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 /******************************************************/
  14 MothurOut* MothurOut::getInstance() {
  15         if( _uniqueInstance == 0) {
  16                 _uniqueInstance = new MothurOut();
  17         }
  18         return _uniqueInstance;
  19 }
  20 /*********************************************************************************************/
  21 void MothurOut::setFileName(string filename)  {
  22         try {
  23                 logFileName = filename;
  24
  25                 #ifdef USE_MPI
  26                         int pid;
  27                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  28
  29                         if (pid == 0) { //only one process should output to screen
  30                 #endif
  31
  32                 openOutputFile(filename, out);
  33
  34                 #ifdef USE_MPI
  35                         }
  36                 #endif
  37         }
  38         catch(exception& e) {
  39                 errorOut(e, "MothurOut", "setFileName");
  40                 exit(1);
  41         }
  42 }
  43 /*********************************************************************************************/
  44 void MothurOut::setDefaultPath(string pathname)  {
  45         try {
  46
  47                 //add / to name if needed
  48                 string lastChar = pathname.substr(pathname.length()-1);
  49                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  50                         if (lastChar != "/") { pathname += "/"; }
  51                 #else
  52                         if (lastChar != "\\") { pathname += "\\"; }
  53                 #endif
  54
  55                 defaultPath = pathname;
  56
  57         }
  58         catch(exception& e) {
  59                 errorOut(e, "MothurOut", "setDefaultPath");
  60                 exit(1);
  61         }
  62 }
  63 /*********************************************************************************************/
  64 void MothurOut::setOutputDir(string pathname)  {
  65         try {
  66                 outputDir = pathname;
  67         }
  68         catch(exception& e) {
  69                 errorOut(e, "MothurOut", "setOutputDir");
  70                 exit(1);
  71         }
  72 }
  73 /*********************************************************************************************/
  74 void MothurOut::closeLog()  {
  75         try {
  76
  77                 #ifdef USE_MPI
  78                         int pid;
  79                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  80
  81                         if (pid == 0) { //only one process should output to screen
  82                 #endif
  83
  84                 out.close();
  85
  86                 #ifdef USE_MPI
  87                         }
  88                 #endif
  89         }
  90         catch(exception& e) {
  91                 errorOut(e, "MothurOut", "closeLog");
  92                 exit(1);
  93         }
  94 }
  95
  96 /*********************************************************************************************/
  97 MothurOut::~MothurOut() {
  98         try {
  99                 _uniqueInstance = 0;
 100
 101         }
 102         catch(exception& e) {
 103                 errorOut(e, "MothurOut", "MothurOut");
 104                 exit(1);
 105         }
 106 }
 107 /*********************************************************************************************/
 108 void MothurOut::mothurOut(string output) {
 109         try {
 110
 111                 #ifdef USE_MPI
 112                         int pid;
 113                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 114
 115                         if (pid == 0) { //only one process should output to screen
 116                 #endif
 117
 118                 cout << output;
 119                 out << output;
 120
 121                 #ifdef USE_MPI
 122                         }
 123                 #endif
 124         }
 125         catch(exception& e) {
 126                 errorOut(e, "MothurOut", "MothurOut");
 127                 exit(1);
 128         }
 129 }
 130 /*********************************************************************************************/
 131 void MothurOut::mothurOutEndLine() {
 132         try {
 133                 #ifdef USE_MPI
 134                         int pid;
 135                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 136
 137                         if (pid == 0) { //only one process should output to screen
 138                 #endif
 139
 140                 cout << endl;
 141                 out << endl;
 142
 143                 #ifdef USE_MPI
 144                         }
 145                 #endif
 146         }
 147         catch(exception& e) {
 148                 errorOut(e, "MothurOut", "MothurOutEndLine");
 149                 exit(1);
 150         }
 151 }
 152 /*********************************************************************************************/
 153 void MothurOut::mothurOutJustToLog(string output) {
 154         try {
 155                 #ifdef USE_MPI
 156                         int pid;
 157                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 158
 159                         if (pid == 0) { //only one process should output to screen
 160                 #endif
 161
 162                 out << output;
 163
 164                 #ifdef USE_MPI
 165                         }
 166                 #endif
 167         }
 168         catch(exception& e) {
 169                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 170                 exit(1);
 171         }
 172 }
 173 /*********************************************************************************************/
 174 void MothurOut::errorOut(exception& e, string object, string function) {
 175         //double vm, rss;
 176         //mem_usage(vm, rss);
 177
 178         mothurOut("[ERROR]: ");
 179         mothurOut(toString(e.what()));
 180         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.");
 181         mothurOutEndLine();
 182 }
 183 /*********************************************************************************************/
 184 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 185 // process_mem_usage(double &, double &) - takes two doubles by reference,
 186 // attempts to read the system-dependent data for a process' virtual memory
 187 // size and resident set size, and return the results in KB.
 188 //
 189 // On failure, returns 0.0, 0.0
 190 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 191   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 192
 193            vm_usage     = 0.0;
 194            resident_set = 0.0;
 195
 196            // 'file' stat seems to give the most reliable results
 197            //
 198            ifstream stat_stream("/proc/self/stat",ios_base::in);
 199
 200            // dummy vars for leading entries in stat that we don't care about
 201            //
 202            string pid, comm, state, ppid, pgrp, session, tty_nr;
 203            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 204            string utime, stime, cutime, cstime, priority, nice;
 205            string O, itrealvalue, starttime;
 206
 207            // the two fields we want
 208            //
 209            unsigned long vsize;
 210            long rss;
 211
 212            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 213                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 214                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 215                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 216
 217            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 218            vm_usage     = vsize / 1024.0;
 219            resident_set = rss * page_size_kb;
 220
 221            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 222                 return 0;
 223
 224         #else
 225 /*              //windows memory usage
 226                 // Get the list of process identifiers.
