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 MothurOut* MothurOut::getInstance() {
  14         if( _uniqueInstance == 0) {
  15                 _uniqueInstance = new MothurOut();
  16         }
  17         return _uniqueInstance;
  18 }
  19 /*********************************************************************************************/
  20 void MothurOut::setFileName(string filename)  {
  21         try {
  22                 logFileName = filename;
  23
  24                 #ifdef USE_MPI
  25                         int pid;
  26                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  27
  28                         if (pid == 0) { //only one process should output to screen
  29                 #endif
  30
  31                 openOutputFile(filename, out);
  32
  33                 #ifdef USE_MPI
  34                         }
  35                 #endif
  36         }
  37         catch(exception& e) {
  38                 errorOut(e, "MothurOut", "setFileName");
  39                 exit(1);
  40         }
  41 }
  42 /*********************************************************************************************/
  43 void MothurOut::setDefaultPath(string pathname)  {
  44         try {
  45
  46                 //add / to name if needed
  47                 string lastChar = pathname.substr(pathname.length()-1);
  48                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  49                         if (lastChar != "/") { pathname += "/"; }
  50                 #else
  51                         if (lastChar != "\\") { pathname += "\\"; }
  52                 #endif
  53
  54                 defaultPath = pathname;
  55
  56         }
  57         catch(exception& e) {
  58                 errorOut(e, "MothurOut", "setDefaultPath");
  59                 exit(1);
  60         }
  61 }
  62 /*********************************************************************************************/
  63 void MothurOut::setOutputDir(string pathname)  {
  64         try {
  65                 outputDir = pathname;
  66         }
  67         catch(exception& e) {
  68                 errorOut(e, "MothurOut", "setOutputDir");
  69                 exit(1);
  70         }
  71 }
  72 /*********************************************************************************************/
  73 void MothurOut::closeLog()  {
  74         try {
  75
  76                 #ifdef USE_MPI
  77                         int pid;
  78                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  79
  80                         if (pid == 0) { //only one process should output to screen
  81                 #endif
  82
  83                 out.close();
  84
  85                 #ifdef USE_MPI
  86                         }
  87                 #endif
  88         }
  89         catch(exception& e) {
  90                 errorOut(e, "MothurOut", "closeLog");
  91                 exit(1);
  92         }
  93 }
  94
  95 /*********************************************************************************************/
  96 MothurOut::~MothurOut() {
  97         try {
  98                 _uniqueInstance = 0;
  99
 100         }
 101         catch(exception& e) {
 102                 errorOut(e, "MothurOut", "MothurOut");
 103                 exit(1);
 104         }
 105 }
 106 /*********************************************************************************************/
 107 void MothurOut::mothurOut(string output) {
 108         try {
 109
 110                 #ifdef USE_MPI
 111                         int pid;
 112                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 113
 114                         if (pid == 0) { //only one process should output to screen
 115                 #endif
 116
 117                 cout << output;
 118                 out << output;
 119
 120                 #ifdef USE_MPI
 121                         }
 122                 #endif
 123         }
 124         catch(exception& e) {
 125                 errorOut(e, "MothurOut", "MothurOut");
 126                 exit(1);
 127         }
 128 }
 129 /*********************************************************************************************/
 130 void MothurOut::mothurOutEndLine() {
 131         try {
 132                 #ifdef USE_MPI
 133                         int pid;
 134                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 135
 136                         if (pid == 0) { //only one process should output to screen
 137                 #endif
 138
 139                 cout << endl;
 140                 out << endl;
 141
 142                 #ifdef USE_MPI
 143                         }
 144                 #endif
 145         }
 146         catch(exception& e) {
 147                 errorOut(e, "MothurOut", "MothurOutEndLine");
 148                 exit(1);
 149         }
 150 }
 151 /*********************************************************************************************/
 152 void MothurOut::mothurOutJustToLog(string output) {
 153         try {
 154                 #ifdef USE_MPI
 155                         int pid;
 156                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 157
 158                         if (pid == 0) { //only one process should output to screen
 159                 #endif
 160
 161                 out << output;
 162
 163                 #ifdef USE_MPI
 164                         }
 165                 #endif
 166         }
 167         catch(exception& e) {
 168                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 169                 exit(1);
 170         }
 171 }
 172 /*********************************************************************************************/
 173 void MothurOut::errorOut(exception& e, string object, string function) {
 174         //double vm, rss;
 175         //mem_usage(vm, rss);
 176
 177         mothurOut("[ERROR]: ");
 178         mothurOut(toString(e.what()));
 179         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.");
 180         mothurOutEndLine();
 181 }
 182 /*********************************************************************************************/
 183 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 184 // process_mem_usage(double &, double &) - takes two doubles by reference,
 185 // attempts to read the system-dependent data for a process' virtual memory
 186 // size and resident set size, and return the results in KB.
 187 //
 188 // On failure, returns 0.0, 0.0
 189 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 190   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 191
 192            vm_usage     = 0.0;
 193            resident_set = 0.0;
 194
 195            // 'file' stat seems to give the most reliable results
 196            //
 197            ifstream stat_stream("/proc/self/stat",ios_base::in);
 198
 199            // dummy vars for leading entries in stat that we don't care about
 200            //
 201            string pid, comm, state, ppid, pgrp, session, tty_nr;
 202            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 203            string utime, stime, cutime, cstime, priority, nice;
 204            string O, itrealvalue, starttime;
 205
 206            // the two fields we want
 207            //
 208            unsigned long vsize;
 209            long rss;
 210
 211            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 212                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 213                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 214                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 215
 216            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 217            vm_usage     = vsize / 1024.0;
 218            resident_set = rss * page_size_kb;
 219
 220            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 221                 return 0;
 222
 223         #else
 224 /*              //windows memory usage
 225                 // Get the list of process identifiers.
