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 unsigned int MothurOut::fromBase36(string base36){
1160         try {
1161                 unsigned int num = 0;
1162
1163                 map<char, int> converts;
1164                 converts['A'] = 0;
1165                 converts['a'] = 0;
1166                 converts['B'] = 1;
1167                 converts['b'] = 1;
1168                 converts['C'] = 2;
1169                 converts['c'] = 2;
1170                 converts['D'] = 3;
1171                 converts['d'] = 3;
1172                 converts['E'] = 4;
1173                 converts['e'] = 4;
1174                 converts['F'] = 5;
1175                 converts['f'] = 5;
1176                 converts['G'] = 6;
1177                 converts['g'] = 6;
1178                 converts['H'] = 7;
1179                 converts['h'] = 7;
1180                 converts['I'] = 8;
1181                 converts['i'] = 8;
1182                 converts['J'] = 9;
1183                 converts['j'] = 9;
1184                 converts['K'] = 10;
1185                 converts['k'] = 10;
1186                 converts['L'] = 11;
1187                 converts['l'] = 11;
1188                 converts['M'] = 12;
1189                 converts['m'] = 12;
1190                 converts['N'] = 13;
1191                 converts['n'] = 13;
1192                 converts['O'] = 14;
1193                 converts['o'] = 14;
1194                 converts['P'] = 15;
1195                 converts['p'] = 15;
1196                 converts['Q'] = 16;
1197                 converts['q'] = 16;
1198                 converts['R'] = 17;
1199                 converts['r'] = 17;
1200                 converts['S'] = 18;
1201                 converts['s'] = 18;
1202                 converts['T'] = 19;
1203                 converts['t'] = 19;
1204                 converts['U'] = 20;
1205                 converts['u'] = 20;
1206                 converts['V'] = 21;
1207                 converts['v'] = 21;
1208                 converts['W'] = 22;
1209                 converts['w'] = 22;
1210                 converts['X'] = 23;
1211                 converts['x'] = 23;
1212                 converts['Y'] = 24;
1213                 converts['y'] = 24;
1214                 converts['Z'] = 25;
1215                 converts['z'] = 25;
1216                 converts['0'] = 26;
1217                 converts['1'] = 27;
1218                 converts['2'] = 28;
1219                 converts['3'] = 29;
1220                 converts['4'] = 30;
1221                 converts['5'] = 31;
1222                 converts['6'] = 32;
1223                 converts['7'] = 33;
1224                 converts['8'] = 34;
1225                 converts['9'] = 35;
1226
1227                 int i = 0;
1228                 while (i < base36.length()) {
1229                         char c = base36[i];
1230                         num = 36 * num + converts[c];
1231                         i++;
1232                 }
1233
1234                 return num;
1235
1236         }
1237         catch(exception& e) {
1238                 errorOut(e, "MothurOut", "fromBase36");
1239                 exit(1);
1240         }
1241 }
1242 /***********************************************************************/
1243
1244 int MothurOut::factorial(int num){
1245         try {
1246                 int total = 1;
1247
1248                 for (int i = 1; i <= num; i++) {
1249                         total *= i;
1250                 }
1251
1252                 return total;
1253         }
1254         catch(exception& e) {
1255                 errorOut(e, "MothurOut", "factorial");
1256                 exit(1);
1257         }
1258 }
1259 /***********************************************************************/
1260
1261 int MothurOut::getNumSeqs(ifstream& file){
1262         try {
1263                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1264                 file.seekg(0);
1265                 return numSeqs;
1266         }
1267         catch(exception& e) {
1268                 errorOut(e, "MothurOut", "getNumSeqs");
1269                 exit(1);
1270         }
1271 }
1272 /***********************************************************************/
1273 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1274         try {
1275                 string input;
1276                 numSeqs = 0;
1277                 while(!file.eof()){
1278                         input = getline(file);
1279                         if (input.length() != 0) {
1280                                 if(input[0] == '>'){ numSeqs++; }
1281                         }
1282                 }
1283         }
1284         catch(exception& e) {
1285                 errorOut(e, "MothurOut", "getNumSeqs");
1286                 exit(1);
1287         }
1288 }
1289 /***********************************************************************/
1290
1291 //This function parses the estimator options and puts them in a vector
1292 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1293         try {
1294                 string individual = "";
1295                 int estimLength = estim.size();
1296                 for(int i=0;i<estimLength;i++){
1297                         if(estim[i] == symbol){
1298                                 container.push_back(individual);
1299                                 individual = "";
1300                         }
1301                         else{
1302                                 individual += estim[i];
1303                         }
1304                 }
1305                 container.push_back(individual);
1306
1307         }
1308         catch(exception& e) {
1309                 errorOut(e, "MothurOut", "splitAtChar");
1310                 exit(1);
1311         }
1312 }
1313
1314 /***********************************************************************/
1315
1316 //This function parses the estimator options and puts them in a vector
1317 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1318         try {
1319                 string individual = "";
1320                 int estimLength = estim.size();
1321                 for(int i=0;i<estimLength;i++){