 227                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 228
 229                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 230
 231                 // Calculate how many process identifiers were returned.
 232                 cProcesses = cbNeeded / sizeof(DWORD);
 233
 234                 // Print the memory usage for each process
 235                 for (int i = 0; i < cProcesses; i++ ) {
 236                         DWORD processID = aProcesses[i];
 237
 238                         PROCESS_MEMORY_COUNTERS pmc;
 239
 240                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 241
 242                         // Print the process identifier.
 243                         printf( "\nProcess ID: %u\n", processID);
 244
 245                         if (NULL != hProcess) {
 246
 247                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 248                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 249                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 250                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 251                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 252                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 253                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 254                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 255                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 256                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 257                                 }
 258                                 CloseHandle(hProcess);
 259                         }
 260                 }
 261 */
 262                         return 0;
 263
 264         #endif
 265 }
 266
 267
 268 /***********************************************************************/
 269 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 270         try {
 271                 fileName = getFullPathName(fileName);
 272
 273                 fileHandle.open(fileName.c_str(), ios::app);
 274                 if(!fileHandle) {
 275                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 276                         return 1;
 277                 }
 278                 else {
 279                         return 0;
 280                 }
 281         }
 282         catch(exception& e) {
 283                 errorOut(e, "MothurOut", "openOutputFileAppend");
 284                 exit(1);
 285         }
 286 }
 287 /***********************************************************************/
 288 void MothurOut::gobble(istream& f){
 289         try {
 290
 291                 char d;
 292                 while(isspace(d=f.get()))               { ;}
 293                 f.putback(d);
 294         }
 295         catch(exception& e) {
 296                 errorOut(e, "MothurOut", "gobble");
 297                 exit(1);
 298         }
 299 }
 300 /***********************************************************************/
 301 void MothurOut::gobble(istringstream& f){
 302         try {
 303                 char d;
 304                 while(isspace(d=f.get()))               {;}
 305                 f.putback(d);
 306         }
 307         catch(exception& e) {
 308                 errorOut(e, "MothurOut", "gobble");
 309                 exit(1);
 310         }
 311 }
 312
 313 /***********************************************************************/
 314
 315 string MothurOut::getline(istringstream& fileHandle) {
 316         try {
 317
 318                 string line = "";
 319
 320                 while (!fileHandle.eof())       {
 321                         //get next character
 322                         char c = fileHandle.get();
 323
 324                         //are you at the end of the line
 325                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 326                         else {          line += c;              }
 327                 }
 328
 329                 return line;
 330
 331         }
 332         catch(exception& e) {
 333                 errorOut(e, "MothurOut", "getline");
 334                 exit(1);
 335         }
 336 }
 337 /***********************************************************************/
 338
 339 string MothurOut::getline(ifstream& fileHandle) {
 340         try {
 341
 342                 string line = "";
 343
 344                 while (!fileHandle.eof())       {
 345                         //get next character
 346                         char c = fileHandle.get();
 347
 348                         //are you at the end of the line
 349                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 350                         else {          line += c;              }
 351                 }
 352
 353                 return line;
 354
 355         }
 356         catch(exception& e) {
 357                 errorOut(e, "MothurOut", "getline");
 358                 exit(1);
 359         }
 360 }
 361 /***********************************************************************/
 362
 363 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 364 #ifdef USE_COMPRESSION
 365 inline bool endsWith(string s, const char * suffix){
 366   size_t suffixLength = strlen(suffix);
 367   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 368 }
 369 #endif
 370 #endif
 371
 372 string MothurOut::getRootName(string longName){
 373         try {
 374
 375                 string rootName = longName;
 376
 377 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 378 #ifdef USE_COMPRESSION
 379     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 380       int pos = rootName.find_last_of('.');
 381       rootName = rootName.substr(0, pos);
 382       cerr << "shortening " << longName << " to " << rootName << "\n";
 383     }
 384 #endif
 385 #endif
 386                 if(rootName.find_last_of(".") != rootName.npos){
 387                         int pos = rootName.find_last_of('.')+1;
 388                         rootName = rootName.substr(0, pos);
 389                 }
 390
 391                 return rootName;
 392         }
 393         catch(exception& e) {
 394                 errorOut(e, "MothurOut", "getRootName");
 395                 exit(1);
 396         }
 397 }
 398 /***********************************************************************/
 399
 400 string MothurOut::getSimpleName(string longName){
 401         try {
 402                 string simpleName = longName;
 403
 404                 size_t found;
 405                 found=longName.find_last_of("/\\");
 406
 407                 if(found != longName.npos){
 408                         simpleName = longName.substr(found+1);
 409                 }
 410
 411                 return simpleName;
 412         }
 413         catch(exception& e) {
 414                 errorOut(e, "MothurOut", "getSimpleName");
 415                 exit(1);
 416         }
 417 }
 418
 419 /***********************************************************************/
 420
 421 string MothurOut::getPathName(string longName){
 422         try {
 423                 string rootPathName = longName;
 424
 425                 if(longName.find_last_of("/\\") != longName.npos){
 426                         int pos = longName.find_last_of("/\\")+1;
 427                         rootPathName = longName.substr(0, pos);
 428                 }
 429
 430                 return rootPathName;
 431         }
 432         catch(exception& e) {
 433                 errorOut(e, "MothurOut", "getPathName");
 434                 exit(1);
 435         }
 436
 437 }
 438 /***********************************************************************/
 439
 440 string MothurOut::hasPath(string longName){
 441         try {
 442                 string path = "";
 443
 444                 size_t found;
 445                 found=longName.find_last_of("~/\\");
 446
 447                 if(found != longName.npos){
 448                         path = longName.substr(0, found+1);
 449                 }
 450
 451                 return path;
 452         }
 453         catch(exception& e) {
 454                 errorOut(e, "MothurOut", "hasPath");
 455                 exit(1);
 456         }
 457 }
 458
 459 /***********************************************************************/
