mothurout.cpp

   1 /*
   2  *  mothurOut.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 2/25/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mothurout.h"
  11
  12 /******************************************************/
  13 MothurOut* MothurOut::getInstance() {
  14         if( _uniqueInstance == 0) {
  15                 _uniqueInstance = new MothurOut();
  16         }
  17         return _uniqueInstance;
  18 }
  19 /*********************************************************************************************/
  20 void MothurOut::setFileName(string filename)  {
  21         try {
  22                 logFileName = filename;
  23
  24                 #ifdef USE_MPI
  25                         int pid;
  26                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  27
  28                         if (pid == 0) { //only one process should output to screen
  29                 #endif
  30
  31                 openOutputFile(filename, out);
  32
  33                 #ifdef USE_MPI
  34                         }
  35                 #endif
  36         }
  37         catch(exception& e) {
  38                 errorOut(e, "MothurOut", "setFileName");
  39                 exit(1);
  40         }
  41 }
  42 /*********************************************************************************************/
  43 void MothurOut::setDefaultPath(string pathname)  {
  44         try {
  45
  46                 //add / to name if needed
  47                 string lastChar = pathname.substr(pathname.length()-1);
  48                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  49                         if (lastChar != "/") { pathname += "/"; }
  50                 #else
  51                         if (lastChar != "\\") { pathname += "\\"; }
  52                 #endif
  53
  54                 defaultPath = pathname;
  55
  56         }
  57         catch(exception& e) {
  58                 errorOut(e, "MothurOut", "setDefaultPath");
  59                 exit(1);
  60         }
  61 }
  62 /*********************************************************************************************/
  63 void MothurOut::setOutputDir(string pathname)  {
  64         try {
  65                 outputDir = pathname;
  66         }
  67         catch(exception& e) {
  68                 errorOut(e, "MothurOut", "setOutputDir");
  69                 exit(1);
  70         }
  71 }
  72 /*********************************************************************************************/
  73 void MothurOut::closeLog()  {
  74         try {
  75
  76                 #ifdef USE_MPI
  77                         int pid;
  78                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  79
  80                         if (pid == 0) { //only one process should output to screen
  81                 #endif
  82
  83                 out.close();
  84
  85                 #ifdef USE_MPI
  86                         }
  87                 #endif
  88         }
  89         catch(exception& e) {
  90                 errorOut(e, "MothurOut", "closeLog");
  91                 exit(1);
  92         }
  93 }
  94
  95 /*********************************************************************************************/
  96 MothurOut::~MothurOut() {
  97         try {
  98                 _uniqueInstance = 0;
  99
 100         }
 101         catch(exception& e) {
 102                 errorOut(e, "MothurOut", "MothurOut");
 103                 exit(1);
 104         }
 105 }
 106 /*********************************************************************************************/
 107 void MothurOut::mothurOut(string output) {
 108         try {
 109
 110                 #ifdef USE_MPI
 111                         int pid;
 112                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 113
 114                         if (pid == 0) { //only one process should output to screen
 115                 #endif
 116
 117                 cout << output;
 118                 out << output;
 119
 120                 #ifdef USE_MPI
 121                         }
 122                 #endif
 123         }
 124         catch(exception& e) {
 125                 errorOut(e, "MothurOut", "MothurOut");
 126                 exit(1);
 127         }
 128 }
 129 /*********************************************************************************************/
 130 void MothurOut::mothurOutEndLine() {
 131         try {
 132                 #ifdef USE_MPI
 133                         int pid;
 134                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 135
 136                         if (pid == 0) { //only one process should output to screen
 137                 #endif
 138
 139                 cout << endl;
 140                 out << endl;
 141
 142                 #ifdef USE_MPI
 143                         }
 144                 #endif
 145         }
 146         catch(exception& e) {
 147                 errorOut(e, "MothurOut", "MothurOutEndLine");
 148                 exit(1);
 149         }
 150 }
 151 /*********************************************************************************************/
 152 void MothurOut::mothurOutJustToLog(string output) {
 153         try {
 154                 #ifdef USE_MPI
 155                         int pid;
 156                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 157
 158                         if (pid == 0) { //only one process should output to screen
 159                 #endif
 160
 161                 out << output;
 162
 163                 #ifdef USE_MPI
 164                         }
 165                 #endif
 166         }
 167         catch(exception& e) {
 168                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 169                 exit(1);
 170         }
 171 }
 172 /*********************************************************************************************/
 173 void MothurOut::errorOut(exception& e, string object, string function) {
 174         //double vm, rss;
 175         //mem_usage(vm, rss);
 176
 177         mothurOut("[ERROR]: ");
 178         mothurOut(toString(e.what()));
 179         mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
 180         mothurOutEndLine();
 181 }
 182 /*********************************************************************************************/
 183 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 184 // process_mem_usage(double &, double &) - takes two doubles by reference,
 185 // attempts to read the system-dependent data for a process' virtual memory
 186 // size and resident set size, and return the results in KB.
