                         ifstream input2;
1034                         openInputFile(tempOutfile, input2);
1035                         openOutputFile(outfile, output);
1036
1037                         while (input2) {
1038                                 input2 >> dist >> firstName >> secondName;
1039                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1040                                 gobble(input2);
1041                         }
1042                         input2.close();
1043                         output.close();
1044
1045                         //remove temp files
1046                         mothurRemove(tempDistFile);
1047                         mothurRemove(tempOutfile);
1048                 #endif
1049
1050                 return outfile;
1051         }
1052         catch(exception& e) {
1053                 errorOut(e, "MothurOut", "sortFile");
1054                 exit(1);
1055         }
1056 }
1057 /**************************************************************************************************/
1058 vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
1059         try {
1060                         vector<unsigned long long> positions;
1061                         ifstream inFASTA;
1062                         //openInputFile(filename, inFASTA);
1063                         inFASTA.open(filename.c_str(), ios::binary);
1064
1065                         string input;
1066                         unsigned long long count = 0;
1067                         while(!inFASTA.eof()){
1068                                 //input = getline(inFASTA);
1069                                 //cout << input << '\t' << inFASTA.tellg() << endl;
1070                                 //if (input.length() != 0) {
1071                                 //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
1072                                 //}
1073                                 //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1074                                 char c = inFASTA.get(); count++;
1075                                 if (c == '>') {
1076                                         positions.push_back(count-1);
1077                                         //cout << count << endl;
1078                                 }
1079                         }
1080                         inFASTA.close();
1081
1082                         num = positions.size();
1083
1084                         /*FILE * pFile;
1085                         long size;
1086
1087                         //get num bytes in file
1088                         pFile = fopen (filename.c_str(),"rb");
1089                         if (pFile==NULL) perror ("Error opening file");
1090                         else{
1091                                 fseek (pFile, 0, SEEK_END);
1092                                 size=ftell (pFile);
1093                                 fclose (pFile);
1094                         }*/
1095
1096                         unsigned long long size = positions[(positions.size()-1)];
1097                         ifstream in;
1098                         openInputFile(filename, in);
1099
1100                         in.seekg(size);
1101
1102                         while(in.get()){
1103                                 if(in.eof())            {       break;  }
1104                                 else                            {       size++; }
1105                         }
1106                         in.close();
1107
1108                         positions.push_back(size);
1109                         positions[0] = 0;
1110
1111                         return positions;
1112         }
1113         catch(exception& e) {
1114                 errorOut(e, "MothurOut", "setFilePosFasta");
1115                 exit(1);
1116         }
1117 }
1118 /**************************************************************************************************/
1119 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
1120         try {
1121                         filename = getFullPathName(filename);
1122
1123                         vector<unsigned long long> positions;
1124                         ifstream in;
1125                         //openInputFile(filename, in);
1126                         in.open(filename.c_str(), ios::binary);
1127
1128                         string input;
1129                         unsigned long long count = 0;
1130                         positions.push_back(0);
1131
1132                         while(!in.eof()){
1133                                 //unsigned long long lastpos = in.tellg();
1134                                 //input = getline(in);
1135                                 //if (input.length() != 0) {
1136                                         //unsigned long long pos = in.tellg();
1137                                         //if (pos != -1) { positions.push_back(pos - input.length() - 1);       }
1138                                         //else {  positions.push_back(lastpos);  }
1139                                 //}
1140                                 //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
1141
1142
1143                                 //getline counting reads
1144                                 char d = in.get(); count++;
1145                                 while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
1146                                         //get next character