 226                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 227
 228                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 229
 230                 // Calculate how many process identifiers were returned.
 231                 cProcesses = cbNeeded / sizeof(DWORD);
 232
 233                 // Print the memory usage for each process
 234                 for (int i = 0; i < cProcesses; i++ ) {
 235                         DWORD processID = aProcesses[i];
 236
 237                         PROCESS_MEMORY_COUNTERS pmc;
 238
 239                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 240
 241                         // Print the process identifier.
 242                         printf( "\nProcess ID: %u\n", processID);
 243
 244                         if (NULL != hProcess) {
 245
 246                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 247                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 248                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 249                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 250                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 251                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 252                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 253                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 254                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 255                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 256                                 }
 257                                 CloseHandle(hProcess);
 258                         }
 259                 }
 260 */
 261                         return 0;
 262
 263         #endif
 264 }
 265
 266
 267 /***********************************************************************/
 268 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 269         try {
 270                 fileName = getFullPathName(fileName);
 271
 272                 fileHandle.open(fileName.c_str(), ios::app);
 273                 if(!fileHandle) {
 274                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 275                         return 1;
 276                 }
 277                 else {
 278                         return 0;
 279                 }
 280         }
 281         catch(exception& e) {
 282                 errorOut(e, "MothurOut", "openOutputFileAppend");
 283                 exit(1);
 284         }
 285 }
 286 /***********************************************************************/
 287 void MothurOut::gobble(istream& f){
 288         try {
 289
 290                 char d;
 291                 while(isspace(d=f.get()))               { ;}
 292                 f.putback(d);
 293         }
 294         catch(exception& e) {
 295                 errorOut(e, "MothurOut", "gobble");
 296                 exit(1);
 297         }
 298 }
 299 /***********************************************************************/
 300 void MothurOut::gobble(istringstream& f){
 301         try {
 302                 char d;
 303                 while(isspace(d=f.get()))               {;}
 304                 f.putback(d);
 305         }
 306         catch(exception& e) {
 307                 errorOut(e, "MothurOut", "gobble");
 308                 exit(1);
 309         }
 310 }
 311
 312 /***********************************************************************/
 313
 314 string MothurOut::getline(istringstream& fileHandle) {
 315         try {
 316
 317                 string line = "";
 318
 319                 while (!fileHandle.eof())       {
 320                         //get next character
 321                         char c = fileHandle.get();
 322
 323                         //are you at the end of the line
 324                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 325                         else {          line += c;              }
 326                 }
 327
 328                 return line;
 329
 330         }
 331         catch(exception& e) {
 332                 errorOut(e, "MothurOut", "getline");
 333                 exit(1);
 334         }
 335 }
 336 /***********************************************************************/
 337
 338 string MothurOut::getline(ifstream& fileHandle) {
 339         try {
 340
 341                 string line = "";
 342
 343                 while (!fileHandle.eof())       {
 344                         //get next character
 345                         char c = fileHandle.get();
 346
 347                         //are you at the end of the line
 348                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 349                         else {          line += c;              }
 350                 }
 351
 352                 return line;
 353
 354         }
 355         catch(exception& e) {
 356                 errorOut(e, "MothurOut", "getline");
 357                 exit(1);
 358         }
 359 }
 360 /***********************************************************************/
 361
 362 #ifdef USE_COMPRESSION
 363 inline bool endsWith(string s, const char * suffix){
 364   size_t suffixLength = strlen(suffix);
 365   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 366 }
 367 #endif
 368
 369 string MothurOut::getRootName(string longName){
 370         try {
 371
 372                 string rootName = longName;
 373
 374 #ifdef USE_COMPRESSION
 375     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 376       int pos = rootName.find_last_of('.');
 377       rootName = rootName.substr(0, pos);
 378       cerr << "shortening " << longName << " to " << rootName << "\n";
 379     }
 380 #endif
 381
 382                 if(rootName.find_last_of(".") != rootName.npos){
 383                         int pos = rootName.find_last_of('.')+1;
 384                         rootName = rootName.substr(0, pos);
 385                 }
 386
 387                 return rootName;
 388         }
 389         catch(exception& e) {
 390                 errorOut(e, "MothurOut", "getRootName");
 391                 exit(1);
 392         }
 393 }
 394 /***********************************************************************/
 395
 396 string MothurOut::getSimpleName(string longName){
 397         try {
 398                 string simpleName = longName;
 399
 400                 size_t found;
 401                 found=longName.find_last_of("/\\");
 402
 403                 if(found != longName.npos){
 404                         simpleName = longName.substr(found+1);
 405                 }
 406
 407                 return simpleName;
 408         }
 409         catch(exception& e) {
 410                 errorOut(e, "MothurOut", "getSimpleName");
 411                 exit(1);
 412         }
 413 }
 414
 415 /***********************************************************************/
 416
 417 string MothurOut::getPathName(string longName){
 418         try {
 419                 string rootPathName = longName;
 420
 421                 if(longName.find_last_of("/\\") != longName.npos){
 422                         int pos = longName.find_last_of("/\\")+1;
 423                         rootPathName = longName.substr(0, pos);
 424                 }
 425
 426                 return rootPathName;
 427         }
 428         catch(exception& e) {
 429                 errorOut(e, "MothurOut", "getPathName");
 430                 exit(1);
 431         }
 432
 433 }
 434 /***********************************************************************/
 435
 436 string MothurOut::hasPath(string longName){
 437         try {
 438                 string path = "";
 439
 440                 size_t found;
 441                 found=longName.find_last_of("~/\\");
 442
 443                 if(found != longName.npos){
 444                         path = longName.substr(0, found+1);
 445                 }
 446
 447                 return path;
 448         }
 449         catch(exception& e) {
 450                 errorOut(e, "MothurOut", "hasPath");
 451                 exit(1);
 452         }
 453 }
 454
 455 /***********************************************************************/
