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 = getenv ("HOME");
 506                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 507                                 return newFileName;
 508                         }else { //find path
 509                                 if (path.rfind("./") == -1) { return fileName; } //already complete name
 510                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 511
 512                                 char* cwdpath = new char[1024];
 513
 514                                 size_t size;
 515                                 cwdpath=getcwd(cwdpath,size);
 516
 517                                 cwd = cwdpath;
 518
 519                                 //rip off first '/'
 520                                 string simpleCWD;
 521                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 522
 523                                 //break apart the current working directory
 524                                 vector<string> dirs;
 525                                 while (simpleCWD.find_first_of('/') != -1) {
 526                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 527                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 528                                         dirs.push_back(dir);
 529                                 }
 530                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 531                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 532
 533
 534                                 int index = dirs.size()-1;
 535
 536                                 while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
 537                                         if (pos == 0) { break;  //you are at the end
 538                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 539                                                 path = path.substr(0, pos-1);
 540                                                 index--;
 541                                                 if (index == 0) {  break; }
 542                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 543                                                 path = path.substr(0, pos);
 544                                         }else if (pos == 1) { break;  //you are at the end
 545                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 546                                 }
 547
 548                                 for (int i = index; i >= 0; i--) {
 549                                         newFileName = dirs[i] +  "/" + newFileName;
 550                                 }
 551
 552                                 newFileName =  "/" +  newFileName;
 553                                 return newFileName;
 554                         }
 555                 #else
 556                         if (path.find("~") != -1) { //go to home directory
 557                                 string homeDir = getenv ("HOMEPATH");
 558                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 559                                 return newFileName;
 560                         }else { //find path
 561                                 if (path.rfind(".\\") == -1) { return fileName; } //already complete name
 562                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 563
 564                                 char *cwdpath = NULL;
 565                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 566                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 567                                 else { cwd = "";  }
 568
 569                                 //break apart the current working directory
 570                                 vector<string> dirs;
 571                                 while (cwd.find_first_of('\\') != -1) {
 572                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 573                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 574                                         dirs.push_back(dir);
 575
 576                                 }
 577                                 //get last one
 578                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 579
 580                                 int index = dirs.size()-1;
 581
 582                                 while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
 583                                         if (pos == 0) { break;  //you are at the end
 584                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 585                                                 path = path.substr(0, pos-1);
 586                                                 index--;
 587                                                 if (index == 0) {  break; }
 588                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 589                                                 path = path.substr(0, pos);
 590                                         }else if (pos == 1) { break;  //you are at the end
 591                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 592                                 }
 593
 594                                 for (int i = index; i >= 0; i--) {
 595                                         newFileName = dirs[i] +  "\\" + newFileName;
 596                                 }
 597
 598                                 return newFileName;
 599                         }
 600
 601                 #endif
 602         }
 603         }
 604         catch(exception& e) {
 605                 errorOut(e, "MothurOut", "getFullPathName");
 606                 exit(1);
 607         }
 608 }
 609 /***********************************************************************/
 610
 611 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 612         try {
 613                         //get full path name
 614                         string completeFileName = getFullPathName(fileName);
 615
 616 #ifdef USE_COMPRESSION
 617       // check for gzipped or bzipped file
 618       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 619         string tempName = string(tmpnam(0));
 620         mkfifo(tempName.c_str(), 0666);
 621         int fork_result = fork();
 622         if (fork_result < 0) {
 623           cerr << "Error forking.\n";
 624           exit(1);
 625         } else if (fork_result == 0) {
 626           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 627           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 628           system(command.c_str());
 629           cerr << "Done decompressing " << completeFileName << "\n";
 630           remove(tempName.c_str());
 631           exit(EXIT_SUCCESS);
 632         } else {
 633           cerr << "waiting on child process " << fork_result << "\n";