 187 //
 188 // On failure, returns 0.0, 0.0
 189 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 190   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 191
 192            vm_usage     = 0.0;
 193            resident_set = 0.0;
 194
 195            // 'file' stat seems to give the most reliable results
 196            //
 197            ifstream stat_stream("/proc/self/stat",ios_base::in);
 198
 199            // dummy vars for leading entries in stat that we don't care about
 200            //
 201            string pid, comm, state, ppid, pgrp, session, tty_nr;
 202            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 203            string utime, stime, cutime, cstime, priority, nice;
 204            string O, itrealvalue, starttime;
 205
 206            // the two fields we want
 207            //
 208            unsigned long vsize;
 209            long rss;
 210
 211            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 212                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 213                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 214                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 215
 216            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 217            vm_usage     = vsize / 1024.0;
 218            resident_set = rss * page_size_kb;
 219
 220            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 221                 return 0;
 222
 223         #else
 224 /*              //windows memory usage
 225                 // Get the list of process identifiers.
 226                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 227
 228                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 229
 230                 // Calculate how many process identifiers were returned.
 231                 cProcesses = cbNeeded / sizeof(DWORD);
 232
 233                 // Print the memory usage for each process
 234                 for (int i = 0; i < cProcesses; i++ ) {
 235                         DWORD processID = aProcesses[i];
 236
 237                         PROCESS_MEMORY_COUNTERS pmc;
 238
 239                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 240
 241                         // Print the process identifier.
 242                         printf( "\nProcess ID: %u\n", processID);
 243
 244                         if (NULL != hProcess) {
 245
 246                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 247                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 248                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 249                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 250                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 251                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 252                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 253                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 254                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 255                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 256                                 }
 257                                 CloseHandle(hProcess);
 258                         }
 259                 }
 260 */
 261                         return 0;
 262
 263         #endif
 264 }
 265
 266
 267 /***********************************************************************/
 268 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 269         try {
 270                 fileName = getFullPathName(fileName);
 271
 272                 fileHandle.open(fileName.c_str(), ios::app);
 273                 if(!fileHandle) {
 274                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 275                         return 1;
 276                 }
 277                 else {
 278                         return 0;
 279                 }
 280         }
 281         catch(exception& e) {
 282                 errorOut(e, "MothurOut", "openOutputFileAppend");
 283                 exit(1);
 284         }
 285 }
 286 /***********************************************************************/
 287 void MothurOut::gobble(istream& f){
 288         try {
 289
 290                 char d;
 291                 while(isspace(d=f.get()))               { ;}
 292                 f.putback(d);
 293         }
 294         catch(exception& e) {
 295                 errorOut(e, "MothurOut", "gobble");
 296                 exit(1);
 297         }
 298 }
 299 /***********************************************************************/
 300 void MothurOut::gobble(istringstream& f){
 301         try {
 302                 char d;
 303                 while(isspace(d=f.get()))               {;}
 304                 f.putback(d);
 305         }
 306         catch(exception& e) {
 307                 errorOut(e, "MothurOut", "gobble");
 308                 exit(1);
 309         }
 310 }
 311
 312 /***********************************************************************/
 313
 314 string MothurOut::getline(istringstream& fileHandle) {
 315         try {
 316
 317                 string line = "";
 318
 319                 while (!fileHandle.eof())       {
 320                         //get next character
 321                         char c = fileHandle.get();
 322
 323                         //are you at the end of the line
 324                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 325                         else {          line += c;              }
 326                 }
 327
 328                 return line;
 329
 330         }
 331         catch(exception& e) {
 332                 errorOut(e, "MothurOut", "getline");
 333                 exit(1);
 334         }
 335 }
 336 /***********************************************************************/
 337
 338 string MothurOut::getline(ifstream& fileHandle) {
 339         try {
 340
 341                 string line = "";
 342
 343                 while (!fileHandle.eof())       {
 344                         //get next character
 345                         char c = fileHandle.get();
 346
 347                         //are you at the end of the line
 348                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 349                         else {          line += c;              }
 350                 }
 351
 352                 return line;
 353
 354         }
 355         catch(exception& e) {
 356                 errorOut(e, "MothurOut", "getline");
 357                 exit(1);
 358         }
 359 }
 360 /***********************************************************************/
 361
 362 #ifdef USE_COMPRESSION
 363 inline bool endsWith(string s, const char * suffix){
 364   size_t suffixLength = strlen(suffix);
 365   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 366 }
 367 #endif
 368
 369 string MothurOut::getRootName(string longName){
 370         try {
 371
 372                 string rootName = longName;
 373
 374 #ifdef USE_COMPRESSION
 375     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 376       int pos = rootName.find_last_of('.');
 377       rootName = rootName.substr(0, pos);
 378       cerr << "shortening " << longName << " to " << rootName << "\n";
 379     }
 380 #endif
 381
 382                 if(rootName.find_last_of(".") != rootName.npos){
 383                         int pos = rootName.find_last_of('.')+1;
 384                         rootName = rootName.substr(0, pos);
 385                 }
 386
 387                 return rootName;
 388         }
 389         catch(exception& e) {
 390                 errorOut(e, "MothurOut", "getRootName");
 391                 exit(1);
 392         }
 393 }
 394 /***********************************************************************/
 395
 396 string MothurOut::getSimpleName(string longName){
 397         try {
 398                 string simpleName = longName;
 399
 400                 size_t found;
 401                 found=longName.find_last_of("/\\");
 402
 403                 if(found != longName.npos){
 404                         simpleName = longName.substr(found+1);
 405                 }
 406
 407                 return simpleName;
 408         }
 409         catch(exception& e) {
 410                 errorOut(e, "MothurOut", "getSimpleName");
 411                 exit(1);
 412         }
 413 }
 414
 415 /***********************************************************************/
 416
 417 string MothurOut::getPathName(string longName){
 418         try {
 419                 string rootPathName = longName;
 420
 421                 if(longName.find_last_of("/\\") != longName.npos){