 456
 457 string MothurOut::getExtension(string longName){
 458         try {
 459                 string extension = longName;
 460
 461                 if(longName.find_last_of('.') != longName.npos){
 462                         int pos = longName.find_last_of('.');
 463                         extension = longName.substr(pos, longName.length());
 464                 }
 465
 466                 return extension;
 467         }
 468         catch(exception& e) {
 469                 errorOut(e, "MothurOut", "getExtension");
 470                 exit(1);
 471         }
 472 }
 473 /***********************************************************************/
 474 bool MothurOut::isBlank(string fileName){
 475         try {
 476
 477                 fileName = getFullPathName(fileName);
 478
 479                 ifstream fileHandle;
 480                 fileHandle.open(fileName.c_str());
 481                 if(!fileHandle) {
 482                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 483                         return false;
 484                 }else {
 485                         //check for blank file
 486                         gobble(fileHandle);
 487                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 488                 }
 489                 return false;
 490         }
 491         catch(exception& e) {
 492                 errorOut(e, "MothurOut", "isBlank");
 493                 exit(1);
 494         }
 495 }
 496 /***********************************************************************/
 497
 498 string MothurOut::getFullPathName(string fileName){
 499         try{
 500
 501         string path = hasPath(fileName);
 502         string newFileName;
 503         int pos;
 504
 505         if (path == "") { return fileName; } //its a simple name
 506         else { //we need to complete the pathname
 507                 // ex. ../../../filename
 508                 // cwd = /user/work/desktop
 509
 510                 string cwd;
 511                 //get current working directory
 512                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 513
 514                         if (path.find("~") != -1) { //go to home directory
 515                                 string homeDir;
 516
 517                                 char *homepath = NULL;
 518                                 homepath = getenv ("HOME");
 519                                 if ( homepath != NULL) { homeDir = homepath; }
 520                                 else { homeDir = "";  }
 521
 522                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 523                                 return newFileName;
 524                         }else { //find path
 525                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 526                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 527
 528                                 //char* cwdpath = new char[1024];
 529                                 //size_t size;
 530                                 //cwdpath=getcwd(cwdpath,size);
 531                                 //cwd = cwdpath;
 532
 533                                 char *cwdpath = NULL;
 534                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 535                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 536                                 else { cwd = "";  }
 537
 538
 539                                 //rip off first '/'
 540                                 string simpleCWD;
 541                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 542
 543                                 //break apart the current working directory
 544                                 vector<string> dirs;
 545                                 while (simpleCWD.find_first_of('/') != string::npos) {
 546                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 547                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 548                                         dirs.push_back(dir);
 549                                 }
 550                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 551                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 552
 553
 554                                 int index = dirs.size()-1;
 555
 556                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 557                                         if (pos == 0) { break;  //you are at the end
 558                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 559                                                 path = path.substr(0, pos-1);
 560                                                 index--;
 561                                                 if (index == 0) {  break; }
 562                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 563                                                 path = path.substr(0, pos);
 564                                         }else if (pos == 1) { break;  //you are at the end
 565                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 566                                 }
 567
 568                                 for (int i = index; i >= 0; i--) {
 569                                         newFileName = dirs[i] +  "/" + newFileName;
 570                                 }
 571
 572                                 newFileName =  "/" +  newFileName;
 573                                 return newFileName;
 574                         }
 575                 #else
 576                         if (path.find("~") != string::npos) { //go to home directory
 577                                 string homeDir = getenv ("HOMEPATH");
 578                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 579                                 return newFileName;
 580                         }else { //find path
 581                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 582                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 583
 584                                 char *cwdpath = NULL;
 585                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 586                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 587                                 else { cwd = "";  }
 588
 589                                 //break apart the current working directory
 590                                 vector<string> dirs;
 591                                 while (cwd.find_first_of('\\') != -1) {
 592                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 593                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 594                                         dirs.push_back(dir);
 595
 596                                 }
 597                                 //get last one
 598                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 599
 600                                 int index = dirs.size()-1;
 601
 602                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 603                                         if (pos == 0) { break;  //you are at the end
 604                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 605                                                 path = path.substr(0, pos-1);
 606                                                 index--;
 607                                                 if (index == 0) {  break; }
 608                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 609                                                 path = path.substr(0, pos);
 610                                         }else if (pos == 1) { break;  //you are at the end
 611                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 612                                 }
 613
 614                                 for (int i = index; i >= 0; i--) {
 615                                         newFileName = dirs[i] +  "\\" + newFileName;
 616                                 }
 617
 618                                 return newFileName;
 619                         }
 620
 621                 #endif
 622         }
 623         }
 624         catch(exception& e) {