 634           completeFileName = tempName;
 635         }
 636       }
 637 #endif
 638
 639                         fileHandle.open(completeFileName.c_str());
 640                         if(!fileHandle) {
 641                                 return 1;
 642                         }else {
 643                                 //check for blank file
 644                                 gobble(fileHandle);
 645                                 return 0;
 646                         }
 647         }
 648         catch(exception& e) {
 649                 errorOut(e, "MothurOut", "openInputFile - no Error");
 650                 exit(1);
 651         }
 652 }
 653 /***********************************************************************/
 654
 655 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 656         try {
 657
 658                 //get full path name
 659                 string completeFileName = getFullPathName(fileName);
 660
 661 #ifdef USE_COMPRESSION
 662   // check for gzipped or bzipped file
 663   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 664     string tempName = string(tmpnam(0));
 665     mkfifo(tempName.c_str(), 0666);
 666     int fork_result = fork();
 667     if (fork_result < 0) {
 668       cerr << "Error forking.\n";
 669       exit(1);
 670     } else if (fork_result == 0) {
 671       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 672       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 673       system(command.c_str());
 674       cerr << "Done decompressing " << completeFileName << "\n";
 675       remove(tempName.c_str());
 676       exit(EXIT_SUCCESS);
 677     } else {
 678       cerr << "waiting on child process " << fork_result << "\n";
 679       completeFileName = tempName;
 680     }
 681   }
 682 #endif
 683
 684
 685                 fileHandle.open(completeFileName.c_str());
 686                 if(!fileHandle) {
 687                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 688                         return 1;
 689                 }
 690                 else {
 691                         //check for blank file
 692                         gobble(fileHandle);
 693                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 694
 695                         return 0;
 696                 }
 697         }
 698         catch(exception& e) {
 699                 errorOut(e, "MothurOut", "openInputFile");
 700                 exit(1);
 701         }
 702 }
 703 /***********************************************************************/
 704
 705 int MothurOut::renameFile(string oldName, string newName){
 706         try {
 707                 ifstream inTest;
 708                 int exist = openInputFile(newName, inTest, "");
 709
 710         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 711                 if (exist == 0) { //you could open it so you want to delete it
 712                         inTest.close();
 713                         string command = "rm " + newName;
 714                         system(command.c_str());
 715                 }
 716
 717                 string command = "mv " + oldName + " " + newName;
 718                 system(command.c_str());
 719         #else
 720                 remove(newName.c_str());
 721                 int renameOk = rename(oldName.c_str(), newName.c_str());
 722         #endif
 723                 return 0;
 724
 725         }
 726         catch(exception& e) {
 727                 errorOut(e, "MothurOut", "renameFile");
 728                 exit(1);
 729         }
 730 }
 731
 732 /***********************************************************************/
 733
 734 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 735         try {
 736
 737                 string completeFileName = getFullPathName(fileName);
 738
 739 #ifdef USE_COMPRESSION
 740     // check for gzipped file
 741     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 742       string tempName = string(tmpnam(0));
 743       mkfifo(tempName.c_str(), 0666);
 744       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 745       int fork_result = fork();
 746       if (fork_result < 0) {
 747         cerr << "Error forking.\n";
 748         exit(1);
 749       } else if (fork_result == 0) {
 750         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 751         system(command.c_str());
 752         exit(0);
 753       } else {
 754         completeFileName = tempName;
 755       }
 756     }
 757 #endif
 758
 759                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 760                 if(!fileHandle) {
 761                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 762                         return 1;
 763                 }
 764                 else {
 765                         return 0;
 766                 }
 767         }
 768         catch(exception& e) {
 769                 errorOut(e, "MothurOut", "openOutputFile");
 770                 exit(1);
 771         }
 772
 773 }
 774
 775 /**************************************************************************************************/
 776 void MothurOut::appendFiles(string temp, string filename) {
 777         try{
 778                 ofstream output;
 779                 ifstream input;
 780
 781                 //open output file in append mode
 782                 openOutputFileAppend(filename, output);
 783                 int ableToOpen = openInputFile(temp, input, "no error");
 784
 785                 if (ableToOpen == 0) { //you opened it
 786                         while(char c = input.get()){
 787                                 if(input.eof())         {       break;                  }
 788                                 else                            {       output << c;    }
 789                         }
 790                         input.close();
 791                 }
 792
 793                 output.close();
 794         }
 795         catch(exception& e) {
 796                 errorOut(e, "MothurOut", "appendFiles");
 797                 exit(1);
 798         }
 799 }
 800
 801 /**************************************************************************************************/
 802 string MothurOut::sortFile(string distFile, string outputDir){
 803         try {
 804
 805                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 806                 string outfile = getRootName(distFile) + "sorted.dist";
 807
 808
 809                 //if you can, use the unix sort since its been optimized for years
 810                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 811                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 812                         system(command.c_str());
 813                 #else //you are stuck with my best attempt...
