mothurout.cpp

   1 /*
   2  *  mothurOut.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 2/25/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mothurout.h"
  11
  12
  13 /******************************************************/
  14 MothurOut* MothurOut::getInstance() {
  15         if( _uniqueInstance == 0) {
  16                 _uniqueInstance = new MothurOut();
  17         }
  18         return _uniqueInstance;
  19 }
  20 /*********************************************************************************************/
  21 void MothurOut::printCurrentFiles()  {
  22         try {
  23                 if (accnosfile != "")           {  mothurOut("accnos=" + accnosfile); mothurOutEndLine();                       }
  24                 if (columnfile != "")           {  mothurOut("column=" + columnfile); mothurOutEndLine();                       }
  25                 if (designfile != "")           {  mothurOut("design=" + designfile); mothurOutEndLine();                       }
  26                 if (fastafile != "")            {  mothurOut("fasta=" + fastafile); mothurOutEndLine();                         }
  27                 if (groupfile != "")            {  mothurOut("group=" + groupfile); mothurOutEndLine();                         }
  28                 if (listfile != "")                     {  mothurOut("list=" + listfile); mothurOutEndLine();                           }
  29                 if (namefile != "")                     {  mothurOut("name=" + namefile); mothurOutEndLine();                           }
  30                 if (oligosfile != "")           {  mothurOut("oligos=" + oligosfile); mothurOutEndLine();                       }
  31                 if (orderfile != "")            {  mothurOut("order=" + orderfile); mothurOutEndLine();                         }
  32                 if (ordergroupfile != "")       {  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();       }
  33                 if (phylipfile != "")           {  mothurOut("phylip=" + phylipfile); mothurOutEndLine();                       }
  34                 if (qualfile != "")                     {  mothurOut("qfile=" + qualfile); mothurOutEndLine();                          }
  35                 if (rabundfile != "")           {  mothurOut("rabund=" + rabundfile); mothurOutEndLine();                       }
  36                 if (relabundfile != "")         {  mothurOut("relabund=" + relabundfile); mothurOutEndLine();           }
  37                 if (sabundfile != "")           {  mothurOut("sabund=" + sabundfile); mothurOutEndLine();                       }
  38                 if (sfffile != "")                      {  mothurOut("sff=" + sfffile); mothurOutEndLine();                                     }
  39                 if (sharedfile != "")           {  mothurOut("shared=" + sharedfile); mothurOutEndLine();                       }
  40                 if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
  41                 if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
  42                 if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
  43                 if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
  44
  45         }
  46         catch(exception& e) {
  47                 errorOut(e, "MothurOut", "printCurrentFiles");
  48                 exit(1);
  49         }
  50 }
  51 /*********************************************************************************************/
  52 bool MothurOut::hasCurrentFiles()  {
  53         try {
  54                 bool hasCurrent = false;
  55
  56                 if (accnosfile != "")           {  return true;                 }
  57                 if (columnfile != "")           {  return true;                 }
  58                 if (designfile != "")           {  return true;                 }
  59                 if (fastafile != "")            {  return true;                 }
  60                 if (groupfile != "")            {  return true;                 }
  61                 if (listfile != "")                     {  return true;                 }
  62                 if (namefile != "")                     {  return true;                 }
  63                 if (oligosfile != "")           {  return true;                 }
  64                 if (orderfile != "")            {  return true;                 }
  65                 if (ordergroupfile != "")       {  return true;                 }
  66                 if (phylipfile != "")           {  return true;                 }
  67                 if (qualfile != "")                     {  return true;                 }
  68                 if (rabundfile != "")           {  return true;                 }
  69                 if (relabundfile != "")         {  return true;                 }
  70                 if (sabundfile != "")           {  return true;                 }
  71                 if (sfffile != "")                      {  return true;                 }
  72                 if (sharedfile != "")           {  return true;                 }
  73                 if (taxonomyfile != "")         {  return true;                 }
  74                 if (treefile != "")                     {  return true;                 }
  75                 if (flowfile != "")                     {  return true;                 }
  76                 if (processors != "1")          {  return true;                 }
  77
  78                 return hasCurrent;
  79
  80         }
  81         catch(exception& e) {
  82                 errorOut(e, "MothurOut", "hasCurrentFiles");
  83                 exit(1);
  84         }
  85 }
  86
  87 /*********************************************************************************************/
  88 void MothurOut::clearCurrentFiles()  {
  89         try {
  90                 phylipfile = "";
  91                 columnfile = "";
  92                 listfile = "";
  93                 rabundfile = "";
  94                 sabundfile = "";
  95                 namefile = "";