 625                 errorOut(e, "MothurOut", "getFullPathName");
 626                 exit(1);
 627         }
 628 }
 629 /***********************************************************************/
 630
 631 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 632         try {
 633                         //get full path name
 634                         string completeFileName = getFullPathName(fileName);
 635
 636 #ifdef USE_COMPRESSION
 637       // check for gzipped or bzipped file
 638       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 639         string tempName = string(tmpnam(0));
 640         mkfifo(tempName.c_str(), 0666);
 641         int fork_result = fork();
 642         if (fork_result < 0) {
 643           cerr << "Error forking.\n";
 644           exit(1);
 645         } else if (fork_result == 0) {
 646           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 647           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 648           system(command.c_str());
 649           cerr << "Done decompressing " << completeFileName << "\n";
 650           remove(tempName.c_str());
 651           exit(EXIT_SUCCESS);
 652         } else {
 653           cerr << "waiting on child process " << fork_result << "\n";
 654           completeFileName = tempName;
 655         }
 656       }
 657 #endif
 658
 659                         fileHandle.open(completeFileName.c_str());
 660                         if(!fileHandle) {
 661                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 662                                 return 1;
 663                         }else {
 664                                 //check for blank file
 665                                 gobble(fileHandle);
 666                                 return 0;
 667                         }
 668         }
 669         catch(exception& e) {
 670                 errorOut(e, "MothurOut", "openInputFile - no Error");
 671                 exit(1);
 672         }
 673 }
 674 /***********************************************************************/
 675
 676 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 677         try {
 678
 679                 //get full path name
 680                 string completeFileName = getFullPathName(fileName);
 681
 682 #ifdef USE_COMPRESSION
 683   // check for gzipped or bzipped file
 684   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 685     string tempName = string(tmpnam(0));
 686     mkfifo(tempName.c_str(), 0666);
 687     int fork_result = fork();
 688     if (fork_result < 0) {
 689       cerr << "Error forking.\n";
 690       exit(1);
 691     } else if (fork_result == 0) {
 692       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 693       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 694       system(command.c_str());
 695       cerr << "Done decompressing " << completeFileName << "\n";
 696       remove(tempName.c_str());
 697       exit(EXIT_SUCCESS);
 698     } else {
 699       cerr << "waiting on child process " << fork_result << "\n";
 700       completeFileName = tempName;
 701     }
 702   }
 703 #endif
 704
 705
 706                 fileHandle.open(completeFileName.c_str());
 707                 if(!fileHandle) {
 708                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 709                         return 1;
 710                 }
 711                 else {
 712                         //check for blank file
 713                         gobble(fileHandle);
 714                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 715
 716                         return 0;
 717                 }
 718         }
 719         catch(exception& e) {
 720                 errorOut(e, "MothurOut", "openInputFile");
 721                 exit(1);
 722         }
 723 }
 724 /***********************************************************************/
 725
 726 int MothurOut::renameFile(string oldName, string newName){
 727         try {
 728                 ifstream inTest;
 729                 int exist = openInputFile(newName, inTest, "");
 730
 731         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 732                 if (exist == 0) { //you could open it so you want to delete it
 733                         inTest.close();
 734                         string command = "rm " + newName;
 735                         system(command.c_str());
 736                 }
 737
 738                 string command = "mv " + oldName + " " + newName;
 739                 system(command.c_str());
 740         #else
 741                 remove(newName.c_str());
 742                 int renameOk = rename(oldName.c_str(), newName.c_str());
 743         #endif
 744                 return 0;
 745
 746         }
 747         catch(exception& e) {
 748                 errorOut(e, "MothurOut", "renameFile");
 749                 exit(1);
 750         }
 751 }
 752
 753 /***********************************************************************/
 754
 755 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 756         try {
 757
 758                 string completeFileName = getFullPathName(fileName);
 759
 760 #ifdef USE_COMPRESSION
 761     // check for gzipped file
 762     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 763       string tempName = string(tmpnam(0));
 764       mkfifo(tempName.c_str(), 0666);
 765       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 766       int fork_result = fork();
 767       if (fork_result < 0) {
 768         cerr << "Error forking.\n";
 769         exit(1);
 770       } else if (fork_result == 0) {
 771         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 772         system(command.c_str());
 773         exit(0);
 774       } else {
 775         completeFileName = tempName;
 776       }
 777     }
 778 #endif
 779
 780                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 781                 if(!fileHandle) {
 782                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 783                         return 1;
 784                 }
 785                 else {
 786                         return 0;
 787                 }
 788         }
 789         catch(exception& e) {
 790                 errorOut(e, "MothurOut", "openOutputFile");
 791                 exit(1);
 792         }
 793
 794 }
 795
 796 /**************************************************************************************************/
 797 void MothurOut::appendFiles(string temp, string filename) {
 798         try{
 799                 ofstream output;
 800                 ifstream input;
 801
 802                 //open output file in append mode
 803                 openOutputFileAppend(filename, output);
 804                 int ableToOpen = openInputFile(temp, input, "no error");
 805                 //int ableToOpen = openInputFile(temp, input);
 806
 807                 if (ableToOpen == 0) { //you opened it
 808                         while(char c = input.get()){
 809                                 if(input.eof())         {       break;                  }
 810                                 else                            {       output << c;    }
 811                         }
 812                         input.close();
 813                 }
 814
 815                 output.close();
 816         }
 817         catch(exception& e) {
 818                 errorOut(e, "MothurOut", "appendFiles");
 819                 exit(1);
 820         }
 821 }
 822
 823 /**************************************************************************************************/
 824 string MothurOut::sortFile(string distFile, string outputDir){
 825         try {
 826
 827                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 828                 string outfile = getRootName(distFile) + "sorted.dist";
 829
 830
 831                 //if you can, use the unix sort since its been optimized for years
 832                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 833                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 834                         system(command.c_str());
 835                 #else //you are stuck with my best attempt...