 814                         //windows sort does not have a way to specify a column, only a character in the line
 815                         //since we cannot assume that the distance will always be at the the same character location on each line
 816                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 817
 818                         //read in file line by file and put distance first
 819                         string tempDistFile = distFile + ".temp";
 820                         ifstream input;
 821                         ofstream output;
 822                         openInputFile(distFile, input);
 823                         openOutputFile(tempDistFile, output);
 824
 825                         string firstName, secondName;
 826                         float dist;
 827                         while (input) {
 828                                 input >> firstName >> secondName >> dist;
 829                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 830                                 gobble(input);
 831                         }
 832                         input.close();
 833                         output.close();
 834
 835
 836                         //sort using windows sort
 837                         string tempOutfile = outfile + ".temp";
 838                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 839                         system(command.c_str());
 840
 841                         //read in sorted file and put distance at end again
 842                         ifstream input2;
 843                         openInputFile(tempOutfile, input2);
 844                         openOutputFile(outfile, output);
 845
 846                         while (input2) {
 847                                 input2 >> dist >> firstName >> secondName;
 848                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 849                                 gobble(input2);
 850                         }
 851                         input2.close();
 852                         output.close();
 853
 854                         //remove temp files
 855                         remove(tempDistFile.c_str());
 856                         remove(tempOutfile.c_str());
 857                 #endif
 858
 859                 return outfile;
 860         }
 861         catch(exception& e) {
 862                 errorOut(e, "MothurOut", "sortFile");
 863                 exit(1);
 864         }
 865 }
 866 /**************************************************************************************************/
 867 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
 868         try {
 869                         vector<unsigned long int> positions;
 870                         ifstream inFASTA;
 871                         openInputFile(filename, inFASTA);
 872
 873                         string input;
 874                         while(!inFASTA.eof()){
 875                                 input = getline(inFASTA);
 876                                 if (input.length() != 0) {
 877                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 878                                 }
 879                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
 880                         }
 881                         inFASTA.close();
 882
 883                         num = positions.size();
 884
 885                         /*FILE * pFile;
 886                         long size;
 887
 888                         //get num bytes in file
 889                         pFile = fopen (filename.c_str(),"rb");
 890                         if (pFile==NULL) perror ("Error opening file");
 891                         else{
 892                                 fseek (pFile, 0, SEEK_END);
 893                                 size=ftell (pFile);
 894                                 fclose (pFile);
 895                         }*/
 896
 897                         unsigned long int size = positions[(positions.size()-1)];
 898                         ifstream in;
 899                         openInputFile(filename, in);
 900
 901                         in.seekg(size);
 902
 903                         while(char c = in.get()){
 904                                 if(in.eof())            {       break;  }
 905                                 else                            {       size++; }
 906                         }
 907                         in.close();
 908
 909                         positions.push_back(size);
 910
 911                         return positions;
 912         }
 913         catch(exception& e) {
 914                 errorOut(e, "MothurOut", "setFilePosFasta");
 915                 exit(1);
 916         }
 917 }
 918 /**************************************************************************************************/
 919 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
 920         try {
 921                         filename = getFullPathName(filename);
 922
 923                         vector<unsigned long int> positions;
 924                         ifstream in;
 925                         openInputFile(filename, in);
 926
 927                         string input;
 928                         while(!in.eof()){
 929                                 unsigned long int lastpos = in.tellg();
 930                                 input = getline(in);
 931                                 if (input.length() != 0) {
 932                                         unsigned long int pos = in.tellg();
 933                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
 934                                         else {  positions.push_back(lastpos);  }
 935                                 }
 936                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
 937                         }
 938                         in.close();
 939
 940                         num = positions.size();
 941
 942                         FILE * pFile;
 943                         unsigned long int size;
 944
 945                         //get num bytes in file
 946                         pFile = fopen (filename.c_str(),"rb");