 460
 461 string MothurOut::getExtension(string longName){
 462         try {
 463                 string extension = longName;
 464
 465                 if(longName.find_last_of('.') != longName.npos){
 466                         int pos = longName.find_last_of('.');
 467                         extension = longName.substr(pos, longName.length());
 468                 }
 469
 470                 return extension;
 471         }
 472         catch(exception& e) {
 473                 errorOut(e, "MothurOut", "getExtension");
 474                 exit(1);
 475         }
 476 }
 477 /***********************************************************************/
 478 bool MothurOut::isBlank(string fileName){
 479         try {
 480
 481                 fileName = getFullPathName(fileName);
 482
 483                 ifstream fileHandle;
 484                 fileHandle.open(fileName.c_str());
 485                 if(!fileHandle) {
 486                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 487                         return false;
 488                 }else {
 489                         //check for blank file
 490                         gobble(fileHandle);
 491                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 492                         fileHandle.close();
 493                 }
 494                 return false;
 495         }
 496         catch(exception& e) {
 497                 errorOut(e, "MothurOut", "isBlank");
 498                 exit(1);
 499         }
 500 }
 501 /***********************************************************************/
 502
 503 string MothurOut::getFullPathName(string fileName){
 504         try{
 505
 506         string path = hasPath(fileName);
 507         string newFileName;
 508         int pos;
 509
 510         if (path == "") { return fileName; } //its a simple name
 511         else { //we need to complete the pathname
 512                 // ex. ../../../filename
 513                 // cwd = /user/work/desktop
 514
 515                 string cwd;
 516                 //get current working directory
 517                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 518
 519                         if (path.find("~") != -1) { //go to home directory
 520                                 string homeDir;
 521
 522                                 char *homepath = NULL;
 523                                 homepath = getenv ("HOME");
 524                                 if ( homepath != NULL) { homeDir = homepath; }
 525                                 else { homeDir = "";  }
 526
 527                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 528                                 return newFileName;
 529                         }else { //find path
 530                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 531                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 532
 533                                 //char* cwdpath = new char[1024];
 534                                 //size_t size;
 535                                 //cwdpath=getcwd(cwdpath,size);
 536                                 //cwd = cwdpath;
 537
 538                                 char *cwdpath = NULL;
 539                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 540                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 541                                 else { cwd = "";  }
 542
 543
 544                                 //rip off first '/'
 545                                 string simpleCWD;
 546                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 547
 548                                 //break apart the current working directory
 549                                 vector<string> dirs;
 550                                 while (simpleCWD.find_first_of('/') != string::npos) {
 551                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 552                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 553                                         dirs.push_back(dir);
 554                                 }
 555                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 556                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 557
 558
 559                                 int index = dirs.size()-1;
 560
 561                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 562                                         if (pos == 0) { break;  //you are at the end
 563                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 564                                                 path = path.substr(0, pos-1);
 565                                                 index--;
 566                                                 if (index == 0) {  break; }
 567                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 568                                                 path = path.substr(0, pos);
 569                                         }else if (pos == 1) { break;  //you are at the end
 570                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 571                                 }
 572
 573                                 for (int i = index; i >= 0; i--) {
 574                                         newFileName = dirs[i] +  "/" + newFileName;
 575                                 }
 576
 577                                 newFileName =  "/" +  newFileName;
 578                                 return newFileName;
 579                         }
 580                 #else
 581                         if (path.find("~") != string::npos) { //go to home directory
 582                                 string homeDir = getenv ("HOMEPATH");
 583                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 584                                 return newFileName;
 585                         }else { //find path
 586                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 587                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 588
 589                                 char *cwdpath = NULL;
 590                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 591                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 592                                 else { cwd = "";  }
 593
 594                                 //break apart the current working directory
 595                                 vector<string> dirs;
 596                                 while (cwd.find_first_of('\\') != -1) {
 597                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 598                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 599                                         dirs.push_back(dir);
 600
 601                                 }
 602                                 //get last one
 603                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 604
 605                                 int index = dirs.size()-1;
 606
 607                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 608                                         if (pos == 0) { break;  //you are at the end
 609                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 610                                                 path = path.substr(0, pos-1);
 611                                                 index--;
 612                                                 if (index == 0) {  break; }
 613                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 614                                                 path = path.substr(0, pos);
 615                                         }else if (pos == 1) { break;  //you are at the end
 616                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 617                                 }
 618
 619                                 for (int i = index; i >= 0; i--) {
 620                                         newFileName = dirs[i] +  "\\" + newFileName;
 621                                 }
 622
 623                                 return newFileName;
 624                         }
 625
 626                 #endif
 627         }
 628         }
 629         catch(exception& e) {
 630                 errorOut(e, "MothurOut", "getFullPathName");
 631                 exit(1);