 836                         //windows sort does not have a way to specify a column, only a character in the line
 837                         //since we cannot assume that the distance will always be at the the same character location on each line
 838                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 839
 840                         //read in file line by file and put distance first
 841                         string tempDistFile = distFile + ".temp";
 842                         ifstream input;
 843                         ofstream output;
 844                         openInputFile(distFile, input);
 845                         openOutputFile(tempDistFile, output);
 846
 847                         string firstName, secondName;
 848                         float dist;
 849                         while (input) {
 850                                 input >> firstName >> secondName >> dist;
 851                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 852                                 gobble(input);
 853                         }
 854                         input.close();
 855                         output.close();
 856
 857
 858                         //sort using windows sort
 859                         string tempOutfile = outfile + ".temp";
 860                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 861                         system(command.c_str());
 862
 863                         //read in sorted file and put distance at end again
 864                         ifstream input2;
 865                         openInputFile(tempOutfile, input2);
 866                         openOutputFile(outfile, output);
 867
 868                         while (input2) {
 869                                 input2 >> dist >> firstName >> secondName;
 870                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 871                                 gobble(input2);
 872                         }
 873                         input2.close();
 874                         output.close();
 875
 876                         //remove temp files
 877                         remove(tempDistFile.c_str());
 878                         remove(tempOutfile.c_str());
 879                 #endif
 880
 881                 return outfile;
 882         }
 883         catch(exception& e) {
 884                 errorOut(e, "MothurOut", "sortFile");
 885                 exit(1);
 886         }
 887 }
 888 /**************************************************************************************************/
 889 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
 890         try {
 891                         vector<unsigned long int> positions;
 892                         ifstream inFASTA;
 893                         openInputFile(filename, inFASTA);
 894
 895                         string input;
 896                         while(!inFASTA.eof()){
 897                                 input = getline(inFASTA);
 898                                 if (input.length() != 0) {
 899                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 900                                 }
 901                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
 902                         }
 903                         inFASTA.close();
 904
 905                         num = positions.size();
 906
 907                         /*FILE * pFile;
 908                         long size;
 909
 910                         //get num bytes in file
 911                         pFile = fopen (filename.c_str(),"rb");
 912                         if (pFile==NULL) perror ("Error opening file");
 913                         else{
 914                                 fseek (pFile, 0, SEEK_END);
 915                                 size=ftell (pFile);
 916                                 fclose (pFile);
 917                         }*/
 918
 919                         unsigned long int size = positions[(positions.size()-1)];
 920                         ifstream in;
 921                         openInputFile(filename, in);
 922
 923                         in.seekg(size);
 924
 925                         while(char c = in.get()){
 926                                 if(in.eof())            {       break;  }
 927                                 else                            {       size++; }
 928                         }
 929                         in.close();
 930
 931                         positions.push_back(size);
 932
 933                         return positions;
 934         }
 935         catch(exception& e) {
 936                 errorOut(e, "MothurOut", "setFilePosFasta");
 937                 exit(1);
 938         }
 939 }
 940 /**************************************************************************************************/
 941 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
 942         try {
 943                         filename = getFullPathName(filename);
 944
 945                         vector<unsigned long int> positions;
 946                         ifstream in;
 947                         openInputFile(filename, in);
 948
 949                         string input;
 950                         while(!in.eof()){
 951                                 unsigned long int lastpos = in.tellg();
 952                                 input = getline(in);
 953                                 if (input.length() != 0) {
 954                                         unsigned long int pos = in.tellg();
 955                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
 956                                         else {  positions.push_back(lastpos);  }
 957                                 }
 958                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
 959                         }
 960                         in.close();
 961
 962                         num = positions.size();
 963
 964                         FILE * pFile;
 965                         unsigned long int size;
 966
 967                         //get num bytes in file
 968                         pFile = fopen (filename.c_str(),"rb");
 969                         if (pFile==NULL) perror ("Error opening file");
 970                         else{
 971                                 fseek (pFile, 0, SEEK_END);
 972                                 size=ftell (pFile);
 973                                 fclose (pFile);
 974                         }
 975
 976                         positions.push_back(size);
 977
 978                         return positions;
 979         }
 980         catch(exception& e) {
 981                 errorOut(e, "MothurOut", "setFilePosEachLine");
 982                 exit(1);
 983         }
 984 }
 985 /**************************************************************************************************/
 986
 987 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 988         try{
 989
 990                 vector<unsigned long int> filePos;
 991                 filePos.push_back(0);
 992
 993                 FILE * pFile;
 994                 unsigned long int size;
 995
 996                 filename = getFullPathName(filename);
 997
 998                 //get num bytes in file
 999                 pFile = fopen (filename.c_str(),"rb");
1000                 if (pFile==NULL) perror ("Error opening file");
1001                 else{
1002                         fseek (pFile, 0, SEEK_END);
1003                         size=ftell (pFile);
1004                         fclose (pFile);