 947                         if (pFile==NULL) perror ("Error opening file");
 948                         else{
 949                                 fseek (pFile, 0, SEEK_END);
 950                                 size=ftell (pFile);
 951                                 fclose (pFile);
 952                         }
 953
 954                         positions.push_back(size);
 955
 956                         return positions;
 957         }
 958         catch(exception& e) {
 959                 errorOut(e, "MothurOut", "setFilePosEachLine");
 960                 exit(1);
 961         }
 962 }
 963 /**************************************************************************************************/
 964
 965 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 966         try{
 967
 968                 vector<unsigned long int> filePos;
 969                 filePos.push_back(0);
 970
 971                 FILE * pFile;
 972                 unsigned long int size;
 973
 974                 filename = getFullPathName(filename);
 975
 976                 //get num bytes in file
 977                 pFile = fopen (filename.c_str(),"rb");
 978                 if (pFile==NULL) perror ("Error opening file");
 979                 else{
 980                         fseek (pFile, 0, SEEK_END);
 981                         size=ftell (pFile);
 982                         fclose (pFile);
 983                 }
 984
 985                 //estimate file breaks
 986                 unsigned long int chunkSize = 0;
 987                 chunkSize = size / proc;
 988
 989                 //file to small to divide by processors
 990                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
 991
 992                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 993                 for (int i = 0; i < proc; i++) {
 994                         unsigned long int spot = (i+1) * chunkSize;
 995
 996                         ifstream in;
 997                         openInputFile(filename, in);
 998                         in.seekg(spot);
 999
1000                         //look for next '>'
1001                         unsigned long int newSpot = spot;
1002                         while (!in.eof()) {
1003                            char c = in.get();
1004                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1005                         }
1006
1007                         //there was not another sequence before the end of the file
1008                         unsigned long int sanityPos = in.tellg();
1009
1010                         if (sanityPos == -1) {  break;  }
1011                         else {  filePos.push_back(newSpot);  }
1012
1013                         in.close();
1014                 }
1015
1016                 //save end pos
1017                 filePos.push_back(size);
1018
1019                 //sanity check filePos
1020                 for (int i = 0; i < (filePos.size()-1); i++) {
1021                         if (filePos[(i+1)] <= filePos[i]) {  cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
1022                 }
1023
1024                 proc = (filePos.size() - 1);
1025
1026                 return filePos;
1027         }
1028         catch(exception& e) {
1029                 errorOut(e, "MothurOut", "divideFile");
1030                 exit(1);
1031         }
1032 }
1033
1034 /***********************************************************************/
1035
1036 bool MothurOut::isTrue(string f){
1037         try {
1038
1039                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1040
1041                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1042                 else {  return false;  }
1043         }
1044         catch(exception& e) {
1045                 errorOut(e, "MothurOut", "isTrue");
1046                 exit(1);
1047         }
1048 }
1049
1050 /***********************************************************************/
1051
1052 float MothurOut::roundDist(float dist, int precision){
1053         try {
1054                 return int(dist * precision + 0.5)/float(precision);
1055         }
1056         catch(exception& e) {
1057                 errorOut(e, "MothurOut", "roundDist");
1058                 exit(1);
1059         }
1060 }
1061 /***********************************************************************/
1062
1063 float MothurOut::ceilDist(float dist, int precision){
1064         try {
1065                 return int(ceil(dist * precision))/float(precision);
1066         }
1067         catch(exception& e) {
1068                 errorOut(e, "MothurOut", "ceilDist");
1069                 exit(1);
1070         }
1071 }
1072
1073 /***********************************************************************/
1074
1075 int MothurOut::getNumNames(string names){
1076         try {
1077                 int count = 0;
1078
1079                 if(names != ""){
1080                         count = 1;
1081                         for(int i=0;i<names.size();i++){
1082                                 if(names[i] == ','){
1083                                         count++;
1084                                 }
1085                         }
1086                 }
1087
1088                 return count;
1089         }
1090         catch(exception& e) {
1091                 errorOut(e, "MothurOut", "getNumNames");
1092                 exit(1);
1093         }
1094 }
1095
1096 /**************************************************************************************************/
1097
1098 vector<vector<double> > MothurOut::binomial(int maxOrder){
1099         try {
1100         vector<vector<double> > binomial(maxOrder+1);
1101
1102     for(int i=0;i<=maxOrder;i++){
1103                 binomial[i].resize(maxOrder+1);
1104                 binomial[i][0]=1;
1105                 binomial[0][i]=0;
1106     }
1107     binomial[0][0]=1;
1108
1109     binomial[1][0]=1;
1110     binomial[1][1]=1;
1111
1112     for(int i=2;i<=maxOrder;i++){
1113                 binomial[1][i]=0;
1114     }
1115
1116     for(int i=2;i<=maxOrder;i++){
1117                 for(int j=1;j<=maxOrder;j++){
1118                         if(i==j){       binomial[i][j]=1;                                                                       }
