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                 }
 493                 return false;
 494         }
 495         catch(exception& e) {
 496                 errorOut(e, "MothurOut", "isBlank");
 497                 exit(1);
 498         }
 499 }
 500 /***********************************************************************/
 501
 502 string MothurOut::getFullPathName(string fileName){
 503         try{
 504
 505         string path = hasPath(fileName);
 506         string newFileName;
 507         int pos;
 508
 509         if (path == "") { return fileName; } //its a simple name
 510         else { //we need to complete the pathname
 511                 // ex. ../../../filename
 512                 // cwd = /user/work/desktop
 513
 514                 string cwd;
 515                 //get current working directory
 516                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 517
 518                         if (path.find("~") != -1) { //go to home directory
 519                                 string homeDir;
 520
 521                                 char *homepath = NULL;
 522                                 homepath = getenv ("HOME");
 523                                 if ( homepath != NULL) { homeDir = homepath; }
 524                                 else { homeDir = "";  }
 525
 526                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 527                                 return newFileName;
 528                         }else { //find path
 529                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 530                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 531
 532                                 //char* cwdpath = new char[1024];
 533                                 //size_t size;
 534                                 //cwdpath=getcwd(cwdpath,size);
 535                                 //cwd = cwdpath;
 536
 537                                 char *cwdpath = NULL;
 538                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 539                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 540                                 else { cwd = "";  }
 541
 542
 543                                 //rip off first '/'
 544                                 string simpleCWD;
 545                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 546
 547                                 //break apart the current working directory
 548                                 vector<string> dirs;
 549                                 while (simpleCWD.find_first_of('/') != string::npos) {
 550                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 551                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 552                                         dirs.push_back(dir);
 553                                 }
 554                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 555                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 556
 557
 558                                 int index = dirs.size()-1;
 559
 560                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 561                                         if (pos == 0) { break;  //you are at the end
 562                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 563                                                 path = path.substr(0, pos-1);
 564                                                 index--;
 565                                                 if (index == 0) {  break; }
 566                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 567                                                 path = path.substr(0, pos);
 568                                         }else if (pos == 1) { break;  //you are at the end
 569                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 570                                 }
 571
 572                                 for (int i = index; i >= 0; i--) {
 573                                         newFileName = dirs[i] +  "/" + newFileName;
 574                                 }
 575
 576                                 newFileName =  "/" +  newFileName;
 577                                 return newFileName;
 578                         }
 579                 #else
 580                         if (path.find("~") != string::npos) { //go to home directory
 581                                 string homeDir = getenv ("HOMEPATH");
 582                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 583                                 return newFileName;
 584                         }else { //find path
 585                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 586                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 587
 588                                 char *cwdpath = NULL;
 589                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 590                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 591                                 else { cwd = "";  }
 592
 593                                 //break apart the current working directory
 594                                 vector<string> dirs;
 595                                 while (cwd.find_first_of('\\') != -1) {
 596                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 597                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 598                                         dirs.push_back(dir);
 599
 600                                 }
 601                                 //get last one
 602                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 603
 604                                 int index = dirs.size()-1;
 605
 606                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 607                                         if (pos == 0) { break;  //you are at the end
 608                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 609                                                 path = path.substr(0, pos-1);
 610                                                 index--;
 611                                                 if (index == 0) {  break; }
 612                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 613                                                 path = path.substr(0, pos);
 614                                         }else if (pos == 1) { break;  //you are at the end
 615                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 616                                 }
 617
 618                                 for (int i = index; i >= 0; i--) {
 619                                         newFileName = dirs[i] +  "\\" + newFileName;
 620                                 }
 621
 622                                 return newFileName;
 623                         }
 624
 625                 #endif
 626         }
 627         }
 628         catch(exception& e) {
 629                 errorOut(e, "MothurOut", "getFullPathName");
 630                 exit(1);
 631         }
 632 }
 633 /***********************************************************************/
 634
 635 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 636         try {
 637                         //get full path name
 638                         string completeFileName = getFullPathName(fileName);
 639 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 640 #ifdef USE_COMPRESSION
 641       // check for gzipped or bzipped file
 642       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 643         string tempName = string(tmpnam(0));
 644         mkfifo(tempName.c_str(), 0666);