1005                 }
1006
1007                 //estimate file breaks
1008                 unsigned long int chunkSize = 0;
1009                 chunkSize = size / proc;
1010
1011                 //file to small to divide by processors
1012                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1013
1014                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1015                 for (int i = 0; i < proc; i++) {
1016                         unsigned long int spot = (i+1) * chunkSize;
1017
1018                         ifstream in;
1019                         openInputFile(filename, in);
1020                         in.seekg(spot);
1021
1022                         //look for next '>'
1023                         unsigned long int newSpot = spot;
1024                         while (!in.eof()) {
1025                            char c = in.get();
1026                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1027                         }
1028
1029                         //there was not another sequence before the end of the file
1030                         unsigned long int sanityPos = in.tellg();
1031
1032                         if (sanityPos == -1) {  break;  }
1033                         else {  filePos.push_back(newSpot);  }
1034
1035                         in.close();
1036                 }
1037
1038                 //save end pos
1039                 filePos.push_back(size);
1040
1041                 //sanity check filePos
1042                 for (int i = 0; i < (filePos.size()-1); i++) {
1043                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1044                 }
1045
1046                 proc = (filePos.size() - 1);
1047
1048                 return filePos;
1049         }
1050         catch(exception& e) {
1051                 errorOut(e, "MothurOut", "divideFile");
1052                 exit(1);
1053         }
1054 }
1055
1056 /***********************************************************************/
1057
1058 bool MothurOut::isTrue(string f){
1059         try {
1060
1061                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1062
1063                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1064                 else {  return false;  }
1065         }
1066         catch(exception& e) {
1067                 errorOut(e, "MothurOut", "isTrue");
1068                 exit(1);
1069         }
1070 }
1071
1072 /***********************************************************************/
1073
1074 float MothurOut::roundDist(float dist, int precision){
1075         try {
1076                 return int(dist * precision + 0.5)/float(precision);
1077         }
1078         catch(exception& e) {
1079                 errorOut(e, "MothurOut", "roundDist");
1080                 exit(1);
1081         }
1082 }
1083 /***********************************************************************/
1084
1085 float MothurOut::ceilDist(float dist, int precision){
1086         try {
1087                 return int(ceil(dist * precision))/float(precision);
1088         }
1089         catch(exception& e) {
1090                 errorOut(e, "MothurOut", "ceilDist");
1091                 exit(1);
1092         }
1093 }
1094
1095 /***********************************************************************/
1096
1097 int MothurOut::getNumNames(string names){
1098         try {
1099                 int count = 0;
1100
1101                 if(names != ""){
1102                         count = 1;
1103                         for(int i=0;i<names.size();i++){
1104                                 if(names[i] == ','){
1105                                         count++;
1106                                 }
1107                         }
1108                 }
1109
1110                 return count;
1111         }
1112         catch(exception& e) {
1113                 errorOut(e, "MothurOut", "getNumNames");
1114                 exit(1);
1115         }
1116 }
1117
1118 /**************************************************************************************************/
1119
1120 vector<vector<double> > MothurOut::binomial(int maxOrder){
1121         try {
1122         vector<vector<double> > binomial(maxOrder+1);
1123
1124     for(int i=0;i<=maxOrder;i++){
1125                 binomial[i].resize(maxOrder+1);
1126                 binomial[i][0]=1;
1127                 binomial[0][i]=0;
1128     }
1129     binomial[0][0]=1;
1130
1131     binomial[1][0]=1;
1132     binomial[1][1]=1;
1133
1134     for(int i=2;i<=maxOrder;i++){
1135                 binomial[1][i]=0;
1136     }
1137
1138     for(int i=2;i<=maxOrder;i++){
1139                 for(int j=1;j<=maxOrder;j++){
1140                         if(i==j){       binomial[i][j]=1;                                                                       }
1141                         if(j>i) {       binomial[i][j]=0;                                                                       }
1142                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1143                 }
1144     }
1145
1146         return binomial;
1147
1148         }
1149         catch(exception& e) {
1150                 errorOut(e, "MothurOut", "binomial");
1151                 exit(1);
1152         }
1153 }
1154
1155 /***********************************************************************/
1156
1157 int MothurOut::factorial(int num){
1158         try {
1159                 int total = 1;
1160
1161                 for (int i = 1; i <= num; i++) {
1162                         total *= i;
1163                 }
1164
1165                 return total;
1166         }
1167         catch(exception& e) {
1168                 errorOut(e, "MothurOut", "factorial");
1169                 exit(1);
1170         }
1171 }
1172 /***********************************************************************/
1173
1174 int MothurOut::getNumSeqs(ifstream& file){
1175         try {
1176                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1177                 file.seekg(0);
1178                 return numSeqs;
1179         }
1180         catch(exception& e) {
1181                 errorOut(e, "MothurOut", "getNumSeqs");
1182                 exit(1);
1183         }
1184 }
1185 /***********************************************************************/
1186 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1187         try {
1188                 string input;
1189                 numSeqs = 0;
1190                 while(!file.eof()){
1191                         input = getline(file);
1192                         if (input.length() != 0) {
1193                                 if(input[0] == '>'){ numSeqs++; }
1194                         }
1195                 }
1196         }
1197         catch(exception& e) {
1198                 errorOut(e, "MothurOut", "getNumSeqs");
1199                 exit(1);
1200         }
1201 }
1202 /***********************************************************************/
1203
1204 //This function parses the estimator options and puts them in a vector
1205 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1206         try {
1207                 string individual = "";
1208                 int estimLength = estim.size();
1209                 for(int i=0;i<estimLength;i++){
1210                         if(estim[i] == symbol){
1211                                 container.push_back(individual);
1212                                 individual = "";
1213                         }
1214                         else{