 422                         int pos = longName.find_last_of("/\\")+1;
 423                         rootPathName = longName.substr(0, pos);
 424                 }
 425
 426                 return rootPathName;
 427         }
 428         catch(exception& e) {
 429                 errorOut(e, "MothurOut", "getPathName");
 430                 exit(1);
 431         }
 432
 433 }
 434 /***********************************************************************/
 435
 436 string MothurOut::hasPath(string longName){
 437         try {
 438                 string path = "";
 439
 440                 size_t found;
 441                 found=longName.find_last_of("~/\\");
 442
 443                 if(found != longName.npos){
 444                         path = longName.substr(0, found+1);
 445                 }
 446
 447                 return path;
 448         }
 449         catch(exception& e) {
 450                 errorOut(e, "MothurOut", "hasPath");
 451                 exit(1);
 452         }
 453 }
 454
 455 /***********************************************************************/
 456
 457 string MothurOut::getExtension(string longName){
 458         try {
 459                 string extension = longName;
 460
 461                 if(longName.find_last_of('.') != longName.npos){
 462                         int pos = longName.find_last_of('.');
 463                         extension = longName.substr(pos, longName.length());
 464                 }
 465
 466                 return extension;
 467         }
 468         catch(exception& e) {
 469                 errorOut(e, "MothurOut", "getExtension");
 470                 exit(1);
 471         }
 472 }
 473 /***********************************************************************/
 474 bool MothurOut::isBlank(string fileName){
 475         try {
 476
 477                 fileName = getFullPathName(fileName);
 478
 479                 ifstream fileHandle;
 480                 fileHandle.open(fileName.c_str());
 481                 if(!fileHandle) {
 482                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 483                         return false;
 484                 }else {
 485                         //check for blank file
 486                         gobble(fileHandle);
 487                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 488                 }
 489                 return false;
 490         }
 491         catch(exception& e) {
 492                 errorOut(e, "MothurOut", "isBlank");
 493                 exit(1);
 494         }
 495 }
 496 /***********************************************************************/
 497
 498 string MothurOut::getFullPathName(string fileName){
 499         try{
 500
 501         string path = hasPath(fileName);
 502         string newFileName;
 503         int pos;
 504
 505         if (path == "") { return fileName; } //its a simple name
 506         else { //we need to complete the pathname
 507                 // ex. ../../../filename
 508                 // cwd = /user/work/desktop
 509
 510                 string cwd;
 511                 //get current working directory
 512                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 513
 514                         if (path.find("~") != -1) { //go to home directory
 515                                 string homeDir;
 516
 517                                 char *homepath = NULL;
 518                                 homepath = getenv ("HOME");
 519                                 if ( homepath != NULL) { homeDir = homepath; }
 520                                 else { homeDir = "";  }
 521
 522                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 523                                 return newFileName;
 524                         }else { //find path
 525                                 if (path.rfind("./") == -1) { return fileName; } //already complete name
 526                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 527
 528                                 //char* cwdpath = new char[1024];
 529                                 //size_t size;
 530                                 //cwdpath=getcwd(cwdpath,size);
 531                                 //cwd = cwdpath;
 532
 533                                 char *cwdpath = NULL;
 534                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 535                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 536                                 else { cwd = "";  }
 537
 538
 539                                 //rip off first '/'
 540                                 string simpleCWD;
 541                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 542
 543                                 //break apart the current working directory
 544                                 vector<string> dirs;
 545                                 while (simpleCWD.find_first_of('/') != -1) {
 546                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 547                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 548                                         dirs.push_back(dir);
 549                                 }
 550                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 551                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 552
 553
 554                                 int index = dirs.size()-1;
 555
 556                                 while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
 557                                         if (pos == 0) { break;  //you are at the end
 558                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 559                                                 path = path.substr(0, pos-1);
 560                                                 index--;
 561                                                 if (index == 0) {  break; }
 562                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 563                                                 path = path.substr(0, pos);
 564                                         }else if (pos == 1) { break;  //you are at the end
 565                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 566                                 }
 567
 568                                 for (int i = index; i >= 0; i--) {
 569                                         newFileName = dirs[i] +  "/" + newFileName;
 570                                 }
 571
 572                                 newFileName =  "/" +  newFileName;
 573                                 return newFileName;
 574                         }
 575                 #else
 576                         if (path.find("~") != -1) { //go to home directory
 577                                 string homeDir = getenv ("HOMEPATH");
 578                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 579                                 return newFileName;
 580                         }else { //find path
 581                                 if (path.rfind(".\\") == -1) { return fileName; } //already complete name
 582                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 583
 584                                 char *cwdpath = NULL;
 585                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 586                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 587                                 else { cwd = "";  }
 588
 589                                 //break apart the current working directory
 590                                 vector<string> dirs;
 591                                 while (cwd.find_first_of('\\') != -1) {
 592                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 593                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 594                                         dirs.push_back(dir);
 595
 596                                 }
 597                                 //get last one
 598                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 599
 600                                 int index = dirs.size()-1;
 601
 602                                 while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
 603                                         if (pos == 0) { break;  //you are at the end
 604                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 605                                                 path = path.substr(0, pos-1);
 606                                                 index--;
 607                                                 if (index == 0) {  break; }
 608                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 609                                                 path = path.substr(0, pos);