 632         }
 633 }
 634 /***********************************************************************/
 635
 636 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 637         try {
 638                         //get full path name
 639                         string completeFileName = getFullPathName(fileName);
 640 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 641 #ifdef USE_COMPRESSION
 642       // check for gzipped or bzipped file
 643       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 644         string tempName = string(tmpnam(0));
 645         mkfifo(tempName.c_str(), 0666);
 646         int fork_result = fork();
 647         if (fork_result < 0) {
 648           cerr << "Error forking.\n";
 649           exit(1);
 650         } else if (fork_result == 0) {
 651           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 652           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 653           system(command.c_str());
 654           cerr << "Done decompressing " << completeFileName << "\n";
 655           remove(tempName.c_str());
 656           exit(EXIT_SUCCESS);
 657         } else {
 658           cerr << "waiting on child process " << fork_result << "\n";
 659           completeFileName = tempName;
 660         }
 661       }
 662 #endif
 663 #endif
 664                         fileHandle.open(completeFileName.c_str());
 665                         if(!fileHandle) {
 666                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 667                                 return 1;
 668                         }else {
 669                                 //check for blank file
 670                                 gobble(fileHandle);
 671                                 return 0;
 672                         }
 673         }
 674         catch(exception& e) {
 675                 errorOut(e, "MothurOut", "openInputFile - no Error");
 676                 exit(1);
 677         }
 678 }
 679 /***********************************************************************/
 680
 681 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 682         try {
 683
 684                 //get full path name
 685                 string completeFileName = getFullPathName(fileName);
 686 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 687 #ifdef USE_COMPRESSION
 688   // check for gzipped or bzipped file
 689   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 690     string tempName = string(tmpnam(0));
 691     mkfifo(tempName.c_str(), 0666);
 692     int fork_result = fork();
 693     if (fork_result < 0) {
 694       cerr << "Error forking.\n";
 695       exit(1);
 696     } else if (fork_result == 0) {
 697       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 698       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 699       system(command.c_str());
 700       cerr << "Done decompressing " << completeFileName << "\n";
 701       remove(tempName.c_str());
 702       exit(EXIT_SUCCESS);
 703     } else {
 704       cerr << "waiting on child process " << fork_result << "\n";
 705       completeFileName = tempName;
 706     }
 707   }
 708 #endif
 709 #endif
 710
 711                 fileHandle.open(completeFileName.c_str());
 712                 if(!fileHandle) {
 713                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 714                         return 1;
 715                 }
 716                 else {
 717                         //check for blank file
 718                         gobble(fileHandle);
 719                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 720
 721                         return 0;
 722                 }
 723         }
 724         catch(exception& e) {
 725                 errorOut(e, "MothurOut", "openInputFile");
 726                 exit(1);
 727         }
 728 }
 729 /***********************************************************************/
 730
 731 int MothurOut::renameFile(string oldName, string newName){
 732         try {
 733                 ifstream inTest;
 734                 int exist = openInputFile(newName, inTest, "");
 735
 736         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 737                 if (exist == 0) { //you could open it so you want to delete it
 738                         inTest.close();
 739                         string command = "rm " + newName;
 740                         system(command.c_str());
 741                 }
 742
 743                 string command = "mv " + oldName + " " + newName;
 744                 system(command.c_str());
 745         #else
 746                 remove(newName.c_str());
 747                 int renameOk = rename(oldName.c_str(), newName.c_str());
 748         #endif
 749                 return 0;
 750
 751         }
 752         catch(exception& e) {
 753                 errorOut(e, "MothurOut", "renameFile");
 754                 exit(1);
 755         }
 756 }
 757
 758 /***********************************************************************/
 759
 760 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 761         try {
 762
 763                 string completeFileName = getFullPathName(fileName);
 764 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 765 #ifdef USE_COMPRESSION
 766     // check for gzipped file
 767     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 768       string tempName = string(tmpnam(0));
 769       mkfifo(tempName.c_str(), 0666);
 770       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 771       int fork_result = fork();
 772       if (fork_result < 0) {
 773         cerr << "Error forking.\n";
 774         exit(1);
 775       } else if (fork_result == 0) {
 776         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 777         system(command.c_str());
 778         exit(0);
 779       } else {
 780         completeFileName = tempName;
 781       }
 782     }
 783 #endif
 784 #endif
 785                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 786                 if(!fileHandle) {
 787                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 788                         return 1;
 789                 }
 790                 else {
 791                         return 0;
 792                 }
 793         }
 794         catch(exception& e) {
 795                 errorOut(e, "MothurOut", "openOutputFile");
 796                 exit(1);
 797         }
 798
 799 }
 800
 801 /**************************************************************************************************/
 802 void MothurOut::appendFiles(string temp, string filename) {
 803         try{
 804                 ofstream output;
 805                 ifstream input;
 806
 807                 //open output file in append mode
 808                 openOutputFileAppend(filename, output);
 809                 int ableToOpen = openInputFile(temp, input, "no error");
 810                 //int ableToOpen = openInputFile(temp, input);
 811
 812                 if (ableToOpen == 0) { //you opened it
 813                         while(char c = input.get()){
 814                                 if(input.eof())         {       break;                  }
 815                                 else                            {       output << c;    }
 816                         }
 817                         input.close();
 818                 }
 819
 820                 output.close();
 821         }
 822         catch(exception& e) {
 823                 errorOut(e, "MothurOut", "appendFiles");
 824                 exit(1);
 825         }
 826 }
 827
 828 /**************************************************************************************************/
 829 string MothurOut::sortFile(string distFile, string outputDir){
 830         try {
 831
 832                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 833                 string outfile = getRootName(distFile) + "sorted.dist";
 834
 835
 836                 //if you can, use the unix sort since its been optimized for years
 837                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 838                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 839                         system(command.c_str());
 840                 #else //you are stuck with my best attempt...
