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                 fileHandle.open(fileName.c_str(), ios::app);
 261                 if(!fileHandle) {
 262                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 263                         return 1;
 264                 }
 265                 else {
 266                         return 0;
 267                 }
 268         }
 269         catch(exception& e) {
 270                 errorOut(e, "MothurOut", "openOutputFileAppend");
 271                 exit(1);
 272         }
 273 }
 274 /***********************************************************************/
 275 void MothurOut::gobble(istream& f){
 276         try {
 277                 char d;
 278                 while(isspace(d=f.get()))               {;}
 279                 f.putback(d);
 280         }
 281         catch(exception& e) {
 282                 errorOut(e, "MothurOut", "gobble");
 283                 exit(1);
 284         }
 285 }
 286 /***********************************************************************/
 287 void MothurOut::gobble(istringstream& f){
 288         try {
 289                 char d;
 290                 while(isspace(d=f.get()))               {;}
 291                 f.putback(d);
 292         }
 293         catch(exception& e) {
 294                 errorOut(e, "MothurOut", "gobble");
 295                 exit(1);
 296         }
 297 }
 298
 299 /***********************************************************************/
 300
 301 string MothurOut::getline(istringstream& fileHandle) {
 302         try {
 303
 304                 string line = "";
 305
 306                 while (!fileHandle.eof())       {
 307                         //get next character
 308                         char c = fileHandle.get();
 309
 310                         //are you at the end of the line
 311                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 312                         else {          line += c;              }
 313                 }
 314
 315                 return line;
 316
 317         }
 318         catch(exception& e) {
 319                 errorOut(e, "MothurOut", "getline");
 320                 exit(1);
 321         }
 322 }
 323 /***********************************************************************/
 324
 325 string MothurOut::getline(ifstream& fileHandle) {
 326         try {
 327
 328                 string line = "";
 329
 330                 while (!fileHandle.eof())       {
 331                         //get next character
 332                         char c = fileHandle.get();
 333
 334                         //are you at the end of the line
 335                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 336                         else {          line += c;              }
 337                 }
 338
 339                 return line;
 340
 341         }
 342         catch(exception& e) {
 343                 errorOut(e, "MothurOut", "getline");
 344                 exit(1);
 345         }
 346 }
 347 /***********************************************************************/
 348
 349 string MothurOut::getRootName(string longName){
 350         try {
 351
 352                 string rootName = longName;
 353
 354                 if(longName.find_last_of(".") != longName.npos){
 355                         int pos = longName.find_last_of('.')+1;
 356                         rootName = longName.substr(0, pos);
 357                 }
 358
 359                 return rootName;
 360         }
 361         catch(exception& e) {
 362                 errorOut(e, "MothurOut", "getRootName");
 363                 exit(1);
 364         }
 365 }
 366 /***********************************************************************/
 367
 368 string MothurOut::getSimpleName(string longName){
 369         try {
 370                 string simpleName = longName;
 371
 372                 size_t found;
 373                 found=longName.find_last_of("/\\");
 374
 375                 if(found != longName.npos){
 376                         simpleName = longName.substr(found+1);
 377                 }
 378
 379                 return simpleName;
 380         }
 381         catch(exception& e) {
 382                 errorOut(e, "MothurOut", "getSimpleName");
 383                 exit(1);
 384         }
 385 }
 386
 387 /***********************************************************************/
 388
 389 string MothurOut::getPathName(string longName){
 390         try {
 391                 string rootPathName = longName;
 392
 393                 if(longName.find_last_of("/\\") != longName.npos){
 394                         int pos = longName.find_last_of("/\\")+1;
 395                         rootPathName = longName.substr(0, pos);
 396                 }
 397
 398                 return rootPathName;
 399         }
 400         catch(exception& e) {
 401                 errorOut(e, "MothurOut", "getPathName");
 402                 exit(1);
 403         }
 404
 405 }
 406 /***********************************************************************/
 407
 408 string MothurOut::hasPath(string longName){
 409         try {
 410                 string path = "";
 411
 412                 size_t found;
 413                 found=longName.find_last_of("~/\\");
 414
 415                 if(found != longName.npos){
 416                         path = longName.substr(0, found+1);
 417                 }
 418
 419                 return path;
 420         }
 421         catch(exception& e) {
 422                 errorOut(e, "MothurOut", "hasPath");
 423                 exit(1);
 424         }
 425 }
 426
 427 /***********************************************************************/
 428
 429 string MothurOut::getExtension(string longName){
 430         try {
 431                 string extension = longName;
 432
 433                 if(longName.find_last_of('.') != longName.npos){
 434                         int pos = longName.find_last_of('.');
 435                         extension = longName.substr(pos, longName.length());
 436                 }
 437
 438                 return extension;
 439         }
 440         catch(exception& e) {
 441                 errorOut(e, "MothurOut", "getExtension");
 442                 exit(1);
 443         }
 444 }