 645         int fork_result = fork();
 646         if (fork_result < 0) {
 647           cerr << "Error forking.\n";
 648           exit(1);
 649         } else if (fork_result == 0) {
 650           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 651           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 652           system(command.c_str());
 653           cerr << "Done decompressing " << completeFileName << "\n";
 654           remove(tempName.c_str());
 655           exit(EXIT_SUCCESS);
 656         } else {
 657           cerr << "waiting on child process " << fork_result << "\n";
 658           completeFileName = tempName;
 659         }
 660       }
 661 #endif
 662 #endif
 663                         fileHandle.open(completeFileName.c_str());
 664                         if(!fileHandle) {
 665                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 666                                 return 1;
 667                         }else {
 668                                 //check for blank file
 669                                 gobble(fileHandle);
 670                                 return 0;
 671                         }
 672         }
 673         catch(exception& e) {
 674                 errorOut(e, "MothurOut", "openInputFile - no Error");
 675                 exit(1);
 676         }
 677 }
 678 /***********************************************************************/
 679
 680 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 681         try {
 682
 683                 //get full path name
 684                 string completeFileName = getFullPathName(fileName);
 685 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 686 #ifdef USE_COMPRESSION
 687   // check for gzipped or bzipped file
 688   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 689     string tempName = string(tmpnam(0));
 690     mkfifo(tempName.c_str(), 0666);
 691     int fork_result = fork();
 692     if (fork_result < 0) {
 693       cerr << "Error forking.\n";
 694       exit(1);
 695     } else if (fork_result == 0) {
 696       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 697       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 698       system(command.c_str());
 699       cerr << "Done decompressing " << completeFileName << "\n";
 700       remove(tempName.c_str());
 701       exit(EXIT_SUCCESS);
 702     } else {
 703       cerr << "waiting on child process " << fork_result << "\n";
 704       completeFileName = tempName;
 705     }
 706   }
 707 #endif
 708 #endif
 709
 710                 fileHandle.open(completeFileName.c_str());
 711                 if(!fileHandle) {
 712                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 713                         return 1;
 714                 }
 715                 else {
 716                         //check for blank file
 717                         gobble(fileHandle);
 718                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 719
 720                         return 0;
 721                 }
 722         }
 723         catch(exception& e) {
 724                 errorOut(e, "MothurOut", "openInputFile");
 725                 exit(1);
 726         }
 727 }
 728 /***********************************************************************/
 729
 730 int MothurOut::renameFile(string oldName, string newName){
 731         try {
 732                 ifstream inTest;
 733                 int exist = openInputFile(newName, inTest, "");
 734
 735         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 736                 if (exist == 0) { //you could open it so you want to delete it
 737                         inTest.close();
 738                         string command = "rm " + newName;
 739                         system(command.c_str());
 740                 }
 741
 742                 string command = "mv " + oldName + " " + newName;
 743                 system(command.c_str());
 744         #else
 745                 remove(newName.c_str());
 746                 int renameOk = rename(oldName.c_str(), newName.c_str());
 747         #endif
 748                 return 0;
 749
 750         }
 751         catch(exception& e) {
 752                 errorOut(e, "MothurOut", "renameFile");
 753                 exit(1);
 754         }
 755 }
 756
 757 /***********************************************************************/
 758
 759 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 760         try {
 761
 762                 string completeFileName = getFullPathName(fileName);
 763 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 764 #ifdef USE_COMPRESSION
 765     // check for gzipped file
 766     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 767       string tempName = string(tmpnam(0));
 768       mkfifo(tempName.c_str(), 0666);
 769       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 770       int fork_result = fork();
 771       if (fork_result < 0) {
 772         cerr << "Error forking.\n";
 773         exit(1);
 774       } else if (fork_result == 0) {
 775         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 776         system(command.c_str());
 777         exit(0);
 778       } else {
 779         completeFileName = tempName;
 780       }
 781     }
 782 #endif
 783 #endif
 784                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 785                 if(!fileHandle) {
 786                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 787                         return 1;
 788                 }
 789                 else {
 790                         return 0;
 791                 }
 792         }
 793         catch(exception& e) {
 794                 errorOut(e, "MothurOut", "openOutputFile");
 795                 exit(1);
 796         }
 797
 798 }
 799
 800 /**************************************************************************************************/
 801 void MothurOut::appendFiles(string temp, string filename) {
 802         try{
 803                 ofstream output;
 804                 ifstream input;
 805
 806                 //open output file in append mode
 807                 openOutputFileAppend(filename, output);
 808                 int ableToOpen = openInputFile(temp, input, "no error");
 809                 //int ableToOpen = openInputFile(temp, input);
 810
 811                 if (ableToOpen == 0) { //you opened it
 812                         while(char c = input.get()){
 813                                 if(input.eof())         {       break;                  }
 814                                 else                            {       output << c;    }
 815                         }
 816                         input.close();
 817                 }
 818
 819                 output.close();
 820         }
 821         catch(exception& e) {
 822                 errorOut(e, "MothurOut", "appendFiles");
 823                 exit(1);
 824         }
 825 }
 826
 827 /**************************************************************************************************/
 828 string MothurOut::sortFile(string distFile, string outputDir){
 829         try {
 830
 831                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 832                 string outfile = getRootName(distFile) + "sorted.dist";
 833
 834
 835                 //if you can, use the unix sort since its been optimized for years
 836                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 837                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 838                         system(command.c_str());
 839                 #else //you are stuck with my best attempt...