 610                                         }else if (pos == 1) { break;  //you are at the end
 611                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 612                                 }
 613
 614                                 for (int i = index; i >= 0; i--) {
 615                                         newFileName = dirs[i] +  "\\" + newFileName;
 616                                 }
 617
 618                                 return newFileName;
 619                         }
 620
 621                 #endif
 622         }
 623         }
 624         catch(exception& e) {
 625                 errorOut(e, "MothurOut", "getFullPathName");
 626                 exit(1);
 627         }
 628 }
 629 /***********************************************************************/
 630
 631 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 632         try {
 633                         //get full path name
 634                         string completeFileName = getFullPathName(fileName);
 635
 636 #ifdef USE_COMPRESSION
 637       // check for gzipped or bzipped file
 638       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 639         string tempName = string(tmpnam(0));
 640         mkfifo(tempName.c_str(), 0666);
 641         int fork_result = fork();
 642         if (fork_result < 0) {
 643           cerr << "Error forking.\n";
 644           exit(1);
 645         } else if (fork_result == 0) {
 646           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 647           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 648           system(command.c_str());
 649           cerr << "Done decompressing " << completeFileName << "\n";
 650           remove(tempName.c_str());
 651           exit(EXIT_SUCCESS);
 652         } else {
 653           cerr << "waiting on child process " << fork_result << "\n";
 654           completeFileName = tempName;
 655         }
 656       }
 657 #endif
 658
 659                         fileHandle.open(completeFileName.c_str());
 660                         if(!fileHandle) {
 661                                 return 1;
 662                         }else {
 663                                 //check for blank file
 664                                 gobble(fileHandle);
 665                                 return 0;
 666                         }
 667         }
 668         catch(exception& e) {
 669                 errorOut(e, "MothurOut", "openInputFile - no Error");
 670                 exit(1);
 671         }
 672 }
 673 /***********************************************************************/
 674
 675 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 676         try {
 677
 678                 //get full path name
 679                 string completeFileName = getFullPathName(fileName);
 680
 681 #ifdef USE_COMPRESSION
 682   // check for gzipped or bzipped file
 683   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 684     string tempName = string(tmpnam(0));
 685     mkfifo(tempName.c_str(), 0666);
 686     int fork_result = fork();
 687     if (fork_result < 0) {
 688       cerr << "Error forking.\n";
 689       exit(1);
 690     } else if (fork_result == 0) {
 691       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 692       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 693       system(command.c_str());
 694       cerr << "Done decompressing " << completeFileName << "\n";
 695       remove(tempName.c_str());
 696       exit(EXIT_SUCCESS);
 697     } else {
 698       cerr << "waiting on child process " << fork_result << "\n";
 699       completeFileName = tempName;
 700     }
 701   }
 702 #endif
 703
 704
 705                 fileHandle.open(completeFileName.c_str());
 706                 if(!fileHandle) {
 707                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 708                         return 1;
 709                 }
 710                 else {
 711                         //check for blank file
 712                         gobble(fileHandle);
 713                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 714
 715                         return 0;
 716                 }
 717         }
 718         catch(exception& e) {
 719                 errorOut(e, "MothurOut", "openInputFile");
 720                 exit(1);
 721         }
 722 }
 723 /***********************************************************************/
 724
 725 int MothurOut::renameFile(string oldName, string newName){
 726         try {
 727                 ifstream inTest;
 728                 int exist = openInputFile(newName, inTest, "");
 729
 730         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 731                 if (exist == 0) { //you could open it so you want to delete it
 732                         inTest.close();
 733                         string command = "rm " + newName;
 734                         system(command.c_str());
 735                 }
 736
 737                 string command = "mv " + oldName + " " + newName;
 738                 system(command.c_str());
 739         #else
 740                 remove(newName.c_str());
 741                 int renameOk = rename(oldName.c_str(), newName.c_str());
 742         #endif
 743                 return 0;
 744
 745         }
 746         catch(exception& e) {
 747                 errorOut(e, "MothurOut", "renameFile");
 748                 exit(1);
 749         }
 750 }
 751
 752 /***********************************************************************/
 753
 754 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 755         try {
 756
 757                 string completeFileName = getFullPathName(fileName);
 758
 759 #ifdef USE_COMPRESSION
 760     // check for gzipped file
 761     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 762       string tempName = string(tmpnam(0));
 763       mkfifo(tempName.c_str(), 0666);
 764       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 765       int fork_result = fork();
 766       if (fork_result < 0) {
 767         cerr << "Error forking.\n";
 768         exit(1);
 769       } else if (fork_result == 0) {
 770         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 771         system(command.c_str());
 772         exit(0);
 773       } else {
 774         completeFileName = tempName;
 775       }
 776     }
 777 #endif
 778
 779                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 780                 if(!fileHandle) {
 781                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 782                         return 1;
 783                 }
 784                 else {
 785                         return 0;
 786                 }
 787         }
 788         catch(exception& e) {
 789                 errorOut(e, "MothurOut", "openOutputFile");
 790                 exit(1);
 791         }
 792
 793 }
 794
 795 /**************************************************************************************************/
 796 void MothurOut::appendFiles(string temp, string filename) {
 797         try{
 798                 ofstream output;
 799                 ifstream input;
 800
 801                 //open output file in append mode
 802                 openOutputFileAppend(filename, output);
 803                 int ableToOpen = openInputFile(temp, input, "no error");
 804
 805                 if (ableToOpen == 0) { //you opened it
 806                         while(char c = input.get()){
 807                                 if(input.eof())         {       break;                  }
 808                                 else                            {       output << c;    }
 809                         }
 810                         input.close();
 811                 }
 812
 813                 output.close();
 814         }
 815         catch(exception& e) {
 816                 errorOut(e, "MothurOut", "appendFiles");
 817                 exit(1);
 818         }
 819 }
 820
 821 /**************************************************************************************************/
 822 string MothurOut::sortFile(string distFile, string outputDir){
 823         try {
 824
 825                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 826                 string outfile = getRootName(distFile) + "sorted.dist";
 827
 828
 829                 //if you can, use the unix sort since its been optimized for years
 830                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 831                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 832                         system(command.c_str());
 833                 #else //you are stuck with my best attempt...