 445 /***********************************************************************/
 446 bool MothurOut::isBlank(string fileName){
 447         try {
 448                 ifstream fileHandle;
 449                 fileHandle.open(fileName.c_str());
 450                 if(!fileHandle) {
 451                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 452                         return false;
 453                 }else {
 454                         //check for blank file
 455                         gobble(fileHandle);
 456                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 457                 }
 458                 return false;
 459         }
 460         catch(exception& e) {
 461                 errorOut(e, "MothurOut", "isBlank");
 462                 exit(1);
 463         }
 464 }
 465 /***********************************************************************/
 466
 467 string MothurOut::getFullPathName(string fileName){
 468         try{
 469
 470         string path = hasPath(fileName);
 471         string newFileName;
 472         int pos;
 473
 474         if (path == "") { return fileName; } //its a simple name
 475         else { //we need to complete the pathname
 476                 // ex. ../../../filename
 477                 // cwd = /user/work/desktop
 478
 479                 string cwd;
 480                 //get current working directory
 481                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 482
 483                         if (path.find("~") != -1) { //go to home directory
 484                                 string homeDir = getenv ("HOME");
 485                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 486                                 return newFileName;
 487                         }else { //find path
 488                                 if (path.rfind("./") == -1) { return fileName; } //already complete name
 489                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 490
 491                                 char* cwdpath = new char[1024];
 492
 493                                 size_t size;
 494                                 cwdpath=getcwd(cwdpath,size);
 495
 496                                 cwd = cwdpath;
 497
 498                                 //rip off first '/'
 499                                 string simpleCWD;
 500                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 501
 502                                 //break apart the current working directory
 503                                 vector<string> dirs;
 504                                 while (simpleCWD.find_first_of('/') != -1) {
 505                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 506                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 507                                         dirs.push_back(dir);
 508                                 }
 509                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 510                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 511
 512
 513                                 int index = dirs.size()-1;
 514
 515                                 while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
 516                                         if (pos == 0) { break;  //you are at the end
 517                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 518                                                 path = path.substr(0, pos-1);
 519                                                 index--;
 520                                                 if (index == 0) {  break; }
 521                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 522                                                 path = path.substr(0, pos);
 523                                         }else if (pos == 1) { break;  //you are at the end
 524                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 525                                 }
 526
 527                                 for (int i = index; i >= 0; i--) {
 528                                         newFileName = dirs[i] +  "/" + newFileName;
 529                                 }
 530
 531                                 newFileName =  "/" +  newFileName;
 532                                 return newFileName;
 533                         }
 534                 #else
 535                         if (path.find("~") != -1) { //go to home directory
 536                                 string homeDir = getenv ("HOMEPATH");
 537                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 538                                 return newFileName;
 539                         }else { //find path
 540                                 if (path.rfind(".\\") == -1) { return fileName; } //already complete name
 541                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 542
 543                                 char *cwdpath = NULL;
 544                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 545                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 546                                 else { cwd = "";  }
 547
 548                                 //break apart the current working directory
 549                                 vector<string> dirs;
 550                                 while (cwd.find_first_of('\\') != -1) {
 551                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 552                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 553                                         dirs.push_back(dir);
 554
 555                                 }
 556                                 //get last one
 557                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 558
 559                                 int index = dirs.size()-1;
 560
 561                                 while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
 562                                         if (pos == 0) { break;  //you are at the end
 563                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 564                                                 path = path.substr(0, pos-1);
 565                                                 index--;
 566                                                 if (index == 0) {  break; }