1147                                         d = in.get();
1148                                         count++;
1149                                 }
1150
1151                                 if (!in.eof()) {
1152                                         d=in.get(); count++;
1153                                         while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
1154                                 }
1155                                 positions.push_back(count-1);
1156                                 //cout << count-1 << endl;
1157                         }
1158                         in.close();
1159
1160                         num = positions.size()-1;
1161
1162                         FILE * pFile;
1163                         unsigned long long size;
1164
1165                         //get num bytes in file
1166                         pFile = fopen (filename.c_str(),"rb");
1167                         if (pFile==NULL) perror ("Error opening file");
1168                         else{
1169                                 fseek (pFile, 0, SEEK_END);
1170                                 size=ftell (pFile);
1171                                 fclose (pFile);
1172                         }
1173
1174                         positions[(positions.size()-1)] = size;
1175
1176                         return positions;
1177         }
1178         catch(exception& e) {
1179                 errorOut(e, "MothurOut", "setFilePosEachLine");
1180                 exit(1);
1181         }
1182 }
1183 /**************************************************************************************************/
1184
1185 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
1186         try{
1187                 vector<unsigned long long> filePos;
1188                 filePos.push_back(0);
1189
1190                 FILE * pFile;
1191                 unsigned long long size;
1192
1193                 filename = getFullPathName(filename);
1194
1195                 //get num bytes in file
1196                 pFile = fopen (filename.c_str(),"rb");
1197                 if (pFile==NULL) perror ("Error opening file");
1198                 else{
1199                         fseek (pFile, 0, SEEK_END);
1200                         size=ftell (pFile);
1201                         fclose (pFile);
1202                 }
1203
1204         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1205
1206                 //estimate file breaks
1207                 unsigned long long chunkSize = 0;
1208                 chunkSize = size / proc;
1209
1210                 //file to small to divide by processors
1211                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1212
1213                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1214                 for (int i = 0; i < proc; i++) {
1215                         unsigned long long spot = (i+1) * chunkSize;
1216
1217                         ifstream in;
1218                         openInputFile(filename, in);
1219                         in.seekg(spot);
1220
1221                         //look for next '>'
1222                         unsigned long long newSpot = spot;
1223                         while (!in.eof()) {
1224                            char c = in.get();
1225
1226                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1227                            else if (int(c) == -1) { break; }
1228
1229                         }
1230
1231                         //there was not another sequence before the end of the file
1232                         unsigned long long sanityPos = in.tellg();
1233
1234                         if (sanityPos == -1) {  break;  }
1235                         else {  filePos.push_back(newSpot);  }
1236
1237                         in.close();
1238                 }
1239
1240                 //save end pos
1241                 filePos.push_back(size);
1242
1243                 //sanity check filePos
1244                 for (int i = 0; i < (filePos.size()-1); i++) {
1245                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1246                 }
1247
1248                 proc = (filePos.size() - 1);
1249 #else
1250                 mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
1251                 proc=1;
1252                 filePos.push_back(size);
1253 #endif
1254                 return filePos;
1255         }
1256         catch(exception& e) {
1257                 errorOut(e, "MothurOut", "divideFile");
1258                 exit(1);
1259         }
1260 }
1261 /**************************************************************************************************/
1262 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1263         try{
1264
1265                 vector<unsigned long long> filePos = divideFile(filename, proc);
1266
1267                 for (int i = 0; i < (filePos.size()-1); i++) {
1268
1269                         //read file chunk
1270                         ifstream in;
1271                         openInputFile(filename, in);
1272                         in.seekg(filePos[i]);
1273                         unsigned long long size = filePos[(i+1)] - filePos[i];
1274                         char* chunk = new char[size];
1275                         in.read(chunk, size);
1276                         in.close();
1277
1278                         //open new file
1279                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1280                         ofstream out;
