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