 834                         //windows sort does not have a way to specify a column, only a character in the line
 835                         //since we cannot assume that the distance will always be at the the same character location on each line
 836                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 837
 838                         //read in file line by file and put distance first
 839                         string tempDistFile = distFile + ".temp";
 840                         ifstream input;
 841                         ofstream output;
 842                         openInputFile(distFile, input);
 843                         openOutputFile(tempDistFile, output);
 844
 845                         string firstName, secondName;
 846                         float dist;
 847                         while (input) {
 848                                 input >> firstName >> secondName >> dist;
 849                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 850                                 gobble(input);
 851                         }
 852                         input.close();
 853                         output.close();
 854
 855
 856                         //sort using windows sort
 857                         string tempOutfile = outfile + ".temp";
 858                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 859                         system(command.c_str());
 860
 861                         //read in sorted file and put distance at end again
 862                         ifstream input2;
 863                         openInputFile(tempOutfile, input2);
 864                         openOutputFile(outfile, output);
 865
 866                         while (input2) {
 867                                 input2 >> dist >> firstName >> secondName;
 868                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 869                                 gobble(input2);
 870                         }
 871                         input2.close();
 872                         output.close();
 873
 874                         //remove temp files
 875                         remove(tempDistFile.c_str());
 876                         remove(tempOutfile.c_str());
 877                 #endif
 878
 879                 return outfile;
 880         }
 881         catch(exception& e) {
 882                 errorOut(e, "MothurOut", "sortFile");
 883                 exit(1);
 884         }
 885 }
 886 /**************************************************************************************************/
 887 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
 888         try {
 889                         vector<unsigned long int> positions;
 890                         ifstream inFASTA;
 891                         openInputFile(filename, inFASTA);
 892
 893                         string input;
 894                         while(!inFASTA.eof()){
 895                                 input = getline(inFASTA);
 896                                 if (input.length() != 0) {
 897                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 898                                 }
 899                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
 900                         }
 901                         inFASTA.close();
 902
 903                         num = positions.size();
 904
 905                         /*FILE * pFile;
 906                         long size;
 907
 908                         //get num bytes in file
 909                         pFile = fopen (filename.c_str(),"rb");
 910                         if (pFile==NULL) perror ("Error opening file");
 911                         else{
 912                                 fseek (pFile, 0, SEEK_END);
 913                                 size=ftell (pFile);
 914                                 fclose (pFile);
 915                         }*/
 916
 917                         unsigned long int size = positions[(positions.size()-1)];
 918                         ifstream in;
 919                         openInputFile(filename, in);
 920
 921                         in.seekg(size);
 922
 923                         while(char c = in.get()){
 924                                 if(in.eof())            {       break;  }
 925                                 else                            {       size++; }
 926                         }
 927                         in.close();
 928
 929                         positions.push_back(size);
 930
 931                         return positions;
 932         }
 933         catch(exception& e) {
 934                 errorOut(e, "MothurOut", "setFilePosFasta");
 935                 exit(1);
 936         }
 937 }
 938 /**************************************************************************************************/
 939 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
 940         try {
 941                         filename = getFullPathName(filename);
 942
 943                         vector<unsigned long int> positions;
 944                         ifstream in;
 945                         openInputFile(filename, in);
 946
 947                         string input;
 948                         while(!in.eof()){
 949                                 unsigned long int lastpos = in.tellg();
 950                                 input = getline(in);
 951                                 if (input.length() != 0) {
 952                                         unsigned long int pos = in.tellg();
 953                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
 954                                         else {  positions.push_back(lastpos);  }
 955                                 }
 956                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
 957                         }
 958                         in.close();
 959
 960                         num = positions.size();
 961
 962                         FILE * pFile;
 963                         unsigned long int size;
 964
 965                         //get num bytes in file
 966                         pFile = fopen (filename.c_str(),"rb");
 967                         if (pFile==NULL) perror ("Error opening file");
 968                         else{
 969                                 fseek (pFile, 0, SEEK_END);
 970                                 size=ftell (pFile);
 971                                 fclose (pFile);
 972                         }
 973
 974                         positions.push_back(size);
 975
 976                         return positions;
 977         }
 978         catch(exception& e) {
 979                 errorOut(e, "MothurOut", "setFilePosEachLine");
 980                 exit(1);
 981         }
 982 }
 983 /**************************************************************************************************/
 984
 985 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 986         try{
 987
 988                 vector<unsigned long int> filePos;
 989                 filePos.push_back(0);
 990
 991                 FILE * pFile;
 992                 unsigned long int size;
 993
 994                 filename = getFullPathName(filename);
 995
 996                 //get num bytes in file
 997                 pFile = fopen (filename.c_str(),"rb");
 998                 if (pFile==NULL) perror ("Error opening file");
 999                 else{
1000                         fseek (pFile, 0, SEEK_END);
1001                         size=ftell (pFile);
1002                         fclose (pFile);