1281                         openOutputFile(fileChunkName, out);
1282
1283                         out << chunk << endl;
1284                         out.close();
1285                         delete[] chunk;
1286
1287                         //save name
1288                         files.push_back(fileChunkName);
1289                 }
1290
1291                 return 0;
1292         }
1293         catch(exception& e) {
1294                 errorOut(e, "MothurOut", "divideFile");
1295                 exit(1);
1296         }
1297 }
1298 /***********************************************************************/
1299
1300 bool MothurOut::isTrue(string f){
1301         try {
1302
1303                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1304
1305                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1306                 else {  return false;  }
1307         }
1308         catch(exception& e) {
1309                 errorOut(e, "MothurOut", "isTrue");
1310                 exit(1);
1311         }
1312 }
1313
1314 /***********************************************************************/
1315
1316 float MothurOut::roundDist(float dist, int precision){
1317         try {
1318                 return int(dist * precision + 0.5)/float(precision);
1319         }
1320         catch(exception& e) {
1321                 errorOut(e, "MothurOut", "roundDist");
1322                 exit(1);
1323         }
1324 }
1325 /***********************************************************************/
1326
1327 float MothurOut::ceilDist(float dist, int precision){
1328         try {
1329                 return int(ceil(dist * precision))/float(precision);
1330         }
1331         catch(exception& e) {
1332                 errorOut(e, "MothurOut", "ceilDist");
1333                 exit(1);
1334         }
1335 }
1336 /**********************************************************************************************************************/
1337 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1338         try {
1339
1340                 //open input file
1341                 ifstream in;
1342                 openInputFile(namefile, in);
1343
1344                 while (!in.eof()) {
1345                         if (control_pressed) { break; }
1346
1347                         string firstCol, secondCol;
1348                         in >> firstCol >> secondCol; gobble(in);
1349
1350                         nameMap[firstCol] = secondCol;
1351                 }
1352                 in.close();
1353
1354                 return 0;
1355
1356         }
1357         catch(exception& e) {
1358                 errorOut(e, "MothurOut", "readNames");
1359                 exit(1);
1360         }
1361 }
1362 /**********************************************************************************************************************/
1363 int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
1364         try {
1365
1366                 //open input file
1367                 ifstream in;
1368                 openInputFile(namefile, in);
1369
1370                 while (!in.eof()) {
1371                         if (control_pressed) { break; }
1372
1373                         string firstCol, secondCol;
1374                         in >> firstCol >> secondCol; gobble(in);
1375
1376                         vector<string> temp;
1377                         splitAtComma(secondCol, temp);
1378
1379                         nameMap[firstCol] = temp;
1380                 }
1381                 in.close();
1382
1383                 return 0;
1384
1385         }
1386         catch(exception& e) {
1387                 errorOut(e, "MothurOut", "readNames");
1388                 exit(1);
1389         }
1390 }
1391 /**********************************************************************************************************************/
1392 map<string, int> MothurOut::readNames(string namefile) {
1393         try {
1394
1395                 map<string, int> nameMap;
1396
1397                 //open input file
1398                 ifstream in;
1399                 openInputFile(namefile, in);
1400
1401                 while (!in.eof()) {
1402                         if (control_pressed) { break; }
1403
1404                         string firstCol, secondCol;
1405                         in >> firstCol >> secondCol; gobble(in);
1406
1407                         int num = getNumNames(secondCol);
1408
1409                         nameMap[firstCol] = num;
1410                 }
1411                 in.close();
1412
1413                 return nameMap;
1414
1415         }
1416         catch(exception& e) {
1417                 errorOut(e, "MothurOut", "readNames");
1418                 exit(1);
1419         }
1420 }
1421 /**********************************************************************************************************************/
1422 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1423         try {
1424                 int error = 0;
1425
1426                 //open input file
1427                 ifstream in;
1428                 openInputFile(namefile, in);
1429
1430                 while (!in.eof()) {
1431                         if (control_pressed) { break; }
1432
1433                         string firstCol, secondCol;
1434                         in >> firstCol >> secondCol; gobble(in);
1435
1436                         int num = getNumNames(secondCol);
1437