1215                                 individual += estim[i];
1216                         }
1217                 }
1218                 container.push_back(individual);
1219
1220                 /*
1221
1222                 while (estim.find_first_of(symbol) != -1) {
1223                         individual = estim.substr(0,estim.find_first_of(symbol));
1224                         if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1225                                 estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
1226                                 container.push_back(individual);
1227                         }
1228                 }
1229                 //get last one
1230                 container.push_back(estim); */
1231         }
1232         catch(exception& e) {
1233                 errorOut(e, "MothurOut", "splitAtChar");
1234                 exit(1);
1235         }
1236 }
1237
1238 /***********************************************************************/
1239
1240 //This function parses the estimator options and puts them in a vector
1241 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1242         try {
1243                 string individual = "";
1244                 int estimLength = estim.size();
1245                 for(int i=0;i<estimLength;i++){
1246                         if(estim[i] == '-'){
1247                                 container.push_back(individual);
1248                                 individual = "";
1249                         }
1250                         else{
1251                                 individual += estim[i];
1252                         }
1253                 }
1254                 container.push_back(individual);
1255
1256
1257         /*      string individual;
1258
1259                 while (estim.find_first_of('-') != -1) {
1260                         individual = estim.substr(0,estim.find_first_of('-'));
1261                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1262                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1263                                 container.push_back(individual);
1264                         }
1265                 }
1266                 //get last one
1267                 container.push_back(estim); */
1268         }
1269         catch(exception& e) {
1270                 errorOut(e, "MothurOut", "splitAtDash");
1271                 exit(1);
1272         }
1273 }
1274
1275 /***********************************************************************/
1276 //This function parses the label options and puts them in a set
1277 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1278         try {
1279                 string individual = "";
1280                 int estimLength = estim.size();
1281                 for(int i=0;i<estimLength;i++){
1282                         if(estim[i] == '-'){
1283                                 container.insert(individual);
1284                                 individual = "";
1285                         }
1286                         else{
1287                                 individual += estim[i];
1288                         }
1289                 }
1290                 container.insert(individual);
1291
1292         //      string individual;
1293
1294         //      while (estim.find_first_of('-') != -1) {
1295         //              individual = estim.substr(0,estim.find_first_of('-'));
1296         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1297         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1298         //                      container.insert(individual);
1299         //              }
1300         //      }
1301                 //get last one
1302         //      container.insert(estim);
1303
1304         }
1305         catch(exception& e) {
1306                 errorOut(e, "MothurOut", "splitAtDash");
1307                 exit(1);
1308         }
1309 }
1310 /***********************************************************************/
1311 //This function parses the line options and puts them in a set
1312 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1313         try {
1314                 string individual;
1315                 int lineNum;
1316
1317                 while (estim.find_first_of('-') != -1) {
1318                         individual = estim.substr(0,estim.find_first_of('-'));
1319                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1320                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1321                                 convert(individual, lineNum); //convert the string to int
1322                                 container.insert(lineNum);
1323                         }
1324                 }
1325                 //get last one
1326                 convert(estim, lineNum); //convert the string to int
1327                 container.insert(lineNum);
1328         }
1329         catch(exception& e) {
1330                 errorOut(e, "MothurOut", "splitAtDash");
1331                 exit(1);
1332         }
1333 }
1334 /***********************************************************************/
1335 //This function parses the a string and puts peices in a vector
1336 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1337         try {
1338                 string individual = "";
1339                 int estimLength = estim.size();
1340                 for(int i=0;i<estimLength;i++){
1341                         if(estim[i] == ','){
1342                                 container.push_back(individual);
1343                                 individual = "";
1344                         }
1345                         else{
1346                                 individual += estim[i];
1347                         }
1348                 }
1349                 container.push_back(individual);
1350
1351
1352
1353
1354 //              string individual;
1355 //
1356 //              while (estim.find_first_of(',') != -1) {
1357 //                      individual = estim.substr(0,estim.find_first_of(','));
1358 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1359 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1360 //                              container.push_back(individual);
1361 //                      }
1362 //              }
1363 //              //get last one
1364 //              container.push_back(estim);
1365         }
1366         catch(exception& e) {
1367                 errorOut(e, "MothurOut", "splitAtComma");
1368                 exit(1);
1369         }
1370 }
1371 /***********************************************************************/
1372
1373 //This function splits up the various option parameters
1374 void MothurOut::splitAtComma(string& prefix, string& suffix){
1375         try {
1376                 prefix = suffix.substr(0,suffix.find_first_of(','));
1377                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1378                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1379                         string space = " ";
1380                         while(suffix.at(0) == ' ')
1381                                 suffix = suffix.substr(1, suffix.length());
1382                 }
1383
1384         }
1385         catch(exception& e) {
1386                 errorOut(e, "MothurOut", "splitAtComma");
1387                 exit(1);
1388         }
1389 }
1390 /***********************************************************************/
1391
1392 //This function separates the key value from the option value i.e. dist=96_...