1119                         if(j>i) {       binomial[i][j]=0;                                                                       }
1120                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1121                 }
1122     }
1123
1124         return binomial;
1125
1126         }
1127         catch(exception& e) {
1128                 errorOut(e, "MothurOut", "binomial");
1129                 exit(1);
1130         }
1131 }
1132
1133 /***********************************************************************/
1134
1135 int MothurOut::factorial(int num){
1136         try {
1137                 int total = 1;
1138
1139                 for (int i = 1; i <= num; i++) {
1140                         total *= i;
1141                 }
1142
1143                 return total;
1144         }
1145         catch(exception& e) {
1146                 errorOut(e, "MothurOut", "factorial");
1147                 exit(1);
1148         }
1149 }
1150 /***********************************************************************/
1151
1152 int MothurOut::getNumSeqs(ifstream& file){
1153         try {
1154                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1155                 file.seekg(0);
1156                 return numSeqs;
1157         }
1158         catch(exception& e) {
1159                 errorOut(e, "MothurOut", "getNumSeqs");
1160                 exit(1);
1161         }
1162 }
1163 /***********************************************************************/
1164 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1165         try {
1166                 string input;
1167                 numSeqs = 0;
1168                 while(!file.eof()){
1169                         input = getline(file);
1170                         if (input.length() != 0) {
1171                                 if(input[0] == '>'){ numSeqs++; }
1172                         }
1173                 }
1174         }
1175         catch(exception& e) {
1176                 errorOut(e, "MothurOut", "getNumSeqs");
1177                 exit(1);
1178         }
1179 }
1180 /***********************************************************************/
1181
1182 //This function parses the estimator options and puts them in a vector
1183 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1184         try {
1185                 string individual = "";
1186                 int estimLength = estim.size();
1187                 for(int i=0;i<estimLength;i++){
1188                         if(estim[i] == symbol){
1189                                 container.push_back(individual);
1190                                 individual = "";
1191                         }
1192                         else{
1193                                 individual += estim[i];
1194                         }
1195                 }
1196                 container.push_back(individual);
1197
1198                 /*
1199
1200                 while (estim.find_first_of(symbol) != -1) {
1201                         individual = estim.substr(0,estim.find_first_of(symbol));
1202                         if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1203                                 estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
1204                                 container.push_back(individual);
1205                         }
1206                 }
1207                 //get last one
1208                 container.push_back(estim); */
1209         }
1210         catch(exception& e) {
1211                 errorOut(e, "MothurOut", "splitAtChar");
1212                 exit(1);
1213         }
1214 }
1215
1216 /***********************************************************************/
1217
1218 //This function parses the estimator options and puts them in a vector
1219 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1220         try {
1221                 string individual = "";
1222                 int estimLength = estim.size();
1223                 for(int i=0;i<estimLength;i++){
1224                         if(estim[i] == '-'){
1225                                 container.push_back(individual);
1226                                 individual = "";
1227                         }
1228                         else{
1229                                 individual += estim[i];
1230                         }
1231                 }
1232                 container.push_back(individual);
1233
1234
1235         /*      string individual;
1236
1237                 while (estim.find_first_of('-') != -1) {
1238                         individual = estim.substr(0,estim.find_first_of('-'));
1239                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1240                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1241                                 container.push_back(individual);
1242                         }
1243                 }
1244                 //get last one
1245                 container.push_back(estim); */
1246         }
1247         catch(exception& e) {
1248                 errorOut(e, "MothurOut", "splitAtDash");
1249                 exit(1);
1250         }
1251 }
1252
1253 /***********************************************************************/
1254 //This function parses the label options and puts them in a set
1255 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1256         try {
1257                 string individual = "";
1258                 int estimLength = estim.size();
1259                 for(int i=0;i<estimLength;i++){
1260                         if(estim[i] == '-'){
1261                                 container.insert(individual);
1262                                 individual = "";
1263                         }
1264                         else{
1265                                 individual += estim[i];
1266                         }
1267                 }
1268                 container.insert(individual);
1269
1270         //      string individual;
1271
1272         //      while (estim.find_first_of('-') != -1) {
1273         //              individual = estim.substr(0,estim.find_first_of('-'));