1438                         map<string, string>::iterator it = fastamap.find(firstCol);
1439                         if (it == fastamap.end()) {
1440                                 error = 1;
1441                                 mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1442                         }else {
1443                                 seqPriorityNode temp(num, it->second, firstCol);
1444                                 nameVector.push_back(temp);
1445                         }
1446                 }
1447                 in.close();
1448
1449                 return error;
1450
1451         }
1452         catch(exception& e) {
1453                 errorOut(e, "MothurOut", "readNames");
1454                 exit(1);
1455         }
1456 }
1457
1458 /***********************************************************************/
1459
1460 int MothurOut::getNumNames(string names){
1461         try {
1462                 int count = 0;
1463
1464                 if(names != ""){
1465                         count = 1;
1466                         for(int i=0;i<names.size();i++){
1467                                 if(names[i] == ','){
1468                                         count++;
1469                                 }
1470                         }
1471                 }
1472
1473                 return count;
1474         }
1475         catch(exception& e) {
1476                 errorOut(e, "MothurOut", "getNumNames");
1477                 exit(1);
1478         }
1479 }
1480 /***********************************************************************/
1481
1482 int MothurOut::getNumChar(string line, char c){
1483         try {
1484                 int count = 0;
1485
1486                 if(line != ""){
1487                         for(int i=0;i<line.size();i++){
1488                                 if(line[i] == c){
1489                                         count++;
1490                                 }
1491                         }
1492                 }
1493
1494                 return count;
1495         }
1496         catch(exception& e) {
1497                 errorOut(e, "MothurOut", "getNumChar");
1498                 exit(1);
1499         }
1500 }
1501 /***********************************************************************/
1502 int MothurOut::mothurRemove(string filename){
1503         try {
1504                 filename = getFullPathName(filename);
1505                 int error = remove(filename.c_str());
1506                 //if (error != 0) {
1507                 //      if (errno != ENOENT) { //ENOENT == file does not exist
1508                 //              string message = "Error deleting file " + filename;
1509                 //              perror(message.c_str());
1510                 //      }
1511                 //}
1512                 return error;
1513         }
1514         catch(exception& e) {
1515                 errorOut(e, "MothurOut", "mothurRemove");
1516                 exit(1);
1517         }
1518 }
1519 /***********************************************************************/
1520 bool MothurOut::mothurConvert(string item, int& num){
1521         try {
1522                 bool error = false;
1523
1524                 if (isNumeric1(item)) {
1525                         convert(item, num);
1526                 }else {
1527                         num = 0;
1528                         error = true;
1529                         mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
1530                         commandInputsConvertError = true;
1531                 }
1532
1533                 return error;
1534         }
1535         catch(exception& e) {
1536                 errorOut(e, "MothurOut", "mothurConvert");
1537                 exit(1);
1538         }
1539 }
1540 /***********************************************************************/
1541 bool MothurOut::isNumeric1(string stringToCheck){
1542         try {
1543                 bool numeric = false;
1544
1545                 if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
1546
1547                 return numeric;
1548         }
1549         catch(exception& e) {
1550                 errorOut(e, "MothurOut", "isNumeric1");
1551                 exit(1);
1552         }
1553
1554 }
1555 /***********************************************************************/
1556 bool MothurOut::mothurConvert(string item, float& num){
1557         try {
1558                 bool error = false;
1559
1560                 if (isNumeric1(item)) {
1561                         convert(item, num);
1562                 }else {
1563                         num = 0;
1564                         error = true;
1565                         mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
1566                         commandInputsConvertError = true;
1567                 }
1568
1569                 return error;
1570         }
1571         catch(exception& e) {
1572                 errorOut(e, "MothurOut", "mothurConvert");
1573                 exit(1);
1574         }
1575 }
1576 /***********************************************************************/
1577 bool MothurOut::mothurConvert(string item, double& num){
1578         try {
1579                 bool error = false;
1580
1581                 if (isNumeric1(item)) {
1582                         convert(item, num);
1583                 }else {
1584                         num = 0;
1585                         error = true;