1393 void MothurOut::splitAtEquals(string& key, string& value){
1394         try {
1395                 if(value.find_first_of('=') != -1){
1396                         key = value.substr(0,value.find_first_of('='));
1397                         if ((value.find_first_of('=')+1) <= value.length()) {
1398                                 value = value.substr(value.find_first_of('=')+1, value.length());
1399                         }
1400                 }else{
1401                         key = value;
1402                         value = 1;
1403                 }
1404         }
1405         catch(exception& e) {
1406                 errorOut(e, "MothurOut", "splitAtEquals");
1407                 exit(1);
1408         }
1409 }
1410
1411 /**************************************************************************************************/
1412
1413 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1414         try {
1415                 for (int i = 0; i < Groups.size(); i++) {
1416                         if (groupname == Groups[i]) { return true; }
1417                 }
1418                 return false;
1419         }
1420         catch(exception& e) {
1421                 errorOut(e, "MothurOut", "inUsersGroups");
1422                 exit(1);
1423         }
1424 }
1425 /**************************************************************************************************/
1426 //returns true if any of the strings in first vector are in second vector
1427 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1428         try {
1429
1430                 for (int i = 0; i < groupnames.size(); i++) {
1431                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1432                 }
1433                 return false;
1434         }
1435         catch(exception& e) {
1436                 errorOut(e, "MothurOut", "inUsersGroups");
1437                 exit(1);
1438         }
1439 }
1440 /***********************************************************************/
1441 //this function determines if the user has given us labels that are smaller than the given label.
1442 //if so then it returns true so that the calling function can run the previous valid distance.
1443 //it's a "smart" distance function.  It also checks for invalid labels.
1444 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1445         try {
1446
1447                 set<string>::iterator it;
1448                 vector<float> orderFloat;
1449                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1450                 map<string, float>::iterator it2;
1451                 float labelFloat;
1452                 bool smaller = false;
1453
1454                 //unique is the smallest line
1455                 if (label == "unique") {  return false;  }
1456                 else {
1457                         if (convertTestFloat(label, labelFloat)) {
1458                                 convert(label, labelFloat);
1459                         }else { //cant convert
1460                                 return false;
1461                         }
1462                 }
1463
1464                 //go through users set and make them floats
1465                 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
1466
1467                         float temp;
1468                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1469                                 convert(*it, temp);
1470                                 orderFloat.push_back(temp);
1471                                 userMap[*it] = temp;
1472                         }else if (*it == "unique") {
1473                                 orderFloat.push_back(-1.0);
1474                                 userMap["unique"] = -1.0;
1475                         }else {
1476                                 if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
1477                                 userLabels.erase(*it);
1478                                 it--;
1479                         }
1480                 }
1481
1482                 //sort order
1483                 sort(orderFloat.begin(), orderFloat.end());
1484
1485                 /*************************************************/
1486                 //is this label bigger than any of the users labels
1487                 /*************************************************/
1488
1489                 //loop through order until you find a label greater than label
1490                 for (int i = 0; i < orderFloat.size(); i++) {
1491                         if (orderFloat[i] < labelFloat) {
1492                                 smaller = true;
1493                                 if (orderFloat[i] == -1) {
1494                                         if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
1495                                         userLabels.erase("unique");
1496                                 }
1497                                 else {
1498                                         if (errorOff == "") { cout << "Your file does not include the label " << endl; }
1499                                         string s = "";
1500                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1501                                                 if (it2->second == orderFloat[i]) {
1502                                                         s = it2->first;
1503                                                         //remove small labels
1504                                                         userLabels.erase(s);
1505                                                         break;
1506                                                 }
1507                                         }
1508                                         if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
1509                                 }
1510                         //since they are sorted once you find a bigger one stop looking
1511                         }else { break; }
1512                 }
1513
1514                 return smaller;
1515
1516         }
1517         catch(exception& e) {
1518                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1519                 exit(1);
1520         }
1521 }
1522
1523 /**************************************************************************************************/
1524 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1525         try {
1526
1527                 bool good = true;
1528
1529                 string line = getline(file);
1530
1531                 //before we added this check
1532                 if (line[0] != '#') {  good = false;  }
1533                 else {
1534                         //rip off #
1535                         line = line.substr(1);
1536
1537                         vector<string> versionVector;
1538                         splitAtChar(version, versionVector, '.');
1539
1540                         //check file version
1541                         vector<string> linesVector;
1542                         splitAtChar(line, linesVector, '.');
1543
1544                         if (versionVector.size() != linesVector.size()) { good = false; }
1545                         else {
1546                                 for (int j = 0; j < versionVector.size(); j++) {
1547                                         int num1, num2;
1548                                         convert(versionVector[j], num1);
1549                                         convert(linesVector[j], num2);
1550
1551                                         //if mothurs version is newer than this files version, then we want to remake it
1552                                         if (num1 > num2) {  good = false; break;  }
1553                                 }
1554                         }
1555
1556                 }
1557
1558                 if (!good) {  file.close();  }
1559                 else { file.seekg(0);  }
1560
1561                 return good;
1562         }
1563         catch(exception& e) {
1564                 errorOut(e, "MothurOut", "checkReleaseVersion");
1565                 exit(1);
1566         }
1567 }
1568
1569 /**************************************************************************************************/
1570
1571
1572
1573
1574