 840                         //windows sort does not have a way to specify a column, only a character in the line
 841                         //since we cannot assume that the distance will always be at the the same character location on each line
 842                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 843
 844                         //read in file line by file and put distance first
 845                         string tempDistFile = distFile + ".temp";
 846                         ifstream input;
 847                         ofstream output;
 848                         openInputFile(distFile, input);
 849                         openOutputFile(tempDistFile, output);
 850
 851                         string firstName, secondName;
 852                         float dist;
 853                         while (input) {
 854                                 input >> firstName >> secondName >> dist;
 855                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 856                                 gobble(input);
 857                         }
 858                         input.close();
 859                         output.close();
 860
 861
 862                         //sort using windows sort
 863                         string tempOutfile = outfile + ".temp";
 864                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 865                         system(command.c_str());
 866
 867                         //read in sorted file and put distance at end again
 868                         ifstream input2;
 869                         openInputFile(tempOutfile, input2);
 870                         openOutputFile(outfile, output);
 871
 872                         while (input2) {
 873                                 input2 >> dist >> firstName >> secondName;
 874                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 875                                 gobble(input2);
 876                         }
 877                         input2.close();
 878                         output.close();
 879
 880                         //remove temp files
 881                         remove(tempDistFile.c_str());
 882                         remove(tempOutfile.c_str());
 883                 #endif
 884
 885                 return outfile;
 886         }
 887         catch(exception& e) {
 888                 errorOut(e, "MothurOut", "sortFile");
 889                 exit(1);
 890         }
 891 }
 892 /**************************************************************************************************/
 893 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
 894         try {
 895                         vector<unsigned long int> positions;
 896                         ifstream inFASTA;
 897                         openInputFile(filename, inFASTA);
 898
 899                         string input;
 900                         while(!inFASTA.eof()){
 901                                 input = getline(inFASTA);
 902                                 if (input.length() != 0) {
 903                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 904                                 }
 905                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
 906                         }
 907                         inFASTA.close();
 908
 909                         num = positions.size();
 910
 911                         /*FILE * pFile;
 912                         long size;
 913
 914                         //get num bytes in file
 915                         pFile = fopen (filename.c_str(),"rb");
 916                         if (pFile==NULL) perror ("Error opening file");
 917                         else{
 918                                 fseek (pFile, 0, SEEK_END);
 919                                 size=ftell (pFile);
 920                                 fclose (pFile);
 921                         }*/
 922
 923                         unsigned long int size = positions[(positions.size()-1)];
 924                         ifstream in;
 925                         openInputFile(filename, in);
 926
 927                         in.seekg(size);
 928
 929                         while(char c = in.get()){
 930                                 if(in.eof())            {       break;  }
 931                                 else                            {       size++; }
 932                         }
 933                         in.close();
 934
 935                         positions.push_back(size);
 936
 937                         return positions;
 938         }
 939         catch(exception& e) {
 940                 errorOut(e, "MothurOut", "setFilePosFasta");
 941                 exit(1);
 942         }
 943 }
 944 /**************************************************************************************************/
 945 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
 946         try {
 947                         filename = getFullPathName(filename);
 948
 949                         vector<unsigned long int> positions;
 950                         ifstream in;
 951                         openInputFile(filename, in);
 952
 953                         string input;
 954                         while(!in.eof()){
 955                                 unsigned long int lastpos = in.tellg();
 956                                 input = getline(in);
 957                                 if (input.length() != 0) {
 958                                         unsigned long int pos = in.tellg();
 959                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
 960                                         else {  positions.push_back(lastpos);  }
 961                                 }
 962                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
 963                         }
 964                         in.close();
 965
 966                         num = positions.size();
 967
 968                         FILE * pFile;
 969                         unsigned long int size;
 970
 971                         //get num bytes in file
 972                         pFile = fopen (filename.c_str(),"rb");