1586                         mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
1587                         commandInputsConvertError = true;
1588                 }
1589
1590                 return error;
1591         }
1592         catch(exception& e) {
1593                 errorOut(e, "MothurOut", "mothurConvert");
1594                 exit(1);
1595         }
1596 }
1597 /**************************************************************************************************/
1598
1599 vector<vector<double> > MothurOut::binomial(int maxOrder){
1600         try {
1601         vector<vector<double> > binomial(maxOrder+1);
1602
1603     for(int i=0;i<=maxOrder;i++){
1604                 binomial[i].resize(maxOrder+1);
1605                 binomial[i][0]=1;
1606                 binomial[0][i]=0;
1607     }
1608     binomial[0][0]=1;
1609
1610     binomial[1][0]=1;
1611     binomial[1][1]=1;
1612
1613     for(int i=2;i<=maxOrder;i++){
1614                 binomial[1][i]=0;
1615     }
1616
1617     for(int i=2;i<=maxOrder;i++){
1618                 for(int j=1;j<=maxOrder;j++){
1619                         if(i==j){       binomial[i][j]=1;                                                                       }
1620                         if(j>i) {       binomial[i][j]=0;                                                                       }
1621                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1622                 }
1623     }
1624
1625         return binomial;
1626
1627         }
1628         catch(exception& e) {
1629                 errorOut(e, "MothurOut", "binomial");
1630                 exit(1);
1631         }
1632 }
1633 /**************************************************************************************************/
1634 unsigned int MothurOut::fromBase36(string base36){
1635         try {
1636                 unsigned int num = 0;
1637
1638                 map<char, int> converts;
1639                 converts['A'] = 0;
1640                 converts['a'] = 0;
1641                 converts['B'] = 1;
1642                 converts['b'] = 1;
1643                 converts['C'] = 2;
1644                 converts['c'] = 2;
1645                 converts['D'] = 3;
1646                 converts['d'] = 3;
1647                 converts['E'] = 4;
1648                 converts['e'] = 4;
1649                 converts['F'] = 5;
1650                 converts['f'] = 5;
1651                 converts['G'] = 6;
1652                 converts['g'] = 6;
1653                 converts['H'] = 7;
1654                 converts['h'] = 7;
1655                 converts['I'] = 8;
1656                 converts['i'] = 8;
1657                 converts['J'] = 9;
1658                 converts['j'] = 9;
1659                 converts['K'] = 10;
1660                 converts['k'] = 10;
1661                 converts['L'] = 11;
1662                 converts['l'] = 11;
1663                 converts['M'] = 12;
1664                 converts['m'] = 12;
1665                 converts['N'] = 13;
1666                 converts['n'] = 13;
1667                 converts['O'] = 14;
1668                 converts['o'] = 14;
1669                 converts['P'] = 15;
1670                 converts['p'] = 15;
1671                 converts['Q'] = 16;
1672                 converts['q'] = 16;
1673                 converts['R'] = 17;
1674                 converts['r'] = 17;
1675                 converts['S'] = 18;
1676                 converts['s'] = 18;
1677                 converts['T'] = 19;
1678                 converts['t'] = 19;
1679                 converts['U'] = 20;
1680                 converts['u'] = 20;
1681                 converts['V'] = 21;
1682                 converts['v'] = 21;
1683                 converts['W'] = 22;
1684                 converts['w'] = 22;
1685                 converts['X'] = 23;
1686                 converts['x'] = 23;
1687                 converts['Y'] = 24;
1688                 converts['y'] = 24;
1689                 converts['Z'] = 25;
1690                 converts['z'] = 25;
1691                 converts['0'] = 26;
1692                 converts['1'] = 27;
1693                 converts['2'] = 28;
1694                 converts['3'] = 29;
1695                 converts['4'] = 30;
1696                 converts['5'] = 31;
1697                 converts['6'] = 32;
1698                 converts['7'] = 33;
1699                 converts['8'] = 34;
1700                 converts['9'] = 35;
1701
1702                 int i = 0;
1703                 while (i < base36.length()) {
1704                         char c = base36[i];
1705                         num = 36 * num + converts[c];
1706                         i++;
1707                 }
1708
1709                 return num;
1710
1711         }
1712         catch(exception& e) {
1713                 errorOut(e, "MothurOut", "fromBase36");
1714                 exit(1);
1715         }
1716 }
1717 /***********************************************************************/
1718
1719 int MothurOut::factorial(int num){
1720         try {
1721                 int total = 1;
1722
1723                 for (int i = 1; i <= num; i++) {
1724                         total *= i;
1725                 }
1726
1727                 return total;
1728         }
1729         catch(exception& e) {
1730                 errorOut(e, "MothurOut", "factorial");
1731                 exit(1);
1732         }
1733 }
1734 /***********************************************************************/