1274         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1275         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1276         //                      container.insert(individual);
1277         //              }
1278         //      }
1279                 //get last one
1280         //      container.insert(estim);
1281
1282         }
1283         catch(exception& e) {
1284                 errorOut(e, "MothurOut", "splitAtDash");
1285                 exit(1);
1286         }
1287 }
1288 /***********************************************************************/
1289 //This function parses the line options and puts them in a set
1290 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1291         try {
1292                 string individual;
1293                 int lineNum;
1294
1295                 while (estim.find_first_of('-') != -1) {
1296                         individual = estim.substr(0,estim.find_first_of('-'));
1297                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1298                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1299                                 convert(individual, lineNum); //convert the string to int
1300                                 container.insert(lineNum);
1301                         }
1302                 }
1303                 //get last one
1304                 convert(estim, lineNum); //convert the string to int
1305                 container.insert(lineNum);
1306         }
1307         catch(exception& e) {
1308                 errorOut(e, "MothurOut", "splitAtDash");
1309                 exit(1);
1310         }
1311 }
1312 /***********************************************************************/
1313 //This function parses the a string and puts peices in a vector
1314 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1315         try {
1316                 string individual = "";
1317                 int estimLength = estim.size();
1318                 for(int i=0;i<estimLength;i++){
1319                         if(estim[i] == ','){
1320                                 container.push_back(individual);
1321                                 individual = "";
1322                         }
1323                         else{
1324                                 individual += estim[i];
1325                         }
1326                 }
1327                 container.push_back(individual);
1328
1329
1330
1331
1332 //              string individual;
1333 //
1334 //              while (estim.find_first_of(',') != -1) {
1335 //                      individual = estim.substr(0,estim.find_first_of(','));
1336 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1337 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1338 //                              container.push_back(individual);
1339 //                      }
1340 //              }
1341 //              //get last one
1342 //              container.push_back(estim);
1343         }
1344         catch(exception& e) {
1345                 errorOut(e, "MothurOut", "splitAtComma");
1346                 exit(1);
1347         }
1348 }
1349 /***********************************************************************/
1350
1351 //This function splits up the various option parameters
1352 void MothurOut::splitAtComma(string& prefix, string& suffix){
1353         try {
1354                 prefix = suffix.substr(0,suffix.find_first_of(','));
1355                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1356                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1357                         string space = " ";
1358                         while(suffix.at(0) == ' ')
1359                                 suffix = suffix.substr(1, suffix.length());
1360                 }
1361
1362         }
1363         catch(exception& e) {
1364                 errorOut(e, "MothurOut", "splitAtComma");
1365                 exit(1);
1366         }
1367 }
1368 /***********************************************************************/
1369
1370 //This function separates the key value from the option value i.e. dist=96_...
1371 void MothurOut::splitAtEquals(string& key, string& value){
1372         try {
1373                 if(value.find_first_of('=') != -1){
1374                         key = value.substr(0,value.find_first_of('='));
1375                         if ((value.find_first_of('=')+1) <= value.length()) {
1376                                 value = value.substr(value.find_first_of('=')+1, value.length());
1377                         }
1378                 }else{
1379                         key = value;
1380                         value = 1;
1381                 }
1382         }
1383         catch(exception& e) {
1384                 errorOut(e, "MothurOut", "splitAtEquals");
1385                 exit(1);
1386         }
1387 }
1388
1389 /**************************************************************************************************/
1390
1391 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1392         try {
1393                 for (int i = 0; i < Groups.size(); i++) {
1394                         if (groupname == Groups[i]) { return true; }
1395                 }
1396                 return false;
1397         }
1398         catch(exception& e) {
1399                 errorOut(e, "MothurOut", "inUsersGroups");
1400                 exit(1);
1401         }
1402 }
1403 /**************************************************************************************************/
1404 //returns true if any of the strings in first vector are in second vector
1405 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1406         try {
1407
1408                 for (int i = 0; i < groupnames.size(); i++) {
1409                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1410                 }
1411                 return false;
1412         }
1413         catch(exception& e) {
1414                 errorOut(e, "MothurOut", "inUsersGroups");
1415                 exit(1);
1416         }
1417 }
1418 /***********************************************************************/
1419 //this function determines if the user has given us labels that are smaller than the given label.