 973                         if (pFile==NULL) perror ("Error opening file");
 974                         else{
 975                                 fseek (pFile, 0, SEEK_END);
 976                                 size=ftell (pFile);
 977                                 fclose (pFile);
 978                         }
 979
 980                         positions.push_back(size);
 981
 982                         return positions;
 983         }
 984         catch(exception& e) {
 985                 errorOut(e, "MothurOut", "setFilePosEachLine");
 986                 exit(1);
 987         }
 988 }
 989 /**************************************************************************************************/
 990
 991 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 992         try{
 993
 994                 vector<unsigned long int> filePos;
 995                 filePos.push_back(0);
 996
 997                 FILE * pFile;
 998                 unsigned long int size;
 999
1000                 filename = getFullPathName(filename);
1001
1002                 //get num bytes in file
1003                 pFile = fopen (filename.c_str(),"rb");
1004                 if (pFile==NULL) perror ("Error opening file");
1005                 else{
1006                         fseek (pFile, 0, SEEK_END);
1007                         size=ftell (pFile);
1008                         fclose (pFile);
1009                 }
1010
1011                 //estimate file breaks
1012                 unsigned long int chunkSize = 0;
1013                 chunkSize = size / proc;
1014
1015                 //file to small to divide by processors
1016                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1017
1018                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1019                 for (int i = 0; i < proc; i++) {
1020                         unsigned long int spot = (i+1) * chunkSize;
1021
1022                         ifstream in;
1023                         openInputFile(filename, in);
1024                         in.seekg(spot);
1025
1026                         //look for next '>'
1027                         unsigned long int newSpot = spot;
1028                         while (!in.eof()) {
1029                            char c = in.get();
1030                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1031                         }
1032
1033                         //there was not another sequence before the end of the file
1034                         unsigned long int sanityPos = in.tellg();
1035
1036                         if (sanityPos == -1) {  break;  }
1037                         else {  filePos.push_back(newSpot);  }
1038
1039                         in.close();
1040                 }
1041
1042                 //save end pos
1043                 filePos.push_back(size);
1044
1045                 //sanity check filePos
1046                 for (int i = 0; i < (filePos.size()-1); i++) {
1047                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1048                 }
1049
1050                 proc = (filePos.size() - 1);
1051
1052                 return filePos;
1053         }
1054         catch(exception& e) {
1055                 errorOut(e, "MothurOut", "divideFile");
1056                 exit(1);
1057         }
1058 }
1059
1060 /***********************************************************************/
1061
1062 bool MothurOut::isTrue(string f){
1063         try {
1064
1065                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1066
1067                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1068                 else {  return false;  }
1069         }
1070         catch(exception& e) {
1071                 errorOut(e, "MothurOut", "isTrue");
1072                 exit(1);
1073         }
1074 }
1075
1076 /***********************************************************************/
1077
1078 float MothurOut::roundDist(float dist, int precision){
1079         try {
1080                 return int(dist * precision + 0.5)/float(precision);
1081         }
1082         catch(exception& e) {
1083                 errorOut(e, "MothurOut", "roundDist");
1084                 exit(1);
1085         }
1086 }
1087 /***********************************************************************/
1088
1089 float MothurOut::ceilDist(float dist, int precision){
1090         try {
1091                 return int(ceil(dist * precision))/float(precision);
1092         }
1093         catch(exception& e) {
1094                 errorOut(e, "MothurOut", "ceilDist");
1095                 exit(1);
1096         }
1097 }
1098
1099 /***********************************************************************/
1100
1101 int MothurOut::getNumNames(string names){
1102         try {
1103                 int count = 0;
1104
1105                 if(names != ""){
1106                         count = 1;
1107                         for(int i=0;i<names.size();i++){
1108                                 if(names[i] == ','){
1109                                         count++;
1110                                 }
1111                         }
1112                 }
1113
1114                 return count;
1115         }
1116         catch(exception& e) {
1117                 errorOut(e, "MothurOut", "getNumNames");
1118                 exit(1);
1119         }
1120 }
1121
1122 /**************************************************************************************************/
1123
1124 vector<vector<double> > MothurOut::binomial(int maxOrder){
1125         try {
1126         vector<vector<double> > binomial(maxOrder+1);
1127
1128     for(int i=0;i<=maxOrder;i++){
1129                 binomial[i].resize(maxOrder+1);
1130                 binomial[i][0]=1;
1131                 binomial[0][i]=0;
1132     }
1133     binomial[0][0]=1;
1134
1135     binomial[1][0]=1;
1136     binomial[1][1]=1;
1137
1138     for(int i=2;i<=maxOrder;i++){
1139                 binomial[1][i]=0;
1140     }
1141
1142     for(int i=2;i<=maxOrder;i++){
1143                 for(int j=1;j<=maxOrder;j++){
1144                         if(i==j){       binomial[i][j]=1;                                                                       }
