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