1420 //if so then it returns true so that the calling function can run the previous valid distance.
1421 //it's a "smart" distance function.  It also checks for invalid labels.
1422 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1423         try {
1424
1425                 set<string>::iterator it;
1426                 vector<float> orderFloat;
1427                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1428                 map<string, float>::iterator it2;
1429                 float labelFloat;
1430                 bool smaller = false;
1431
1432                 //unique is the smallest line
1433                 if (label == "unique") {  return false;  }
1434                 else {
1435                         if (convertTestFloat(label, labelFloat)) {
1436                                 convert(label, labelFloat);
1437                         }else { //cant convert
1438                                 return false;
1439                         }
1440                 }
1441
1442                 //go through users set and make them floats
1443                 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
1444
1445                         float temp;
1446                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1447                                 convert(*it, temp);
1448                                 orderFloat.push_back(temp);
1449                                 userMap[*it] = temp;
1450                         }else if (*it == "unique") {
1451                                 orderFloat.push_back(-1.0);
1452                                 userMap["unique"] = -1.0;
1453                         }else {
1454                                 if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
1455                                 userLabels.erase(*it);
1456                                 it--;
1457                         }
1458                 }
1459
1460                 //sort order
1461                 sort(orderFloat.begin(), orderFloat.end());
1462
1463                 /*************************************************/
1464                 //is this label bigger than any of the users labels
1465                 /*************************************************/
1466
1467                 //loop through order until you find a label greater than label
1468                 for (int i = 0; i < orderFloat.size(); i++) {
1469                         if (orderFloat[i] < labelFloat) {
1470                                 smaller = true;
1471                                 if (orderFloat[i] == -1) {
1472                                         if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
1473                                         userLabels.erase("unique");
1474                                 }
1475                                 else {
1476                                         if (errorOff == "") { cout << "Your file does not include the label " << endl; }
1477                                         string s = "";
1478                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1479                                                 if (it2->second == orderFloat[i]) {
1480                                                         s = it2->first;
1481                                                         //remove small labels
1482                                                         userLabels.erase(s);
1483                                                         break;
1484                                                 }
1485                                         }
1486                                         if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
1487                                 }
1488                         //since they are sorted once you find a bigger one stop looking
1489                         }else { break; }
1490                 }
1491
1492                 return smaller;
1493
1494         }
1495         catch(exception& e) {
1496                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1497                 exit(1);
1498         }
1499 }
1500
1501 /**************************************************************************************************/
1502 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1503         try {
1504
1505                 bool good = true;
1506
1507                 string line = getline(file);
1508
1509                 //before we added this check
1510                 if (line[0] != '#') {  good = false;  }
1511                 else {
1512                         //rip off #
1513                         line = line.substr(1);
1514
1515                         vector<string> versionVector;
1516                         splitAtChar(version, versionVector, '.');
1517
1518                         //check file version
1519                         vector<string> linesVector;
1520                         splitAtChar(line, linesVector, '.');
1521
1522                         if (versionVector.size() != linesVector.size()) { good = false; }
1523                         else {
1524                                 for (int j = 0; j < versionVector.size(); j++) {
1525                                         int num1, num2;
1526                                         convert(versionVector[j], num1);
1527                                         convert(linesVector[j], num2);
1528
1529                                         //if mothurs version is newer than this files version, then we want to remake it
1530                                         if (num1 > num2) {  good = false; break;  }
1531                                 }
1532                         }
1533
1534                 }
1535
1536                 if (!good) {  file.close();  }
1537                 else { file.seekg(0);  }
1538
1539                 return good;
1540         }
1541         catch(exception& e) {
1542                 errorOut(e, "MothurOut", "checkReleaseVersion");
1543                 exit(1);
1544         }
1545 }
1546 /**************************************************************************************************/
1547
1548
1549
1550
1551