1145                         if(j>i) {       binomial[i][j]=0;                                                                       }
1146                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1147                 }
1148     }
1149
1150         return binomial;
1151
1152         }
1153         catch(exception& e) {
1154                 errorOut(e, "MothurOut", "binomial");
1155                 exit(1);
1156         }
1157 }
1158
1159 /***********************************************************************/
1160
1161 int MothurOut::factorial(int num){
1162         try {
1163                 int total = 1;
1164
1165                 for (int i = 1; i <= num; i++) {
1166                         total *= i;
1167                 }
1168
1169                 return total;
1170         }
1171         catch(exception& e) {
1172                 errorOut(e, "MothurOut", "factorial");
1173                 exit(1);
1174         }
1175 }
1176 /***********************************************************************/
1177
1178 int MothurOut::getNumSeqs(ifstream& file){
1179         try {
1180                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1181                 file.seekg(0);
1182                 return numSeqs;
1183         }
1184         catch(exception& e) {
1185                 errorOut(e, "MothurOut", "getNumSeqs");
1186                 exit(1);
1187         }
1188 }
1189 /***********************************************************************/
1190 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1191         try {
1192                 string input;
1193                 numSeqs = 0;
1194                 while(!file.eof()){
1195                         input = getline(file);
1196                         if (input.length() != 0) {
1197                                 if(input[0] == '>'){ numSeqs++; }
1198                         }
1199                 }
1200         }
1201         catch(exception& e) {
1202                 errorOut(e, "MothurOut", "getNumSeqs");
1203                 exit(1);
1204         }
1205 }
1206 /***********************************************************************/
1207
1208 //This function parses the estimator options and puts them in a vector
1209 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1210         try {
1211                 string individual = "";
1212                 int estimLength = estim.size();
1213                 for(int i=0;i<estimLength;i++){
1214                         if(estim[i] == symbol){
1215                                 container.push_back(individual);
1216                                 individual = "";
1217                         }
1218                         else{
1219                                 individual += estim[i];
1220                         }
1221                 }
1222                 container.push_back(individual);
1223
1224                 /*
1225
1226                 while (estim.find_first_of(symbol) != -1) {
1227                         individual = estim.substr(0,estim.find_first_of(symbol));
1228                         if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1229                                 estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
1230                                 container.push_back(individual);
1231                         }
1232                 }
1233                 //get last one
1234                 container.push_back(estim); */
1235         }
1236         catch(exception& e) {
1237                 errorOut(e, "MothurOut", "splitAtChar");
1238                 exit(1);
1239         }
1240 }
1241
1242 /***********************************************************************/
1243
1244 //This function parses the estimator options and puts them in a vector
1245 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1246         try {
1247                 string individual = "";
1248                 int estimLength = estim.size();
1249                 for(int i=0;i<estimLength;i++){
1250                         if(estim[i] == '-'){
1251                                 container.push_back(individual);
1252                                 individual = "";
1253                         }
1254                         else{
1255                                 individual += estim[i];
1256                         }
1257                 }
1258                 container.push_back(individual);
1259
1260
1261         /*      string individual;
1262
1263                 while (estim.find_first_of('-') != -1) {
1264                         individual = estim.substr(0,estim.find_first_of('-'));
1265                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1266                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1267                                 container.push_back(individual);
1268                         }
1269                 }
1270                 //get last one
1271                 container.push_back(estim); */
1272         }
1273         catch(exception& e) {
1274                 errorOut(e, "MothurOut", "splitAtDash");
1275                 exit(1);
1276         }
1277 }
1278
1279 /***********************************************************************/
1280 //This function parses the label options and puts them in a set
1281 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1282         try {
1283                 string individual = "";
1284                 int estimLength = estim.size();
1285                 for(int i=0;i<estimLength;i++){
1286                         if(estim[i] == '-'){
1287                                 container.insert(individual);
1288                                 individual = "";
1289                         }
1290                         else{
1291                                 individual += estim[i];
1292                         }
1293                 }
1294                 container.insert(individual);
1295
1296         //      string individual;
1297
1298         //      while (estim.find_first_of('-') != -1) {
1299         //              individual = estim.substr(0,estim.find_first_of('-'));