1003                 }
1004
1005                 //estimate file breaks
1006                 unsigned long int chunkSize = 0;
1007                 chunkSize = size / proc;
1008
1009                 //file to small to divide by processors
1010                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1011
1012                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1013                 for (int i = 0; i < proc; i++) {
1014                         unsigned long int spot = (i+1) * chunkSize;
1015
1016                         ifstream in;
1017                         openInputFile(filename, in);
1018                         in.seekg(spot);
1019
1020                         //look for next '>'
1021                         unsigned long int newSpot = spot;
1022                         while (!in.eof()) {
1023                            char c = in.get();
1024                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1025                         }
1026
1027                         //there was not another sequence before the end of the file
1028                         unsigned long int sanityPos = in.tellg();
1029
1030                         if (sanityPos == -1) {  break;  }
1031                         else {  filePos.push_back(newSpot);  }
1032
1033                         in.close();
1034                 }
1035
1036                 //save end pos
1037                 filePos.push_back(size);
1038
1039                 //sanity check filePos
1040                 for (int i = 0; i < (filePos.size()-1); i++) {
1041                         if (filePos[(i+1)] <= filePos[i]) {  cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
1042                 }
1043
1044                 proc = (filePos.size() - 1);
1045
1046                 return filePos;
1047         }
1048         catch(exception& e) {
1049                 errorOut(e, "MothurOut", "divideFile");
1050                 exit(1);
1051         }
1052 }
1053
1054 /***********************************************************************/
1055
1056 bool MothurOut::isTrue(string f){
1057         try {
1058
1059                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1060
1061                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1062                 else {  return false;  }
1063         }
1064         catch(exception& e) {
1065                 errorOut(e, "MothurOut", "isTrue");
1066                 exit(1);
1067         }
1068 }
1069
1070 /***********************************************************************/
1071
1072 float MothurOut::roundDist(float dist, int precision){
1073         try {
1074                 return int(dist * precision + 0.5)/float(precision);
1075         }
1076         catch(exception& e) {
1077                 errorOut(e, "MothurOut", "roundDist");
1078                 exit(1);
1079         }
1080 }
1081 /***********************************************************************/
1082
1083 float MothurOut::ceilDist(float dist, int precision){
1084         try {
1085                 return int(ceil(dist * precision))/float(precision);
1086         }
1087         catch(exception& e) {
1088                 errorOut(e, "MothurOut", "ceilDist");
1089                 exit(1);
1090         }
1091 }
1092
1093 /***********************************************************************/
1094
1095 int MothurOut::getNumNames(string names){
1096         try {
1097                 int count = 0;
1098
1099                 if(names != ""){
1100                         count = 1;
1101                         for(int i=0;i<names.size();i++){
1102                                 if(names[i] == ','){
1103                                         count++;
1104                                 }
1105                         }
1106                 }
1107
1108                 return count;
1109         }
1110         catch(exception& e) {
1111                 errorOut(e, "MothurOut", "getNumNames");
1112                 exit(1);
1113         }
1114 }
1115
1116 /**************************************************************************************************/
1117
1118 vector<vector<double> > MothurOut::binomial(int maxOrder){
1119         try {
1120         vector<vector<double> > binomial(maxOrder+1);
1121
1122     for(int i=0;i<=maxOrder;i++){
1123                 binomial[i].resize(maxOrder+1);
1124                 binomial[i][0]=1;
1125                 binomial[0][i]=0;
1126     }
1127     binomial[0][0]=1;
1128
1129     binomial[1][0]=1;
1130     binomial[1][1]=1;
1131
1132     for(int i=2;i<=maxOrder;i++){
1133                 binomial[1][i]=0;
1134     }
1135
1136     for(int i=2;i<=maxOrder;i++){
1137                 for(int j=1;j<=maxOrder;j++){
1138                         if(i==j){       binomial[i][j]=1;                                                                       }
1139                         if(j>i) {       binomial[i][j]=0;                                                                       }
1140                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1141                 }
1142     }
1143
1144         return binomial;
1145
1146         }
1147         catch(exception& e) {
1148                 errorOut(e, "MothurOut", "binomial");
1149                 exit(1);
1150         }
1151 }
1152
1153 /***********************************************************************/
1154
1155 int MothurOut::factorial(int num){
1156         try {
1157                 int total = 1;
1158
1159                 for (int i = 1; i <= num; i++) {
1160                         total *= i;
1161                 }
1162
1163                 return total;
1164         }
1165         catch(exception& e) {
1166                 errorOut(e, "MothurOut", "factorial");
1167                 exit(1);
1168         }
1169 }
1170 /***********************************************************************/
1171
1172 int MothurOut::getNumSeqs(ifstream& file){
1173         try {
1174                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1175                 file.seekg(0);
1176                 return numSeqs;
1177         }
1178         catch(exception& e) {
1179                 errorOut(e, "MothurOut", "getNumSeqs");
1180                 exit(1);
1181         }
1182 }
1183 /***********************************************************************/
1184 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1185         try {
1186                 string input;
1187                 numSeqs = 0;
1188                 while(!file.eof()){
1189                         input = getline(file);
1190                         if (input.length() != 0) {
1191                                 if(input[0] == '>'){ numSeqs++; }
1192                         }
1193                 }
1194         }
1195         catch(exception& e) {
1196                 errorOut(e, "MothurOut", "getNumSeqs");
1197                 exit(1);
1198         }
1199 }
1200 /***********************************************************************/
1201
1202 //This function parses the estimator options and puts them in a vector
1203 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1204         try {
1205                 string individual = "";
1206                 int estimLength = estim.size();
1207                 for(int i=0;i<estimLength;i++){
1208                         if(estim[i] == symbol){
1209                                 container.push_back(individual);
1210                                 individual = "";
1211                         }