 567                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 568                                                 path = path.substr(0, pos);
 569                                         }else if (pos == 1) { break;  //you are at the end
 570                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 571                                 }
 572
 573                                 for (int i = index; i >= 0; i--) {
 574                                         newFileName = dirs[i] +  "\\" + newFileName;
 575                                 }
 576
 577                                 return newFileName;
 578                         }
 579
 580                 #endif
 581         }
 582         }
 583         catch(exception& e) {
 584                 errorOut(e, "MothurOut", "getFullPathName");
 585                 exit(1);
 586         }
 587 }
 588 /***********************************************************************/
 589
 590 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 591         try {
 592                         //get full path name
 593                         string completeFileName = getFullPathName(fileName);
 594
 595                         fileHandle.open(completeFileName.c_str());
 596                         if(!fileHandle) {
 597                                 return 1;
 598                         }else {
 599                                 //check for blank file
 600                                 gobble(fileHandle);
 601                                 return 0;
 602                         }
 603         }
 604         catch(exception& e) {
 605                 errorOut(e, "MothurOut", "openInputFile - no Error");
 606                 exit(1);
 607         }
 608 }
 609 /***********************************************************************/
 610
 611 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 612         try {
 613                 //get full path name
 614                 string completeFileName = getFullPathName(fileName);
 615
 616                 fileHandle.open(completeFileName.c_str());
 617                 if(!fileHandle) {
 618                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 619                         return 1;
 620                 }
 621                 else {
 622                         //check for blank file
 623                         gobble(fileHandle);
 624                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 625
 626                         return 0;
 627                 }
 628         }
 629         catch(exception& e) {
 630                 errorOut(e, "MothurOut", "openInputFile");
 631                 exit(1);
 632         }
 633 }
 634 /***********************************************************************/
 635
 636 int MothurOut::renameFile(string oldName, string newName){
 637         try {
 638                 ifstream inTest;
 639                 int exist = openInputFile(newName, inTest, "");
 640
 641         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 642                 if (exist == 0) { //you could open it so you want to delete it
 643                         inTest.close();
 644                         string command = "rm " + newName;
 645                         system(command.c_str());
 646                 }
 647
 648                 string command = "mv " + oldName + " " + newName;
 649                 system(command.c_str());
 650         #else
 651                 remove(newName.c_str());
 652                 int renameOk = rename(oldName.c_str(), newName.c_str());
 653         #endif
 654                 return 0;
 655
 656         }
 657         catch(exception& e) {
 658                 errorOut(e, "MothurOut", "renameFile");
 659                 exit(1);
 660         }
 661 }
 662
 663 /***********************************************************************/
 664
 665 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 666         try {
 667
 668                 string completeFileName = getFullPathName(fileName);
 669
 670                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 671                 if(!fileHandle) {
 672                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 673                         return 1;
 674                 }
 675                 else {
 676                         return 0;
 677                 }
 678         }
 679         catch(exception& e) {
 680                 errorOut(e, "MothurOut", "openOutputFile");
 681                 exit(1);
 682         }
 683
 684 }
 685
 686 /**************************************************************************************************/
 687 void MothurOut::appendFiles(string temp, string filename) {
 688         try{
 689                 ofstream output;
 690                 ifstream input;
 691
 692                 //open output file in append mode
 693                 openOutputFileAppend(filename, output);
 694                 int ableToOpen = openInputFile(temp, input, "no error");
 695
 696                 if (ableToOpen == 0) { //you opened it
 697                         while(char c = input.get()){
 698                                 if(input.eof())         {       break;                  }
 699                                 else                            {       output << c;    }
 700                         }
 701                         input.close();
 702                 }
 703
 704                 output.close();
 705         }
 706         catch(exception& e) {
 707                 errorOut(e, "MothurOut", "appendFiles");
 708                 exit(1);
 709         }
 710 }
 711
 712 /**************************************************************************************************/
 713 string MothurOut::sortFile(string distFile, string outputDir){
 714         try {
 715
 716                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 717                 string outfile = getRootName(distFile) + "sorted.dist";
 718
 719
 720                 //if you can, use the unix sort since its been optimized for years
 721                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 722                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 723                         system(command.c_str());
 724                 #else //you are stuck with my best attempt...