1300         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1301         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1302         //                      container.insert(individual);
1303         //              }
1304         //      }
1305                 //get last one
1306         //      container.insert(estim);
1307
1308         }
1309         catch(exception& e) {
1310                 errorOut(e, "MothurOut", "splitAtDash");
1311                 exit(1);
1312         }
1313 }
1314 /***********************************************************************/
1315 //This function parses the line options and puts them in a set
1316 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1317         try {
1318                 string individual;
1319                 int lineNum;
1320
1321                 while (estim.find_first_of('-') != -1) {
1322                         individual = estim.substr(0,estim.find_first_of('-'));
1323                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1324                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1325                                 convert(individual, lineNum); //convert the string to int
1326                                 container.insert(lineNum);
1327                         }
1328                 }
1329                 //get last one
1330                 convert(estim, lineNum); //convert the string to int
1331                 container.insert(lineNum);
1332         }
1333         catch(exception& e) {
1334                 errorOut(e, "MothurOut", "splitAtDash");
1335                 exit(1);
1336         }
1337 }
1338 /***********************************************************************/
1339 //This function parses the a string and puts peices in a vector
1340 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1341         try {
1342                 string individual = "";
1343                 int estimLength = estim.size();
1344                 for(int i=0;i<estimLength;i++){
1345                         if(estim[i] == ','){
1346                                 container.push_back(individual);
1347                                 individual = "";
1348                         }
1349                         else{
1350                                 individual += estim[i];
1351                         }
1352                 }
1353                 container.push_back(individual);
1354
1355
1356
1357
1358 //              string individual;
1359 //
1360 //              while (estim.find_first_of(',') != -1) {
1361 //                      individual = estim.substr(0,estim.find_first_of(','));
1362 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1363 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1364 //                              container.push_back(individual);
1365 //                      }
1366 //              }
1367 //              //get last one
1368 //              container.push_back(estim);
1369         }
1370         catch(exception& e) {
1371                 errorOut(e, "MothurOut", "splitAtComma");
1372                 exit(1);
1373         }
1374 }
1375 /***********************************************************************/
1376
1377 //This function splits up the various option parameters
1378 void MothurOut::splitAtComma(string& prefix, string& suffix){
1379         try {
1380                 prefix = suffix.substr(0,suffix.find_first_of(','));
1381                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1382                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1383                         string space = " ";
1384                         while(suffix.at(0) == ' ')
1385                                 suffix = suffix.substr(1, suffix.length());
1386                 }
1387
1388         }
1389         catch(exception& e) {
1390                 errorOut(e, "MothurOut", "splitAtComma");
1391                 exit(1);
1392         }
1393 }
1394 /***********************************************************************/
1395
1396 //This function separates the key value from the option value i.e. dist=96_...
1397 void MothurOut::splitAtEquals(string& key, string& value){
1398         try {
1399                 if(value.find_first_of('=') != -1){
1400                         key = value.substr(0,value.find_first_of('='));
1401                         if ((value.find_first_of('=')+1) <= value.length()) {
1402                                 value = value.substr(value.find_first_of('=')+1, value.length());
1403                         }
1404                 }else{
1405                         key = value;
1406                         value = 1;
1407                 }
1408         }
1409         catch(exception& e) {
1410                 errorOut(e, "MothurOut", "splitAtEquals");
1411                 exit(1);
1412         }
1413 }
1414
1415 /**************************************************************************************************/
1416
1417 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1418         try {
1419                 for (int i = 0; i < Groups.size(); i++) {
1420                         if (groupname == Groups[i]) { return true; }
1421                 }
1422                 return false;
1423         }
1424         catch(exception& e) {
1425                 errorOut(e, "MothurOut", "inUsersGroups");
1426                 exit(1);
1427         }
1428 }
1429 /**************************************************************************************************/
1430 //returns true if any of the strings in first vector are in second vector
1431 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1432         try {
1433
1434                 for (int i = 0; i < groupnames.size(); i++) {
1435                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1436                 }
1437                 return false;
1438         }
1439         catch(exception& e) {
1440                 errorOut(e, "MothurOut", "inUsersGroups");
1441                 exit(1);
1442         }
1443 }
1444 /***********************************************************************/
1445 //this function determines if the user has given us labels that are smaller than the given label.
