mothurout.cpp

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