 725                         //windows sort does not have a way to specify a column, only a character in the line
 726                         //since we cannot assume that the distance will always be at the the same character location on each line
 727                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 728
 729                         //read in file line by file and put distance first
 730                         string tempDistFile = distFile + ".temp";
 731                         ifstream input;
 732                         ofstream output;
 733                         openInputFile(distFile, input);
 734                         openOutputFile(tempDistFile, output);
 735
 736                         string firstName, secondName;
 737                         float dist;
 738                         while (input) {
 739                                 input >> firstName >> secondName >> dist;
 740                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 741                                 gobble(input);
 742                         }
 743                         input.close();
 744                         output.close();
 745
 746
 747                         //sort using windows sort
 748                         string tempOutfile = outfile + ".temp";
 749                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 750                         system(command.c_str());
 751
 752                         //read in sorted file and put distance at end again
 753                         ifstream input2;
 754                         openInputFile(tempOutfile, input2);
 755                         openOutputFile(outfile, output);
 756
 757                         while (input2) {
 758                                 input2 >> dist >> firstName >> secondName;
 759                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 760                                 gobble(input2);
 761                         }
 762                         input2.close();
 763                         output.close();
 764
 765                         //remove temp files
 766                         remove(tempDistFile.c_str());
 767                         remove(tempOutfile.c_str());
 768                 #endif
 769
 770                 return outfile;
 771         }
 772         catch(exception& e) {
 773                 errorOut(e, "MothurOut", "sortFile");
 774                 exit(1);
 775         }
 776 }
 777 /**************************************************************************************************/
 778 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
 779         try {
 780                         vector<unsigned long int> positions;
 781                         ifstream inFASTA;
 782                         openInputFile(filename, inFASTA);
 783
 784                         string input;
 785                         while(!inFASTA.eof()){
 786                                 input = getline(inFASTA);
 787                                 if (input.length() != 0) {
 788                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
 789                                 }
 790                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
 791                         }
 792                         inFASTA.close();
 793
 794                         num = positions.size();
 795
 796                         /*FILE * pFile;
 797                         long size;
 798
 799                         //get num bytes in file
 800                         pFile = fopen (filename.c_str(),"rb");
 801                         if (pFile==NULL) perror ("Error opening file");
 802                         else{
 803                                 fseek (pFile, 0, SEEK_END);
 804                                 size=ftell (pFile);
 805                                 fclose (pFile);
 806                         }*/
 807
 808                         unsigned long int size = positions[(positions.size()-1)];
 809                         ifstream in;
 810                         openInputFile(filename, in);
 811
 812                         in.seekg(size);
 813
 814                         while(char c = in.get()){
 815                                 if(in.eof())            {       break;  }
 816                                 else                            {       size++; }
 817                         }
 818                         in.close();
 819
 820                         positions.push_back(size);
 821
 822                         return positions;
 823         }
 824         catch(exception& e) {
 825                 errorOut(e, "MothurOut", "setFilePosFasta");
 826                 exit(1);
 827         }
 828 }
 829 /**************************************************************************************************/
 830 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
 831         try {
 832
 833                         vector<unsigned long int> positions;
 834                         ifstream in;
 835                         openInputFile(filename, in);
 836
 837                         string input;
 838                         while(!in.eof()){
 839                                 unsigned long int lastpos = in.tellg();
 840                                 input = getline(in);
 841                                 if (input.length() != 0) {
 842                                         unsigned long int pos = in.tellg();
 843                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
 844                                         else {  positions.push_back(lastpos);  }