 841                         //windows sort does not have a way to specify a column, only a character in the line
 842                         //since we cannot assume that the distance will always be at the the same character location on each line
 843                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 844
 845                         //read in file line by file and put distance first
 846                         string tempDistFile = distFile + ".temp";
 847                         ifstream input;
 848                         ofstream output;
 849                         openInputFile(distFile, input);
 850                         openOutputFile(tempDistFile, output);
 851
 852                         string firstName, secondName;
 853                         float dist;
 854                         while (input) {
 855                                 input >> firstName >> secondName >> dist;
 856                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 857                                 gobble(input);
 858                         }
 859                         input.close();
 860                         output.close();
 861
 862
 863                         //sort using windows sort
 864                         string tempOutfile = outfile + ".temp";
 865                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 866                         system(command.c_str());
 867
 868                         //read in sorted file and put distance at end again
 869                         ifstream input2;
 870                         openInputFile(tempOutfile, input2);
 871                         openOutputFile(outfile, output);
 872
 873                         while (input2) {
 874                                 input2 >> dist >> firstName >> secondName;
 875                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 876                                 gobble(input2);
 877                         }
 878                         input2.close();
 879                         output.close();
 880
 881                         //remove temp files
 882                         remove(tempDistFile.c_str());
 883                         remove(tempOutfile.c_str());
 884                 #endif
 885
 886                 return outfile;
 887         }
 888         catch(exception& e) {
 889                 errorOut(e, "MothurOut", "sortFile");
 890                 exit(1);
 891         }
 892 }
 893 /**************************************************************************************************/
 894 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
 895         try {
 896                         vector<unsigned long int> positions;
 897                         ifstream inFASTA;
 898                         openInputFile(filename, inFASTA);
 899
 900                         string input;
 901                         while(!inFASTA.eof()){
 902                                 input = getline(inFASTA);
 903                                 if (input.length() != 0) {
 904                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 905                                 }
 906                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
 907                         }
 908                         inFASTA.close();
 909
 910                         num = positions.size();
 911
 912                         /*FILE * pFile;
 913                         long size;
 914
 915                         //get num bytes in file
 916                         pFile = fopen (filename.c_str(),"rb");
 917                         if (pFile==NULL) perror ("Error opening file");
 918                         else{
 919                                 fseek (pFile, 0, SEEK_END);
 920                                 size=ftell (pFile);
 921                                 fclose (pFile);
 922                         }*/
 923
 924                         unsigned long int size = positions[(positions.size()-1)];
 925                         ifstream in;
 926                         openInputFile(filename, in);
 927
 928                         in.seekg(size);
 929
 930                         while(in.get()){
 931                                 if(in.eof())            {       break;  }
 932                                 else                            {       size++; }
 933                         }
 934                         in.close();
 935
 936                         positions.push_back(size);
 937
 938                         return positions;
 939         }
 940         catch(exception& e) {
 941                 errorOut(e, "MothurOut", "setFilePosFasta");
 942                 exit(1);
 943         }
 944 }
 945 /**************************************************************************************************/
 946 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
 947         try {
 948                         filename = getFullPathName(filename);
 949
 950                         vector<unsigned long int> positions;
 951                         ifstream in;
 952                         openInputFile(filename, in);
 953
 954                         string input;
 955                         while(!in.eof()){
 956                                 unsigned long int lastpos = in.tellg();
 957                                 input = getline(in);
 958                                 if (input.length() != 0) {
 959                                         unsigned long int pos = in.tellg();
 960                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
 961                                         else {  positions.push_back(lastpos);  }
 962                                 }
 963                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
 964                         }
 965                         in.close();
 966
 967                         num = positions.size();
 968
 969                         FILE * pFile;
 970                         unsigned long int size;
 971
 972                         //get num bytes in file
 973                         pFile = fopen (filename.c_str(),"rb");
 974                         if (pFile==NULL) perror ("Error opening file");
 975                         else{
 976                                 fseek (pFile, 0, SEEK_END);
 977                                 size=ftell (pFile);
 978                                 fclose (pFile);
 979                         }
 980
 981                         positions.push_back(size);
 982
 983                         return positions;
 984         }
 985         catch(exception& e) {
 986                 errorOut(e, "MothurOut", "setFilePosEachLine");
 987                 exit(1);
 988         }
 989 }
 990 /**************************************************************************************************/
 991
 992 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 993         try{
 994
 995                 vector<unsigned long int> filePos;
 996                 filePos.push_back(0);
 997
 998                 FILE * pFile;
 999                 unsigned long int size;
1000
1001                 filename = getFullPathName(filename);
1002
1003                 //get num bytes in file
1004                 pFile = fopen (filename.c_str(),"rb");
1005                 if (pFile==NULL) perror ("Error opening file");
1006                 else{
1007                         fseek (pFile, 0, SEEK_END);
1008                         size=ftell (pFile);
1009                         fclose (pFile);
1010                 }
1011
1012                 //estimate file breaks
1013                 unsigned long int chunkSize = 0;
1014                 chunkSize = size / proc;
1015
1016                 //file to small to divide by processors
1017                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1018
1019                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1020                 for (int i = 0; i < proc; i++) {
1021                         unsigned long int spot = (i+1) * chunkSize;
1022
1023                         ifstream in;
1024                         openInputFile(filename, in);
1025                         in.seekg(spot);
1026
1027                         //look for next '>'
1028                         unsigned long int newSpot = spot;
1029                         while (!in.eof()) {
1030                            char c = in.get();