1446 //if so then it returns true so that the calling function can run the previous valid distance.
1447 //it's a "smart" distance function.  It also checks for invalid labels.
1448 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1449         try {
1450
1451                 set<string>::iterator it;
1452                 vector<float> orderFloat;
1453                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1454                 map<string, float>::iterator it2;
1455                 float labelFloat;
1456                 bool smaller = false;
1457
1458                 //unique is the smallest line
1459                 if (label == "unique") {  return false;  }
1460                 else {
1461                         if (convertTestFloat(label, labelFloat)) {
1462                                 convert(label, labelFloat);
1463                         }else { //cant convert
1464                                 return false;
1465                         }
1466                 }
1467
1468                 //go through users set and make them floats
1469                 for(it = userLabels.begin(); it != userLabels.end();) {
1470
1471                         float temp;
1472                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1473                                 convert(*it, temp);
1474                                 orderFloat.push_back(temp);
1475                                 userMap[*it] = temp;
1476                                 it++;
1477                         }else if (*it == "unique") {
1478                                 orderFloat.push_back(-1.0);
1479                                 userMap["unique"] = -1.0;
1480                                 it++;
1481                         }else {
1482                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1483                                 userLabels.erase(it++);
1484                         }
1485                 }
1486
1487                 //sort order
1488                 sort(orderFloat.begin(), orderFloat.end());
1489
1490                 /*************************************************/
1491                 //is this label bigger than any of the users labels
1492                 /*************************************************/
1493
1494                 //loop through order until you find a label greater than label
1495                 for (int i = 0; i < orderFloat.size(); i++) {
1496                         if (orderFloat[i] < labelFloat) {
1497                                 smaller = true;
1498                                 if (orderFloat[i] == -1) {
1499                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1500                                         userLabels.erase("unique");
1501                                 }
1502                                 else {
1503                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1504                                         string s = "";
1505                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1506                                                 if (it2->second == orderFloat[i]) {
1507                                                         s = it2->first;
1508                                                         //remove small labels
1509                                                         userLabels.erase(s);
1510                                                         break;
1511                                                 }
1512                                         }
1513                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1514                                 }
1515                         //since they are sorted once you find a bigger one stop looking
1516                         }else { break; }
1517                 }
1518
1519                 return smaller;
1520
1521         }
1522         catch(exception& e) {
1523                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1524                 exit(1);
1525         }
1526 }
1527
1528 /**************************************************************************************************/
1529 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1530         try {
1531
1532                 bool good = true;
1533
1534                 string line = getline(file);
1535
1536                 //before we added this check
1537                 if (line[0] != '#') {  good = false;  }
1538                 else {
1539                         //rip off #
1540                         line = line.substr(1);
1541
1542                         vector<string> versionVector;
1543                         splitAtChar(version, versionVector, '.');
1544
1545                         //check file version
1546                         vector<string> linesVector;
1547                         splitAtChar(line, linesVector, '.');
1548
1549                         if (versionVector.size() != linesVector.size()) { good = false; }
1550                         else {
1551                                 for (int j = 0; j < versionVector.size(); j++) {
1552                                         int num1, num2;
1553                                         convert(versionVector[j], num1);
1554                                         convert(linesVector[j], num2);
1555
1556                                         //if mothurs version is newer than this files version, then we want to remake it
1557                                         if (num1 > num2) {  good = false; break;  }
1558                                 }
1559                         }
1560
1561                 }
1562
1563                 if (!good) {  file.close();  }
1564                 else { file.seekg(0);  }
1565
1566                 return good;
1567         }
1568         catch(exception& e) {
1569                 errorOut(e, "MothurOut", "checkReleaseVersion");
1570                 exit(1);
1571         }
1572 }
1573
1574 /**************************************************************************************************/
1575
1576
1577
1578
1579