 845                                 }
 846                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
 847                         }
 848                         in.close();
 849
 850                         num = positions.size();
 851
 852                         FILE * pFile;
 853                         unsigned long int size;
 854
 855                         //get num bytes in file
 856                         pFile = fopen (filename.c_str(),"rb");
 857                         if (pFile==NULL) perror ("Error opening file");
 858                         else{
 859                                 fseek (pFile, 0, SEEK_END);
 860                                 size=ftell (pFile);
 861                                 fclose (pFile);
 862                         }
 863
 864                         positions.push_back(size);
 865
 866                         return positions;
 867         }
 868         catch(exception& e) {
 869                 errorOut(e, "MothurOut", "setFilePosEachLine");
 870                 exit(1);
 871         }
 872 }
 873 /**************************************************************************************************/
 874
 875 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 876         try{
 877
 878                 vector<unsigned long int> filePos;
 879                 filePos.push_back(0);
 880
 881                 FILE * pFile;
 882                 unsigned long int size;
 883
 884                 //get num bytes in file
 885                 pFile = fopen (filename.c_str(),"rb");
 886                 if (pFile==NULL) perror ("Error opening file");
 887                 else{
 888                         fseek (pFile, 0, SEEK_END);
 889                         size=ftell (pFile);
 890                         fclose (pFile);
 891                 }
 892
 893                 //estimate file breaks
 894                 unsigned long int chunkSize = 0;
 895                 chunkSize = size / proc;
 896
 897                 //file to small to divide by processors
 898                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
 899
 900                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 901                 for (int i = 0; i < proc; i++) {
 902                         unsigned long int spot = (i+1) * chunkSize;
 903
 904                         ifstream in;
 905                         openInputFile(filename, in);
 906                         in.seekg(spot);
 907
 908                         //look for next '>'
 909                         unsigned long int newSpot = spot;
 910                         while (!in.eof()) {
 911                            char c = in.get();
 912                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
 913                         }
 914
 915                         //there was not another sequence before the end of the file
 916                         unsigned long int sanityPos = in.tellg();
 917                         if (sanityPos = -1) {   break;  }
 918                         else {   filePos.push_back(newSpot);  }
 919
 920                         in.close();
 921                 }
 922
 923                 //save end pos
 924                 filePos.push_back(size);
 925
 926                 //sanity check filePos
 927                 for (int i = 0; i < (filePos.size()-1); i++) {
 928                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 929                 }
 930
 931                 proc = (filePos.size() - 1);
 932
 933                 return filePos;
 934         }
 935         catch(exception& e) {
 936                 errorOut(e, "MothurOut", "divideFile");
 937                 exit(1);
 938         }
 939 }
 940
 941 /***********************************************************************/
 942
 943 bool MothurOut::isTrue(string f){
 944         try {
 945
 946                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
 947
 948                 if ((f == "TRUE") || (f == "T")) {      return true;    }
 949                 else {  return false;  }
 950         }
 951         catch(exception& e) {
 952                 errorOut(e, "MothurOut", "isTrue");
 953                 exit(1);
 954         }
 955 }
 956
 957 /***********************************************************************/
 958
 959 float MothurOut::roundDist(float dist, int precision){
 960         try {
 961                 return int(dist * precision + 0.5)/float(precision);
 962         }
 963         catch(exception& e) {
 964                 errorOut(e, "MothurOut", "roundDist");
 965                 exit(1);
 966         }
 967 }
 968 /***********************************************************************/
 969
 970 float MothurOut::ceilDist(float dist, int precision){
 971         try {
 972                 return int(ceil(dist * precision))/float(precision);
 973         }
 974         catch(exception& e) {
 975                 errorOut(e, "MothurOut", "ceilDist");
 976                 exit(1);
 977         }
 978 }
 979
 980 /***********************************************************************/
 981
 982 int MothurOut::getNumNames(string names){
 983         try {
 984                 int count = 0;
 985
 986                 if(names != ""){
 987                         count = 1;
 988                         for(int i=0;i<names.size();i++){
 989                                 if(names[i] == ','){
 990                                         count++;
 991                                 }
 992                         }
 993                 }
 994