1031                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1032                         }
1033
1034                         //there was not another sequence before the end of the file
1035                         unsigned long int sanityPos = in.tellg();
1036
1037                         if (sanityPos == -1) {  break;  }
1038                         else {  filePos.push_back(newSpot);  }
1039
1040                         in.close();
1041                 }
1042
1043                 //save end pos
1044                 filePos.push_back(size);
1045
1046                 //sanity check filePos
1047                 for (int i = 0; i < (filePos.size()-1); i++) {
1048                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1049                 }
1050
1051                 proc = (filePos.size() - 1);
1052
1053                 return filePos;
1054         }
1055         catch(exception& e) {
1056                 errorOut(e, "MothurOut", "divideFile");
1057                 exit(1);
1058         }
1059 }
1060
1061 /***********************************************************************/
1062
1063 bool MothurOut::isTrue(string f){
1064         try {
1065
1066                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1067
1068                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1069                 else {  return false;  }
1070         }
1071         catch(exception& e) {
1072                 errorOut(e, "MothurOut", "isTrue");
1073                 exit(1);
1074         }
1075 }
1076
1077 /***********************************************************************/
1078
1079 float MothurOut::roundDist(float dist, int precision){
1080         try {
1081                 return int(dist * precision + 0.5)/float(precision);
1082         }
1083         catch(exception& e) {
1084                 errorOut(e, "MothurOut", "roundDist");
1085                 exit(1);
1086         }
1087 }
1088 /***********************************************************************/
1089
1090 float MothurOut::ceilDist(float dist, int precision){
1091         try {
1092                 return int(ceil(dist * precision))/float(precision);
1093         }
1094         catch(exception& e) {
1095                 errorOut(e, "MothurOut", "ceilDist");
1096                 exit(1);
1097         }
1098 }
1099
1100 /***********************************************************************/
1101
1102 int MothurOut::getNumNames(string names){
1103         try {
1104                 int count = 0;
1105
1106                 if(names != ""){
1107                         count = 1;
1108                         for(int i=0;i<names.size();i++){
1109                                 if(names[i] == ','){
1110                                         count++;
1111                                 }
1112                         }
1113                 }
1114
1115                 return count;
1116         }
1117         catch(exception& e) {
1118                 errorOut(e, "MothurOut", "getNumNames");
1119                 exit(1);
1120         }
1121 }
1122
1123 /**************************************************************************************************/
1124
1125 vector<vector<double> > MothurOut::binomial(int maxOrder){
1126         try {
1127         vector<vector<double> > binomial(maxOrder+1);
1128
1129     for(int i=0;i<=maxOrder;i++){
1130                 binomial[i].resize(maxOrder+1);
1131                 binomial[i][0]=1;
1132                 binomial[0][i]=0;
1133     }
1134     binomial[0][0]=1;
1135
1136     binomial[1][0]=1;
1137     binomial[1][1]=1;
1138
1139     for(int i=2;i<=maxOrder;i++){
1140                 binomial[1][i]=0;
1141     }
1142
1143     for(int i=2;i<=maxOrder;i++){
1144                 for(int j=1;j<=maxOrder;j++){
1145                         if(i==j){       binomial[i][j]=1;                                                                       }
1146                         if(j>i) {       binomial[i][j]=0;                                                                       }
1147                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1148                 }
1149     }
1150
1151         return binomial;
1152
1153         }
1154         catch(exception& e) {
1155                 errorOut(e, "MothurOut", "binomial");
1156                 exit(1);
1157         }
1158 }
1159 /**************************************************************************************************/
1160 unsigned int MothurOut::fromBase36(string base36){
1161         try {
1162                 unsigned int num = 0;
1163
1164                 map<char, int> converts;
1165                 converts['A'] = 0;
1166                 converts['a'] = 0;
1167                 converts['B'] = 1;
1168                 converts['b'] = 1;
1169                 converts['C'] = 2;
1170                 converts['c'] = 2;
1171                 converts['D'] = 3;
1172                 converts['d'] = 3;
1173                 converts['E'] = 4;
1174                 converts['e'] = 4;
1175                 converts['F'] = 5;
1176                 converts['f'] = 5;
1177                 converts['G'] = 6;
1178                 converts['g'] = 6;
1179                 converts['H'] = 7;
1180                 converts['h'] = 7;
1181                 converts['I'] = 8;
1182                 converts['i'] = 8;
1183                 converts['J'] = 9;
1184                 converts['j'] = 9;
1185                 converts['K'] = 10;
1186                 converts['k'] = 10;
1187                 converts['L'] = 11;
1188                 converts['l'] = 11;
1189                 converts['M'] = 12;
1190                 converts['m'] = 12;
1191                 converts['N'] = 13;
1192                 converts['n'] = 13;
1193                 converts['O'] = 14;
1194                 converts['o'] = 14;
1195                 converts['P'] = 15;
1196                 converts['p'] = 15;
1197                 converts['Q'] = 16;
1198                 converts['q'] = 16;
1199                 converts['R'] = 17;
1200                 converts['r'] = 17;
1201                 converts['S'] = 18;
1202                 converts['s'] = 18;
1203                 converts['T'] = 19;
1204                 converts['t'] = 19;
1205                 converts['U'] = 20;
1206                 converts['u'] = 20;
1207                 converts['V'] = 21;
1208                 converts['v'] = 21;
1209                 converts['W'] = 22;
1210                 converts['w'] = 22;
1211                 converts['X'] = 23;
1212                 converts['x'] = 23;
1213                 converts['Y'] = 24;
1214                 converts['y'] = 24;
1215                 converts['Z'] = 25;
1216                 converts['z'] = 25;
1217                 converts['0'] = 26;
1218                 converts['1'] = 27;
1219                 converts['2'] = 28;
1220                 converts['3'] = 29;
1221                 converts['4'] = 30;
1222                 converts['5'] = 31;
1223                 converts['6'] = 32;
1224                 converts['7'] = 33;
1225                 converts['8'] = 34;
1226                 converts['9'] = 35;
1227
1228                 int i = 0;
1229                 while (i < base36.length()) {
1230                         char c = base36[i];
1231                         num = 36 * num + converts[c];
1232                         i++;
1233                 }
1234
1235                 return num;
1236
1237         }
1238         catch(exception& e) {
1239                 errorOut(e, "MothurOut", "fromBase36");
1240                 exit(1);
1241         }
1242 }
1243 /***********************************************************************/
1244
1245 int MothurOut::factorial(int num){
1246         try {
1247                 int total = 1;
1248
1249                 for (int i = 1; i <= num; i++) {
1250                         total *= i;
1251                 }
1252
1253                 return total;
1254         }
1255         catch(exception& e) {
1256                 errorOut(e, "MothurOut", "factorial");
1257                 exit(1);
1258         }
1259 }
1260 /***********************************************************************/
1261
1262 int MothurOut::getNumSeqs(ifstream& file){
1263         try {
1264                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1265                 file.seekg(0);
1266                 return numSeqs;