1322                         if(estim[i] == '-'){
1323                                 container.push_back(individual);
1324                                 individual = "";
1325                         }
1326                         else{
1327                                 individual += estim[i];
1328                         }
1329                 }
1330                 container.push_back(individual);
1331
1332
1333         /*      string individual;
1334
1335                 while (estim.find_first_of('-') != -1) {
1336                         individual = estim.substr(0,estim.find_first_of('-'));
1337                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1338                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1339                                 container.push_back(individual);
1340                         }
1341                 }
1342                 //get last one
1343                 container.push_back(estim); */
1344         }
1345         catch(exception& e) {
1346                 errorOut(e, "MothurOut", "splitAtDash");
1347                 exit(1);
1348         }
1349 }
1350
1351 /***********************************************************************/
1352 //This function parses the label options and puts them in a set
1353 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1354         try {
1355                 string individual = "";
1356                 int estimLength = estim.size();
1357                 for(int i=0;i<estimLength;i++){
1358                         if(estim[i] == '-'){
1359                                 container.insert(individual);
1360                                 individual = "";
1361                         }
1362                         else{
1363                                 individual += estim[i];
1364                         }
1365                 }
1366                 container.insert(individual);
1367
1368         //      string individual;
1369
1370         //      while (estim.find_first_of('-') != -1) {
1371         //              individual = estim.substr(0,estim.find_first_of('-'));
1372         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1373         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1374         //                      container.insert(individual);
1375         //              }
1376         //      }
1377                 //get last one
1378         //      container.insert(estim);
1379
1380         }
1381         catch(exception& e) {
1382                 errorOut(e, "MothurOut", "splitAtDash");
1383                 exit(1);
1384         }
1385 }
1386 /***********************************************************************/
1387 //This function parses the line options and puts them in a set
1388 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1389         try {
1390                 string individual;
1391                 int lineNum;
1392
1393                 while (estim.find_first_of('-') != -1) {
1394                         individual = estim.substr(0,estim.find_first_of('-'));
1395                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1396                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1397                                 convert(individual, lineNum); //convert the string to int
1398                                 container.insert(lineNum);
1399                         }
1400                 }
1401                 //get last one
1402                 convert(estim, lineNum); //convert the string to int
1403                 container.insert(lineNum);
1404         }
1405         catch(exception& e) {
1406                 errorOut(e, "MothurOut", "splitAtDash");
1407                 exit(1);
1408         }
1409 }
1410 /***********************************************************************/
1411 //This function parses the a string and puts peices in a vector
1412 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1413         try {
1414                 string individual = "";
1415                 int estimLength = estim.size();
1416                 for(int i=0;i<estimLength;i++){
1417                         if(estim[i] == ','){
1418                                 container.push_back(individual);
1419                                 individual = "";
1420                         }
1421                         else{
1422                                 individual += estim[i];
1423                         }
1424                 }
1425                 container.push_back(individual);
1426
1427
1428
1429
1430 //              string individual;
1431 //
1432 //              while (estim.find_first_of(',') != -1) {
1433 //                      individual = estim.substr(0,estim.find_first_of(','));
1434 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1435 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1436 //                              container.push_back(individual);
1437 //                      }
1438 //              }
1439 //              //get last one
1440 //              container.push_back(estim);
1441         }
1442         catch(exception& e) {
1443                 errorOut(e, "MothurOut", "splitAtComma");
1444                 exit(1);
1445         }
1446 }
1447 /***********************************************************************/
1448
1449 //This function splits up the various option parameters
1450 void MothurOut::splitAtComma(string& prefix, string& suffix){
1451         try {
1452                 prefix = suffix.substr(0,suffix.find_first_of(','));
1453                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1454                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1455                         string space = " ";
1456                         while(suffix.at(0) == ' ')
1457                                 suffix = suffix.substr(1, suffix.length());
1458                 }
1459
1460         }
1461         catch(exception& e) {
1462                 errorOut(e, "MothurOut", "splitAtComma");
1463                 exit(1);
1464         }
1465 }
1466 /***********************************************************************/
1467
1468 //This function separates the key value from the option value i.e. dist=96_...