1735
1736 int MothurOut::getNumSeqs(ifstream& file){
1737         try {
1738                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1739                 file.seekg(0);
1740                 return numSeqs;
1741         }
1742         catch(exception& e) {
1743                 errorOut(e, "MothurOut", "getNumSeqs");
1744                 exit(1);
1745         }
1746 }
1747 /***********************************************************************/
1748 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1749         try {
1750                 string input;
1751                 numSeqs = 0;
1752                 while(!file.eof()){
1753                         input = getline(file);
1754                         if (input.length() != 0) {
1755                                 if(input[0] == '>'){ numSeqs++; }
1756                         }
1757                 }
1758         }
1759         catch(exception& e) {
1760                 errorOut(e, "MothurOut", "getNumSeqs");
1761                 exit(1);
1762         }
1763 }
1764 /***********************************************************************/
1765
1766 //This function parses the estimator options and puts them in a vector
1767 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1768         try {
1769                 string individual = "";
1770                 int estimLength = estim.size();
1771                 for(int i=0;i<estimLength;i++){
1772                         if(estim[i] == symbol){
1773                                 container.push_back(individual);
1774                                 individual = "";
1775                         }
1776                         else{
1777                                 individual += estim[i];
1778                         }
1779                 }
1780                 container.push_back(individual);
1781
1782         }
1783         catch(exception& e) {
1784                 errorOut(e, "MothurOut", "splitAtChar");
1785                 exit(1);
1786         }
1787 }
1788
1789 /***********************************************************************/
1790
1791 //This function parses the estimator options and puts them in a vector
1792 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1793         try {
1794                 string individual = "";
1795                 int estimLength = estim.size();
1796                 for(int i=0;i<estimLength;i++){
1797                         if(estim[i] == '-'){
1798                                 container.push_back(individual);
1799                                 individual = "";
1800                         }
1801                         else{
1802                                 individual += estim[i];
1803                         }
1804                 }
1805                 container.push_back(individual);
1806
1807
1808         /*      string individual;
1809
1810                 while (estim.find_first_of('-') != -1) {
1811                         individual = estim.substr(0,estim.find_first_of('-'));
1812                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1813                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1814                                 container.push_back(individual);
1815                         }
1816                 }
1817                 //get last one
1818                 container.push_back(estim); */
1819         }
1820         catch(exception& e) {
1821                 errorOut(e, "MothurOut", "splitAtDash");
1822                 exit(1);
1823         }
1824 }
1825
1826 /***********************************************************************/
1827 //This function parses the label options and puts them in a set
1828 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1829         try {
1830                 string individual = "";
1831                 int estimLength = estim.size();
1832                 for(int i=0;i<estimLength;i++){
1833                         if(estim[i] == '-'){
1834                                 container.insert(individual);
1835                                 individual = "";
1836                         }
1837                         else{
1838                                 individual += estim[i];
1839                         }
1840                 }
1841                 container.insert(individual);
1842
1843         //      string individual;
1844
1845         //      while (estim.find_first_of('-') != -1) {
1846         //              individual = estim.substr(0,estim.find_first_of('-'));
1847         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1848         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1849         //                      container.insert(individual);
1850         //              }
1851         //      }
1852                 //get last one
1853         //      container.insert(estim);
1854
1855         }
1856         catch(exception& e) {
1857                 errorOut(e, "MothurOut", "splitAtDash");
1858                 exit(1);
1859         }
1860 }
1861 /***********************************************************************/
1862 //This function parses the line options and puts them in a set
1863 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1864         try {
1865                 string individual;
1866                 int lineNum;
1867
1868                 while (estim.find_first_of('-') != -1) {
1869                         individual = estim.substr(0,estim.find_first_of('-'));