 995                 return count;
 996         }
 997         catch(exception& e) {
 998                 errorOut(e, "MothurOut", "getNumNames");
 999                 exit(1);
1000         }
1001 }
1002
1003 /**************************************************************************************************/
1004
1005 vector<vector<double> > MothurOut::binomial(int maxOrder){
1006         try {
1007         vector<vector<double> > binomial(maxOrder+1);
1008
1009     for(int i=0;i<=maxOrder;i++){
1010                 binomial[i].resize(maxOrder+1);
1011                 binomial[i][0]=1;
1012                 binomial[0][i]=0;
1013     }
1014     binomial[0][0]=1;
1015
1016     binomial[1][0]=1;
1017     binomial[1][1]=1;
1018
1019     for(int i=2;i<=maxOrder;i++){
1020                 binomial[1][i]=0;
1021     }
1022
1023     for(int i=2;i<=maxOrder;i++){
1024                 for(int j=1;j<=maxOrder;j++){
1025                         if(i==j){       binomial[i][j]=1;                                                                       }
1026                         if(j>i) {       binomial[i][j]=0;                                                                       }
1027                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1028                 }
1029     }
1030
1031         return binomial;
1032
1033         }
1034         catch(exception& e) {
1035                 errorOut(e, "MothurOut", "binomial");
1036                 exit(1);
1037         }
1038 }
1039
1040 /***********************************************************************/
1041
1042 int MothurOut::factorial(int num){
1043         try {
1044                 int total = 1;
1045
1046                 for (int i = 1; i <= num; i++) {
1047                         total *= i;
1048                 }
1049
1050                 return total;
1051         }
1052         catch(exception& e) {
1053                 errorOut(e, "MothurOut", "factorial");
1054                 exit(1);
1055         }
1056 }
1057 /***********************************************************************/
1058
1059 int MothurOut::getNumSeqs(ifstream& file){
1060         try {
1061                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1062                 file.seekg(0);
1063                 return numSeqs;
1064         }
1065         catch(exception& e) {
1066                 errorOut(e, "MothurOut", "getNumSeqs");
1067                 exit(1);
1068         }
1069 }
1070 /***********************************************************************/
1071 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1072         try {
1073                 string input;
1074                 numSeqs = 0;
1075                 while(!file.eof()){
1076                         input = getline(file);
1077                         if (input.length() != 0) {
1078                                 if(input[0] == '>'){ numSeqs++; }
1079                         }
1080                 }
1081         }
1082         catch(exception& e) {
1083                 errorOut(e, "MothurOut", "getNumSeqs");
1084                 exit(1);
1085         }
1086 }
1087 /***********************************************************************/
1088
1089 //This function parses the estimator options and puts them in a vector
1090 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1091         try {
1092                 string individual;
1093
1094                 while (estim.find_first_of(symbol) != -1) {
1095                         individual = estim.substr(0,estim.find_first_of(symbol));
1096                         if ((estim.find_first_of(symbol)+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1097                                 estim = estim.substr(estim.find_first_of(symbol)+1, estim.length());
1098                                 container.push_back(individual);
1099                         }
1100                 }
1101                 //get last one
1102                 container.push_back(estim);
1103         }
1104         catch(exception& e) {
1105                 errorOut(e, "MothurOut", "splitAtChar");
1106                 exit(1);
1107         }
1108 }
1109
1110 /***********************************************************************/
1111
1112 //This function parses the estimator options and puts them in a vector
1113 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1114         try {
1115                 string individual;
1116
1117                 while (estim.find_first_of('-') != -1) {
1118                         individual = estim.substr(0,estim.find_first_of('-'));
1119                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1120                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1121                                 container.push_back(individual);
1122                         }
1123                 }
1124                 //get last one
1125                 container.push_back(estim);
1126         }
1127         catch(exception& e) {
1128                 errorOut(e, "MothurOut", "splitAtDash");
1129                 exit(1);
1130         }
1131 }
1132
1133 /***********************************************************************/
1134 //This function parses the label options and puts them in a set
1135 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1136         try {
1137                 string individual;
1138
1139                 while (estim.find_first_of('-') != -1) {
1140                         individual = estim.substr(0,estim.find_first_of('-'));