1469 void MothurOut::splitAtEquals(string& key, string& value){
1470         try {
1471                 if(value.find_first_of('=') != -1){
1472                         key = value.substr(0,value.find_first_of('='));
1473                         if ((value.find_first_of('=')+1) <= value.length()) {
1474                                 value = value.substr(value.find_first_of('=')+1, value.length());
1475                         }
1476                 }else{
1477                         key = value;
1478                         value = 1;
1479                 }
1480         }
1481         catch(exception& e) {
1482                 errorOut(e, "MothurOut", "splitAtEquals");
1483                 exit(1);
1484         }
1485 }
1486
1487 /**************************************************************************************************/
1488
1489 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1490         try {
1491                 for (int i = 0; i < Groups.size(); i++) {
1492                         if (groupname == Groups[i]) { return true; }
1493                 }
1494                 return false;
1495         }
1496         catch(exception& e) {
1497                 errorOut(e, "MothurOut", "inUsersGroups");
1498                 exit(1);
1499         }
1500 }
1501 /**************************************************************************************************/
1502 //returns true if any of the strings in first vector are in second vector
1503 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1504         try {
1505
1506                 for (int i = 0; i < groupnames.size(); i++) {
1507                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1508                 }
1509                 return false;
1510         }
1511         catch(exception& e) {
1512                 errorOut(e, "MothurOut", "inUsersGroups");
1513                 exit(1);
1514         }
1515 }
1516 /***********************************************************************/
1517 //this function determines if the user has given us labels that are smaller than the given label.
1518 //if so then it returns true so that the calling function can run the previous valid distance.
1519 //it's a "smart" distance function.  It also checks for invalid labels.
1520 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1521         try {
1522
1523                 set<string>::iterator it;
1524                 vector<float> orderFloat;
1525                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1526                 map<string, float>::iterator it2;
1527                 float labelFloat;
1528                 bool smaller = false;
1529
1530                 //unique is the smallest line
1531                 if (label == "unique") {  return false;  }
1532                 else {
1533                         if (convertTestFloat(label, labelFloat)) {
1534                                 convert(label, labelFloat);
1535                         }else { //cant convert
1536                                 return false;
1537                         }
1538                 }
1539
1540                 //go through users set and make them floats
1541                 for(it = userLabels.begin(); it != userLabels.end();) {
1542
1543                         float temp;
1544                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1545                                 convert(*it, temp);
1546                                 orderFloat.push_back(temp);
1547                                 userMap[*it] = temp;
1548                                 it++;
1549                         }else if (*it == "unique") {
1550                                 orderFloat.push_back(-1.0);
1551                                 userMap["unique"] = -1.0;
1552                                 it++;
1553                         }else {
1554                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1555                                 userLabels.erase(it++);
1556                         }
1557                 }
1558
1559                 //sort order
1560                 sort(orderFloat.begin(), orderFloat.end());
1561
1562                 /*************************************************/
1563                 //is this label bigger than any of the users labels
1564                 /*************************************************/
1565
1566                 //loop through order until you find a label greater than label
1567                 for (int i = 0; i < orderFloat.size(); i++) {
1568                         if (orderFloat[i] < labelFloat) {
1569                                 smaller = true;
1570                                 if (orderFloat[i] == -1) {
1571                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1572                                         userLabels.erase("unique");
1573                                 }
1574                                 else {
1575                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1576                                         string s = "";
1577                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1578                                                 if (it2->second == orderFloat[i]) {
1579                                                         s = it2->first;
1580                                                         //remove small labels
1581                                                         userLabels.erase(s);
1582                                                         break;
1583                                                 }
1584                                         }
1585                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1586                                 }
1587                         //since they are sorted once you find a bigger one stop looking
1588                         }else { break; }
1589                 }
1590
1591                 return smaller;
1592
1593         }
1594         catch(exception& e) {
1595                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1596                 exit(1);
1597         }
1598 }
1599
1600 /**************************************************************************************************/
1601 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1602         try {
1603
1604                 bool good = true;
1605
1606                 string line = getline(file);
1607
1608                 //before we added this check
1609                 if (line[0] != '#') {  good = false;  }
1610                 else {
1611                         //rip off #
1612                         line = line.substr(1);
1613
1614                         vector<string> versionVector;
1615                         splitAtChar(version, versionVector, '.');
1616
1617                         //check file version
1618                         vector<string> linesVector;
1619                         splitAtChar(line, linesVector, '.');
1620
1621                         if (versionVector.size() != linesVector.size()) { good = false; }
1622                         else {
1623                                 for (int j = 0; j < versionVector.size(); j++) {
1624                                         int num1, num2;
1625                                         convert(versionVector[j], num1);
1626                                         convert(linesVector[j], num2);
1627
1628                                         //if mothurs version is newer than this files version, then we want to remake it
1629                                         if (num1 > num2) {  good = false; break;  }
1630                                 }
1631                         }
1632
1633                 }
1634
1635                 if (!good) {  file.close();  }
1636                 else { file.seekg(0);  }
1637
1638                 return good;
1639         }
1640         catch(exception& e) {
1641                 errorOut(e, "MothurOut", "checkReleaseVersion");
1642                 exit(1);
1643         }
1644 }
1645
1646 /**************************************************************************************************/
1647
1648
1649
1650
1651