1212                         else{
1213                                 individual += estim[i];
1214                         }
1215                 }
1216                 container.push_back(individual);
1217
1218                 /*
1219
1220                 while (estim.find_first_of(symbol) != -1) {
1221                         individual = estim.substr(0,estim.find_first_of(symbol));
1222                         if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1223                                 estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
1224                                 container.push_back(individual);
1225                         }
1226                 }
1227                 //get last one
1228                 container.push_back(estim); */
1229         }
1230         catch(exception& e) {
1231                 errorOut(e, "MothurOut", "splitAtChar");
1232                 exit(1);
1233         }
1234 }
1235
1236 /***********************************************************************/
1237
1238 //This function parses the estimator options and puts them in a vector
1239 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1240         try {
1241                 string individual = "";
1242                 int estimLength = estim.size();
1243                 for(int i=0;i<estimLength;i++){
1244                         if(estim[i] == '-'){
1245                                 container.push_back(individual);
1246                                 individual = "";
1247                         }
1248                         else{
1249                                 individual += estim[i];
1250                         }
1251                 }
1252                 container.push_back(individual);
1253
1254
1255         /*      string individual;
1256
1257                 while (estim.find_first_of('-') != -1) {
1258                         individual = estim.substr(0,estim.find_first_of('-'));
1259                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1260                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1261                                 container.push_back(individual);
1262                         }
1263                 }
1264                 //get last one
1265                 container.push_back(estim); */
1266         }
1267         catch(exception& e) {
1268                 errorOut(e, "MothurOut", "splitAtDash");
1269                 exit(1);
1270         }
1271 }
1272
1273 /***********************************************************************/
1274 //This function parses the label options and puts them in a set
1275 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1276         try {
1277                 string individual = "";
1278                 int estimLength = estim.size();
1279                 for(int i=0;i<estimLength;i++){
1280                         if(estim[i] == '-'){
1281                                 container.insert(individual);
1282                                 individual = "";
1283                         }
1284                         else{
1285                                 individual += estim[i];
1286                         }
1287                 }
1288                 container.insert(individual);
1289
1290         //      string individual;
1291
1292         //      while (estim.find_first_of('-') != -1) {
1293         //              individual = estim.substr(0,estim.find_first_of('-'));
1294         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1295         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1296         //                      container.insert(individual);
1297         //              }
1298         //      }
1299                 //get last one
1300         //      container.insert(estim);
1301
1302         }
1303         catch(exception& e) {
1304                 errorOut(e, "MothurOut", "splitAtDash");
1305                 exit(1);
1306         }
1307 }
1308 /***********************************************************************/
1309 //This function parses the line options and puts them in a set
1310 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1311         try {
1312                 string individual;
1313                 int lineNum;
1314
1315                 while (estim.find_first_of('-') != -1) {
1316                         individual = estim.substr(0,estim.find_first_of('-'));
1317                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1318                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1319                                 convert(individual, lineNum); //convert the string to int
1320                                 container.insert(lineNum);
1321                         }
1322                 }
1323                 //get last one
1324                 convert(estim, lineNum); //convert the string to int
1325                 container.insert(lineNum);
1326         }
1327         catch(exception& e) {
1328                 errorOut(e, "MothurOut", "splitAtDash");
1329                 exit(1);
1330         }
1331 }
1332 /***********************************************************************/
1333 //This function parses the a string and puts peices in a vector
1334 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1335         try {
1336                 string individual = "";
1337                 int estimLength = estim.size();
1338                 for(int i=0;i<estimLength;i++){
1339                         if(estim[i] == ','){
1340                                 container.push_back(individual);
1341                                 individual = "";
1342                         }
1343                         else{
1344                                 individual += estim[i];
1345                         }
1346                 }
1347                 container.push_back(individual);
1348
1349
1350
1351
1352 //              string individual;
1353 //
1354 //              while (estim.find_first_of(',') != -1) {
1355 //                      individual = estim.substr(0,estim.find_first_of(','));
1356 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1357 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1358 //                              container.push_back(individual);
1359 //                      }
1360 //              }
1361 //              //get last one
1362 //              container.push_back(estim);
1363         }
1364         catch(exception& e) {
1365                 errorOut(e, "MothurOut", "splitAtComma");
1366                 exit(1);
1367         }
1368 }
1369 /***********************************************************************/
1370
1371 //This function splits up the various option parameters
1372 void MothurOut::splitAtComma(string& prefix, string& suffix){
1373         try {
1374                 prefix = suffix.substr(0,suffix.find_first_of(','));
1375                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1376                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1377                         string space = " ";
1378                         while(suffix.at(0) == ' ')
1379                                 suffix = suffix.substr(1, suffix.length());
1380                 }
1381
1382         }
1383         catch(exception& e) {
1384                 errorOut(e, "MothurOut", "splitAtComma");
1385                 exit(1);
1386         }
1387 }
1388 /***********************************************************************/
1389
1390 //This function separates the key value from the option value i.e. dist=96_...