1267         }
1268         catch(exception& e) {
1269                 errorOut(e, "MothurOut", "getNumSeqs");
1270                 exit(1);
1271         }
1272 }
1273 /***********************************************************************/
1274 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1275         try {
1276                 string input;
1277                 numSeqs = 0;
1278                 while(!file.eof()){
1279                         input = getline(file);
1280                         if (input.length() != 0) {
1281                                 if(input[0] == '>'){ numSeqs++; }
1282                         }
1283                 }
1284         }
1285         catch(exception& e) {
1286                 errorOut(e, "MothurOut", "getNumSeqs");
1287                 exit(1);
1288         }
1289 }
1290 /***********************************************************************/
1291
1292 //This function parses the estimator options and puts them in a vector
1293 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1294         try {
1295                 string individual = "";
1296                 int estimLength = estim.size();
1297                 for(int i=0;i<estimLength;i++){
1298                         if(estim[i] == symbol){
1299                                 container.push_back(individual);
1300                                 individual = "";
1301                         }
1302                         else{
1303                                 individual += estim[i];
1304                         }
1305                 }
1306                 container.push_back(individual);
1307
1308         }
1309         catch(exception& e) {
1310                 errorOut(e, "MothurOut", "splitAtChar");
1311                 exit(1);
1312         }
1313 }
1314
1315 /***********************************************************************/
1316
1317 //This function parses the estimator options and puts them in a vector
1318 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1319         try {
1320                 string individual = "";
1321                 int estimLength = estim.size();
1322                 for(int i=0;i<estimLength;i++){
1323                         if(estim[i] == '-'){
1324                                 container.push_back(individual);
1325                                 individual = "";
1326                         }
1327                         else{
1328                                 individual += estim[i];
1329                         }
1330                 }
1331                 container.push_back(individual);
1332
1333
1334         /*      string individual;
1335
1336                 while (estim.find_first_of('-') != -1) {
1337                         individual = estim.substr(0,estim.find_first_of('-'));
1338                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1339                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1340                                 container.push_back(individual);
1341                         }
1342                 }
1343                 //get last one
1344                 container.push_back(estim); */
1345         }
1346         catch(exception& e) {
1347                 errorOut(e, "MothurOut", "splitAtDash");
1348                 exit(1);
1349         }
1350 }
1351
1352 /***********************************************************************/
1353 //This function parses the label options and puts them in a set
1354 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1355         try {
1356                 string individual = "";
1357                 int estimLength = estim.size();
1358                 for(int i=0;i<estimLength;i++){
1359                         if(estim[i] == '-'){
1360                                 container.insert(individual);
1361                                 individual = "";
1362                         }
1363                         else{
1364                                 individual += estim[i];
1365                         }
1366                 }
1367                 container.insert(individual);
1368
1369         //      string individual;
1370
1371         //      while (estim.find_first_of('-') != -1) {
1372         //              individual = estim.substr(0,estim.find_first_of('-'));
1373         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1374         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1375         //                      container.insert(individual);
1376         //              }
1377         //      }
1378                 //get last one
1379         //      container.insert(estim);
1380
1381         }
1382         catch(exception& e) {
1383                 errorOut(e, "MothurOut", "splitAtDash");
1384                 exit(1);
1385         }
1386 }
1387 /***********************************************************************/
1388 //This function parses the line options and puts them in a set
1389 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1390         try {
1391                 string individual;
1392                 int lineNum;
1393
1394                 while (estim.find_first_of('-') != -1) {
1395                         individual = estim.substr(0,estim.find_first_of('-'));
1396                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1397                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1398                                 convert(individual, lineNum); //convert the string to int
1399                                 container.insert(lineNum);
1400                         }
1401                 }
1402                 //get last one
1403                 convert(estim, lineNum); //convert the string to int
1404                 container.insert(lineNum);
1405         }
1406         catch(exception& e) {
1407                 errorOut(e, "MothurOut", "splitAtDash");
1408                 exit(1);
1409         }
1410 }
1411 /***********************************************************************/
1412 //This function parses the a string and puts peices in a vector
1413 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1414         try {
1415                 string individual = "";
1416                 int estimLength = estim.size();
1417                 for(int i=0;i<estimLength;i++){
1418                         if(estim[i] == ','){
1419                                 container.push_back(individual);
1420                                 individual = "";
1421                         }
1422                         else{
1423                                 individual += estim[i];
1424                         }
1425                 }
1426                 container.push_back(individual);
1427
1428
1429
1430
1431 //              string individual;
1432 //
1433 //              while (estim.find_first_of(',') != -1) {
1434 //                      individual = estim.substr(0,estim.find_first_of(','));
1435 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1436 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1437 //                              container.push_back(individual);
1438 //                      }
1439 //              }
1440 //              //get last one
1441 //              container.push_back(estim);
1442         }
1443         catch(exception& e) {
1444                 errorOut(e, "MothurOut", "splitAtComma");
1445                 exit(1);
1446         }
1447 }
1448 /***********************************************************************/
1449
1450 //This function splits up the various option parameters
1451 void MothurOut::splitAtComma(string& prefix, string& suffix){
1452         try {
1453                 prefix = suffix.substr(0,suffix.find_first_of(','));
1454                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1455                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1456                         string space = " ";
1457                         while(suffix.at(0) == ' ')
1458                                 suffix = suffix.substr(1, suffix.length());
1459                 }
1460
1461         }
1462         catch(exception& e) {
1463                 errorOut(e, "MothurOut", "splitAtComma");
1464                 exit(1);
1465         }
1466 }
1467 /***********************************************************************/
1468
1469 //This function separates the key value from the option value i.e. dist=96_...