1141                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1142                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1143                                 container.insert(individual);
1144                         }
1145                 }
1146                 //get last one
1147                 container.insert(estim);
1148         }
1149         catch(exception& e) {
1150                 errorOut(e, "MothurOut", "splitAtDash");
1151                 exit(1);
1152         }
1153 }
1154 /***********************************************************************/
1155 //This function parses the line options and puts them in a set
1156 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1157         try {
1158                 string individual;
1159                 int lineNum;
1160
1161                 while (estim.find_first_of('-') != -1) {
1162                         individual = estim.substr(0,estim.find_first_of('-'));
1163                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1164                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1165                                 convert(individual, lineNum); //convert the string to int
1166                                 container.insert(lineNum);
1167                         }
1168                 }
1169                 //get last one
1170                 convert(estim, lineNum); //convert the string to int
1171                 container.insert(lineNum);
1172         }
1173         catch(exception& e) {
1174                 errorOut(e, "MothurOut", "splitAtDash");
1175                 exit(1);
1176         }
1177 }
1178 /***********************************************************************/
1179 //This function parses the a string and puts peices in a vector
1180 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1181         try {
1182                 string individual;
1183
1184                 while (estim.find_first_of(',') != -1) {
1185                         individual = estim.substr(0,estim.find_first_of(','));
1186                         if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1187                                 estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1188                                 container.push_back(individual);
1189                         }
1190                 }
1191                 //get last one
1192                 container.push_back(estim);
1193         }
1194         catch(exception& e) {
1195                 errorOut(e, "MothurOut", "splitAtComma");
1196                 exit(1);
1197         }
1198 }
1199 /***********************************************************************/
1200
1201 //This function splits up the various option parameters
1202 void MothurOut::splitAtComma(string& prefix, string& suffix){
1203         try {
1204                 prefix = suffix.substr(0,suffix.find_first_of(','));
1205                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1206                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1207                         string space = " ";
1208                         while(suffix.at(0) == ' ')
1209                                 suffix = suffix.substr(1, suffix.length());
1210                 }
1211
1212         }
1213         catch(exception& e) {
1214                 errorOut(e, "MothurOut", "splitAtComma");
1215                 exit(1);
1216         }
1217 }
1218 /***********************************************************************/
1219
1220 //This function separates the key value from the option value i.e. dist=96_...
1221 void MothurOut::splitAtEquals(string& key, string& value){
1222         try {
1223                 if(value.find_first_of('=') != -1){
1224                         key = value.substr(0,value.find_first_of('='));
1225                         if ((value.find_first_of('=')+1) <= value.length()) {
1226                                 value = value.substr(value.find_first_of('=')+1, value.length());
1227                         }
1228                 }else{
1229                         key = value;
1230                         value = 1;
1231                 }
1232         }
1233         catch(exception& e) {
1234                 errorOut(e, "MothurOut", "splitAtEquals");
1235                 exit(1);
1236         }
1237 }
1238
1239 /**************************************************************************************************/
1240
1241 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1242         try {
1243                 for (int i = 0; i < Groups.size(); i++) {
1244                         if (groupname == Groups[i]) { return true; }
1245                 }
1246                 return false;
1247         }
1248         catch(exception& e) {
1249                 errorOut(e, "MothurOut", "inUsersGroups");
1250                 exit(1);
1251         }
1252 }
1253 /**************************************************************************************************/
1254 //returns true if any of the strings in first vector are in second vector
1255 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1256         try {
1257
1258                 for (int i = 0; i < groupnames.size(); i++) {
1259                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1260                 }
1261                 return false;
1262         }
1263         catch(exception& e) {
1264                 errorOut(e, "MothurOut", "inUsersGroups");
1265                 exit(1);
1266         }
1267 }
1268 /***********************************************************************/
1269 //this function determines if the user has given us labels that are smaller than the given label.