1391 void MothurOut::splitAtEquals(string& key, string& value){
1392         try {
1393                 if(value.find_first_of('=') != -1){
1394                         key = value.substr(0,value.find_first_of('='));
1395                         if ((value.find_first_of('=')+1) <= value.length()) {
1396                                 value = value.substr(value.find_first_of('=')+1, value.length());
1397                         }
1398                 }else{
1399                         key = value;
1400                         value = 1;
1401                 }
1402         }
1403         catch(exception& e) {
1404                 errorOut(e, "MothurOut", "splitAtEquals");
1405                 exit(1);
1406         }
1407 }
1408
1409 /**************************************************************************************************/
1410
1411 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1412         try {
1413                 for (int i = 0; i < Groups.size(); i++) {
1414                         if (groupname == Groups[i]) { return true; }
1415                 }
1416                 return false;
1417         }
1418         catch(exception& e) {
1419                 errorOut(e, "MothurOut", "inUsersGroups");
1420                 exit(1);
1421         }
1422 }
1423 /**************************************************************************************************/
1424 //returns true if any of the strings in first vector are in second vector
1425 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1426         try {
1427
1428                 for (int i = 0; i < groupnames.size(); i++) {
1429                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1430                 }
1431                 return false;
1432         }
1433         catch(exception& e) {
1434                 errorOut(e, "MothurOut", "inUsersGroups");
1435                 exit(1);
1436         }
1437 }
1438 /***********************************************************************/
1439 //this function determines if the user has given us labels that are smaller than the given label.
1440 //if so then it returns true so that the calling function can run the previous valid distance.
1441 //it's a "smart" distance function.  It also checks for invalid labels.
1442 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1443         try {
1444
1445                 set<string>::iterator it;
1446                 vector<float> orderFloat;
1447                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1448                 map<string, float>::iterator it2;
1449                 float labelFloat;
1450                 bool smaller = false;
1451
1452                 //unique is the smallest line
1453                 if (label == "unique") {  return false;  }
1454                 else {
1455                         if (convertTestFloat(label, labelFloat)) {
1456                                 convert(label, labelFloat);
1457                         }else { //cant convert
1458                                 return false;
1459                         }
1460                 }
1461
1462                 //go through users set and make them floats
1463                 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
1464
1465                         float temp;
1466                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1467                                 convert(*it, temp);
1468                                 orderFloat.push_back(temp);
1469                                 userMap[*it] = temp;
1470                         }else if (*it == "unique") {
1471                                 orderFloat.push_back(-1.0);
1472                                 userMap["unique"] = -1.0;
1473                         }else {
1474                                 if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
1475                                 userLabels.erase(*it);
1476                                 it--;
1477                         }
1478                 }
1479
1480                 //sort order
1481                 sort(orderFloat.begin(), orderFloat.end());
1482
1483                 /*************************************************/
1484                 //is this label bigger than any of the users labels
1485                 /*************************************************/
1486
1487                 //loop through order until you find a label greater than label
1488                 for (int i = 0; i < orderFloat.size(); i++) {
1489                         if (orderFloat[i] < labelFloat) {
1490                                 smaller = true;
1491                                 if (orderFloat[i] == -1) {
1492                                         if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
1493                                         userLabels.erase("unique");
1494                                 }
1495                                 else {
1496                                         if (errorOff == "") { cout << "Your file does not include the label " << endl; }
1497                                         string s = "";
1498                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1499                                                 if (it2->second == orderFloat[i]) {
1500                                                         s = it2->first;
1501                                                         //remove small labels
1502                                                         userLabels.erase(s);
1503                                                         break;
1504                                                 }
1505                                         }
1506                                         if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
1507                                 }
1508                         //since they are sorted once you find a bigger one stop looking
1509                         }else { break; }
1510                 }
1511
1512                 return smaller;
1513
1514         }
1515         catch(exception& e) {
1516                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1517                 exit(1);
1518         }
1519 }
1520
1521 /**************************************************************************************************/
1522 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1523         try {
1524
1525                 bool good = true;
1526
1527                 string line = getline(file);
1528
1529                 //before we added this check
1530                 if (line[0] != '#') {  good = false;  }
1531                 else {
1532                         //rip off #
1533                         line = line.substr(1);
1534
1535                         vector<string> versionVector;
1536                         splitAtChar(version, versionVector, '.');
1537
1538                         //check file version
1539                         vector<string> linesVector;
1540                         splitAtChar(line, linesVector, '.');
1541
1542                         if (versionVector.size() != linesVector.size()) { good = false; }
1543                         else {
1544                                 for (int j = 0; j < versionVector.size(); j++) {
1545                                         int num1, num2;
1546                                         convert(versionVector[j], num1);
1547                                         convert(linesVector[j], num2);
1548
1549                                         //if mothurs version is newer than this files version, then we want to remake it
1550                                         if (num1 > num2) {  good = false; break;  }
1551                                 }
1552                         }
1553
1554                 }
1555
1556                 if (!good) {  file.close();  }
1557                 else { file.seekg(0);  }
1558
1559                 return good;
1560         }
1561         catch(exception& e) {
1562                 errorOut(e, "MothurOut", "checkReleaseVersion");
1563                 exit(1);
1564         }
1565 }
1566 /**************************************************************************************************/
1567
1568
1569
1570
1571