1470 void MothurOut::splitAtEquals(string& key, string& value){
1471         try {
1472                 if(value.find_first_of('=') != -1){
1473                         key = value.substr(0,value.find_first_of('='));
1474                         if ((value.find_first_of('=')+1) <= value.length()) {
1475                                 value = value.substr(value.find_first_of('=')+1, value.length());
1476                         }
1477                 }else{
1478                         key = value;
1479                         value = 1;
1480                 }
1481         }
1482         catch(exception& e) {
1483                 errorOut(e, "MothurOut", "splitAtEquals");
1484                 exit(1);
1485         }
1486 }
1487
1488 /**************************************************************************************************/
1489
1490 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1491         try {
1492                 for (int i = 0; i < Groups.size(); i++) {
1493                         if (groupname == Groups[i]) { return true; }
1494                 }
1495                 return false;
1496         }
1497         catch(exception& e) {
1498                 errorOut(e, "MothurOut", "inUsersGroups");
1499                 exit(1);
1500         }
1501 }
1502 /**************************************************************************************************/
1503 //returns true if any of the strings in first vector are in second vector
1504 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1505         try {
1506
1507                 for (int i = 0; i < groupnames.size(); i++) {
1508                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1509                 }
1510                 return false;
1511         }
1512         catch(exception& e) {
1513                 errorOut(e, "MothurOut", "inUsersGroups");
1514                 exit(1);
1515         }
1516 }
1517 /***********************************************************************/
1518 //this function determines if the user has given us labels that are smaller than the given label.
1519 //if so then it returns true so that the calling function can run the previous valid distance.
1520 //it's a "smart" distance function.  It also checks for invalid labels.
1521 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1522         try {
1523
1524                 set<string>::iterator it;
1525                 vector<float> orderFloat;
1526                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1527                 map<string, float>::iterator it2;
1528                 float labelFloat;
1529                 bool smaller = false;
1530
1531                 //unique is the smallest line
1532                 if (label == "unique") {  return false;  }
1533                 else {
1534                         if (convertTestFloat(label, labelFloat)) {
1535                                 convert(label, labelFloat);
1536                         }else { //cant convert
1537                                 return false;
1538                         }
1539                 }
1540
1541                 //go through users set and make them floats
1542                 for(it = userLabels.begin(); it != userLabels.end();) {
1543
1544                         float temp;
1545                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1546                                 convert(*it, temp);
1547                                 orderFloat.push_back(temp);
1548                                 userMap[*it] = temp;
1549                                 it++;
1550                         }else if (*it == "unique") {
1551                                 orderFloat.push_back(-1.0);
1552                                 userMap["unique"] = -1.0;
1553                                 it++;
1554                         }else {
1555                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1556                                 userLabels.erase(it++);
1557                         }
1558                 }
1559
1560                 //sort order
1561                 sort(orderFloat.begin(), orderFloat.end());
1562
1563                 /*************************************************/
1564                 //is this label bigger than any of the users labels
1565                 /*************************************************/
1566
1567                 //loop through order until you find a label greater than label
1568                 for (int i = 0; i < orderFloat.size(); i++) {
1569                         if (orderFloat[i] < labelFloat) {
1570                                 smaller = true;
1571                                 if (orderFloat[i] == -1) {
1572                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1573                                         userLabels.erase("unique");
1574                                 }
1575                                 else {
1576                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1577                                         string s = "";
1578                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1579                                                 if (it2->second == orderFloat[i]) {
1580                                                         s = it2->first;
1581                                                         //remove small labels
1582                                                         userLabels.erase(s);
1583                                                         break;
1584                                                 }
1585                                         }
1586                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1587                                 }
1588                         //since they are sorted once you find a bigger one stop looking
1589                         }else { break; }
1590                 }
1591
1592                 return smaller;
1593
1594         }
1595         catch(exception& e) {
1596                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1597                 exit(1);
1598         }
1599 }
1600
1601 /**************************************************************************************************/
1602 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1603         try {
1604
1605                 bool good = true;
1606
1607                 string line = getline(file);
1608
1609                 //before we added this check
1610                 if (line[0] != '#') {  good = false;  }
1611                 else {
1612                         //rip off #
1613                         line = line.substr(1);
1614
1615                         vector<string> versionVector;
1616                         splitAtChar(version, versionVector, '.');
1617
1618                         //check file version
1619                         vector<string> linesVector;
1620                         splitAtChar(line, linesVector, '.');
1621
1622                         if (versionVector.size() != linesVector.size()) { good = false; }
1623                         else {
1624                                 for (int j = 0; j < versionVector.size(); j++) {
1625                                         int num1, num2;
1626                                         convert(versionVector[j], num1);
1627                                         convert(linesVector[j], num2);
1628
1629                                         //if mothurs version is newer than this files version, then we want to remake it
1630                                         if (num1 > num2) {  good = false; break;  }
1631                                 }
1632                         }
1633
1634                 }
1635
1636                 if (!good) {  file.close();  }
1637                 else { file.seekg(0);  }
1638
1639                 return good;
1640         }
1641         catch(exception& e) {
1642                 errorOut(e, "MothurOut", "checkReleaseVersion");
1643                 exit(1);
1644         }
1645 }
1646
1647 /**************************************************************************************************/
1648
1649
1650
1651
1652