1870                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1871                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1872                                 convert(individual, lineNum); //convert the string to int
1873                                 container.insert(lineNum);
1874                         }
1875                 }
1876                 //get last one
1877                 convert(estim, lineNum); //convert the string to int
1878                 container.insert(lineNum);
1879         }
1880         catch(exception& e) {
1881                 errorOut(e, "MothurOut", "splitAtDash");
1882                 exit(1);
1883         }
1884 }
1885 /***********************************************************************/
1886 //This function parses the a string and puts peices in a vector
1887 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1888         try {
1889                 string individual = "";
1890                 int estimLength = estim.size();
1891                 for(int i=0;i<estimLength;i++){
1892                         if(estim[i] == ','){
1893                                 container.push_back(individual);
1894                                 individual = "";
1895                         }
1896                         else{
1897                                 individual += estim[i];
1898                         }
1899                 }
1900                 container.push_back(individual);
1901
1902
1903
1904
1905 //              string individual;
1906 //
1907 //              while (estim.find_first_of(',') != -1) {
1908 //                      individual = estim.substr(0,estim.find_first_of(','));
1909 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1910 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1911 //                              container.push_back(individual);
1912 //                      }
1913 //              }
1914 //              //get last one
1915 //              container.push_back(estim);
1916         }
1917         catch(exception& e) {
1918                 errorOut(e, "MothurOut", "splitAtComma");
1919                 exit(1);
1920         }
1921 }
1922 /***********************************************************************/
1923
1924 //This function splits up the various option parameters
1925 void MothurOut::splitAtComma(string& prefix, string& suffix){
1926         try {
1927                 prefix = suffix.substr(0,suffix.find_first_of(','));
1928                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1929                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1930                         string space = " ";
1931                         while(suffix.at(0) == ' ')
1932                                 suffix = suffix.substr(1, suffix.length());
1933                 }
1934
1935         }
1936         catch(exception& e) {
1937                 errorOut(e, "MothurOut", "splitAtComma");
1938                 exit(1);
1939         }
1940 }
1941 /***********************************************************************/
1942
1943 //This function separates the key value from the option value i.e. dist=96_...
1944 void MothurOut::splitAtEquals(string& key, string& value){
1945         try {
1946                 if(value.find_first_of('=') != -1){
1947                         key = value.substr(0,value.find_first_of('='));
1948                         if ((value.find_first_of('=')+1) <= value.length()) {
1949                                 value = value.substr(value.find_first_of('=')+1, value.length());
1950                         }
1951                 }else{
1952                         key = value;
1953                         value = 1;
1954                 }
1955         }
1956         catch(exception& e) {
1957                 errorOut(e, "MothurOut", "splitAtEquals");
1958                 exit(1);
1959         }
1960 }
1961
1962 /**************************************************************************************************/
1963
1964 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1965         try {
1966                 for (int i = 0; i < Groups.size(); i++) {
1967                         if (groupname == Groups[i]) { return true; }
1968                 }
1969                 return false;
1970         }
1971         catch(exception& e) {
1972                 errorOut(e, "MothurOut", "inUsersGroups");
1973                 exit(1);
1974         }
1975 }
1976 /**************************************************************************************************/
1977 //returns true if any of the strings in first vector are in second vector
1978 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1979         try {
1980
1981                 for (int i = 0; i < groupnames.size(); i++) {
1982                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1983                 }
1984                 return false;
1985         }
1986         catch(exception& e) {
1987                 errorOut(e, "MothurOut", "inUsersGroups");
1988                 exit(1);
1989         }
1990 }
1991 /***********************************************************************/
1992 //this function determines if the user has given us labels that are smaller than the given label.
1993 //if so then it returns true so that the calling function can run the previous valid distance.
1994 //it's a "smart" distance function.  It also checks for invalid labels.