1270 //if so then it returns true so that the calling function can run the previous valid distance.
1271 //it's a "smart" distance function.  It also checks for invalid labels.
1272 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1273         try {
1274
1275                 set<string>::iterator it;
1276                 vector<float> orderFloat;
1277                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1278                 map<string, float>::iterator it2;
1279                 float labelFloat;
1280                 bool smaller = false;
1281
1282                 //unique is the smallest line
1283                 if (label == "unique") {  return false;  }
1284                 else {
1285                         if (convertTestFloat(label, labelFloat)) {
1286                                 convert(label, labelFloat);
1287                         }else { //cant convert
1288                                 return false;
1289                         }
1290                 }
1291
1292                 //go through users set and make them floats
1293                 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
1294
1295                         float temp;
1296                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1297                                 convert(*it, temp);
1298                                 orderFloat.push_back(temp);
1299                                 userMap[*it] = temp;
1300                         }else if (*it == "unique") {
1301                                 orderFloat.push_back(-1.0);
1302                                 userMap["unique"] = -1.0;
1303                         }else {
1304                                 if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
1305                                 userLabels.erase(*it);
1306                                 it--;
1307                         }
1308                 }
1309
1310                 //sort order
1311                 sort(orderFloat.begin(), orderFloat.end());
1312
1313                 /*************************************************/
1314                 //is this label bigger than any of the users labels
1315                 /*************************************************/
1316
1317                 //loop through order until you find a label greater than label
1318                 for (int i = 0; i < orderFloat.size(); i++) {
1319                         if (orderFloat[i] < labelFloat) {
1320                                 smaller = true;
1321                                 if (orderFloat[i] == -1) {
1322                                         if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
1323                                         userLabels.erase("unique");
1324                                 }
1325                                 else {
1326                                         if (errorOff == "") { cout << "Your file does not include the label " << endl; }
1327                                         string s = "";
1328                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1329                                                 if (it2->second == orderFloat[i]) {
1330                                                         s = it2->first;
1331                                                         //remove small labels
1332                                                         userLabels.erase(s);
1333                                                         break;
1334                                                 }
1335                                         }
1336                                         if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
1337                                 }
1338                         //since they are sorted once you find a bigger one stop looking
1339                         }else { break; }
1340                 }
1341
1342                 return smaller;
1343
1344         }
1345         catch(exception& e) {
1346                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1347                 exit(1);
1348         }
1349 }
1350
1351 /**************************************************************************************************/
1352 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1353         try {
1354
1355                 bool good = true;
1356
1357                 string line = getline(file);
1358
1359                 //before we added this check
1360                 if (line[0] != '#') {  good = false;  }
1361                 else {
1362                         //rip off #
1363                         line = line.substr(1);
1364
1365                         vector<string> versionVector;
1366                         splitAtChar(version, versionVector, '.');
1367
1368                         //check file version
1369                         vector<string> linesVector;
1370                         splitAtChar(line, linesVector, '.');
1371
1372                         if (versionVector.size() != linesVector.size()) { good = false; }
1373                         else {
1374                                 for (int j = 0; j < versionVector.size(); j++) {
1375                                         int num1, num2;
1376                                         convert(versionVector[j], num1);
1377                                         convert(linesVector[j], num2);
1378
1379                                         //if mothurs version is newer than this files version, then we want to remake it
1380                                         if (num1 > num2) {  good = false; break;  }
1381                                 }
1382                         }
1383
1384                 }
1385
1386                 if (!good) {  file.close();  }
1387                 else { file.seekg(0);  }
1388
1389                 return good;
1390         }
1391         catch(exception& e) {
1392                 errorOut(e, "MothurOut", "checkReleaseVersion");
1393                 exit(1);
1394         }
1395 }
1396 /**************************************************************************************************/
1397
1398
1399
1400
1401