1995 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1996         try {
1997
1998                 set<string>::iterator it;
1999                 vector<float> orderFloat;
2000                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
2001                 map<string, float>::iterator it2;
2002                 float labelFloat;
2003                 bool smaller = false;
2004
2005                 //unique is the smallest line
2006                 if (label == "unique") {  return false;  }
2007                 else {
2008                         if (convertTestFloat(label, labelFloat)) {
2009                                 convert(label, labelFloat);
2010                         }else { //cant convert
2011                                 return false;
2012                         }
2013                 }
2014
2015                 //go through users set and make them floats
2016                 for(it = userLabels.begin(); it != userLabels.end();) {
2017
2018                         float temp;
2019                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
2020                                 convert(*it, temp);
2021                                 orderFloat.push_back(temp);
2022                                 userMap[*it] = temp;
2023                                 it++;
2024                         }else if (*it == "unique") {
2025                                 orderFloat.push_back(-1.0);
2026                                 userMap["unique"] = -1.0;
2027                                 it++;
2028                         }else {
2029                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
2030                                 userLabels.erase(it++);
2031                         }
2032                 }
2033
2034                 //sort order
2035                 sort(orderFloat.begin(), orderFloat.end());
2036
2037                 /*************************************************/
2038                 //is this label bigger than any of the users labels
2039                 /*************************************************/
2040
2041                 //loop through order until you find a label greater than label
2042                 for (int i = 0; i < orderFloat.size(); i++) {
2043                         if (orderFloat[i] < labelFloat) {
2044                                 smaller = true;
2045                                 if (orderFloat[i] == -1) {
2046                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
2047                                         userLabels.erase("unique");
2048                                 }
2049                                 else {
2050                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
2051                                         string s = "";
2052                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
2053                                                 if (it2->second == orderFloat[i]) {
2054                                                         s = it2->first;
2055                                                         //remove small labels
2056                                                         userLabels.erase(s);
2057                                                         break;
2058                                                 }
2059                                         }
2060                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
2061                                 }
2062                         //since they are sorted once you find a bigger one stop looking
2063                         }else { break; }
2064                 }
2065
2066                 return smaller;
2067
2068         }
2069         catch(exception& e) {
2070                 errorOut(e, "MothurOut", "anyLabelsToProcess");
2071                 exit(1);
2072         }
2073 }
2074
2075 /**************************************************************************************************/
2076 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
2077         try {
2078
2079                 bool good = true;
2080
2081                 string line = getline(file);
2082
2083                 //before we added this check
2084                 if (line[0] != '#') {  good = false;  }
2085                 else {
2086                         //rip off #
2087                         line = line.substr(1);
2088
2089                         vector<string> versionVector;
2090                         splitAtChar(version, versionVector, '.');
2091
2092                         //check file version
2093                         vector<string> linesVector;
2094                         splitAtChar(line, linesVector, '.');
2095
2096                         if (versionVector.size() != linesVector.size()) { good = false; }
2097                         else {
2098                                 for (int j = 0; j < versionVector.size(); j++) {
2099                                         int num1, num2;
2100                                         convert(versionVector[j], num1);
2101                                         convert(linesVector[j], num2);
2102
2103                                         //if mothurs version is newer than this files version, then we want to remake it
2104                                         if (num1 > num2) {  good = false; break;  }
2105                                 }
2106                         }
2107
2108                 }
2109
2110                 if (!good) {  file.close();  }
2111                 else { file.seekg(0);  }
2112
2113                 return good;
2114         }
2115         catch(exception& e) {
2116                 errorOut(e, "MothurOut", "checkReleaseVersion");
2117                 exit(1);
2118         }
2119 }
2120 /**************************************************************************************************/
2121 bool MothurOut::isContainingOnlyDigits(string input) {
2122         try{
2123
2124                 //are you a digit in ascii code
2125                 for (int i = 0;i < input.length(); i++){
2126                         if( input[i]>47 && input[i]<58){}
2127                         else { return false; }
2128                 }
2129
2130                 return true;
2131         }
2132         catch(exception& e) {
2133                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
2134                 exit(1);
2135         }
2136 }
2137 /**************************************************************************************************/
2138 int MothurOut::removeConfidences(string& tax) {
2139         try {
2140
2141                 string taxon;
2142                 string newTax = "";
2143
2144                 while (tax.find_first_of(';') != -1) {
2145
2146                         if (control_pressed) { return 0; }
2147
2148                         //get taxon
2149                         taxon = tax.substr(0,tax.find_first_of(';'));
2150
2151                         int pos = taxon.find_last_of('(');
2152                         if (pos != -1) {
2153                                 //is it a number?
2154                                 int pos2 = taxon.find_last_of(')');
2155                                 if (pos2 != -1) {
2156                                         string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
2157                                         if (isNumeric1(confidenceScore)) {
2158                                                 taxon = taxon.substr(0, pos); //rip off confidence
2159                                         }
2160                                 }
2161                         }
2162                         taxon += ";";
2163
2164                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
2165                         newTax += taxon;
2166                 }
2167
2168                 tax = newTax;
2169
2170                 return 0;
2171         }
2172         catch(exception& e) {
2173                 errorOut(e, "MothurOut", "removeConfidences");
2174                 exit(1);
2175         }
2176 }
2177 /**************************************************************************************************/
2178
2179
2180
2181
2182