  96                 groupfile = "";
  97                 designfile = "";
  98                 orderfile = "";
  99                 treefile = "";
 100                 sharedfile = "";
 101                 ordergroupfile = "";
 102                 relabundfile = "";
 103                 fastafile = "";
 104                 qualfile = "";
 105                 sfffile = "";
 106                 oligosfile = "";
 107                 accnosfile = "";
 108                 taxonomyfile = "";
 109                 flowfile = "";
 110                 processors = "1";
 111         }
 112         catch(exception& e) {
 113                 errorOut(e, "MothurOut", "clearCurrentFiles");
 114                 exit(1);
 115         }
 116 }
 117 /*********************************************************************************************/
 118 void MothurOut::setFileName(string filename)  {
 119         try {
 120                 logFileName = filename;
 121
 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                 openOutputFile(filename, out);
 130
 131                 #ifdef USE_MPI
 132                         }
 133                 #endif
 134         }
 135         catch(exception& e) {
 136                 errorOut(e, "MothurOut", "setFileName");
 137                 exit(1);
 138         }
 139 }
 140 /*********************************************************************************************/
 141 void MothurOut::setDefaultPath(string pathname)  {
 142         try {
 143
 144                 //add / to name if needed
 145                 string lastChar = pathname.substr(pathname.length()-1);
 146                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 147                         if (lastChar != "/") { pathname += "/"; }
 148                 #else
 149                         if (lastChar != "\\") { pathname += "\\"; }
 150                 #endif
 151
 152                 defaultPath = pathname;
 153
 154         }
 155         catch(exception& e) {
 156                 errorOut(e, "MothurOut", "setDefaultPath");
 157                 exit(1);
 158         }
 159 }
 160 /*********************************************************************************************/
 161 void MothurOut::setOutputDir(string pathname)  {
 162         try {
 163                 outputDir = pathname;
 164         }
 165         catch(exception& e) {
 166                 errorOut(e, "MothurOut", "setOutputDir");
 167                 exit(1);
 168         }
 169 }
 170 /*********************************************************************************************/
 171 void MothurOut::closeLog()  {
 172         try {
 173
 174                 #ifdef USE_MPI
 175                         int pid;
 176                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 177
 178                         if (pid == 0) { //only one process should output to screen
 179                 #endif
 180
 181                 out.close();
 182
 183                 #ifdef USE_MPI
 184                         }
 185                 #endif
 186         }
 187         catch(exception& e) {
 188                 errorOut(e, "MothurOut", "closeLog");
 189                 exit(1);
 190         }
 191 }
 192
 193 /*********************************************************************************************/
 194 MothurOut::~MothurOut() {
 195         try {
 196                 _uniqueInstance = 0;
 197
 198         }
 199         catch(exception& e) {
 200                 errorOut(e, "MothurOut", "MothurOut");
 201                 exit(1);
 202         }
 203 }
 204 /*********************************************************************************************/
 205 void MothurOut::mothurOut(string output) {
 206         try {
 207
 208                 #ifdef USE_MPI
 209                         int pid;
 210                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 211
 212                         if (pid == 0) { //only one process should output to screen
 213                 #endif
 214
 215                 cout << output;
 216                 out << output;
 217
 218                 #ifdef USE_MPI
 219                         }
 220                 #endif
 221         }
 222         catch(exception& e) {
 223                 errorOut(e, "MothurOut", "MothurOut");
 224                 exit(1);
 225         }
 226 }
 227 /*********************************************************************************************/
 228 void MothurOut::mothurOutEndLine() {
 229         try {
 230                 #ifdef USE_MPI
 231                         int pid;
 232                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 233
 234                         if (pid == 0) { //only one process should output to screen
 235                 #endif
 236
 237                 cout << endl;
 238                 out << endl;
 239
 240                 #ifdef USE_MPI
 241                         }
 242                 #endif
 243         }
 244         catch(exception& e) {
 245                 errorOut(e, "MothurOut", "MothurOutEndLine");
 246                 exit(1);
 247         }
 248 }
 249 /*********************************************************************************************/
 250 void MothurOut::mothurOut(string output, ofstream& outputFile) {
 251         try {
 252
 253 #ifdef USE_MPI
 254                 int pid;
 255                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 256
 257                 if (pid == 0) { //only one process should output to screen
 258 #endif
 259
 260                         cout << output;
 261                         out << output;
 262                         outputFile << output;
 263
 264 #ifdef USE_MPI
 265                 }
 266 #endif
 267         }
 268         catch(exception& e) {
 269                 errorOut(e, "MothurOut", "MothurOut");
 270                 exit(1);
 271         }
 272 }
 273 /*********************************************************************************************/
 274 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 275         try {
 276 #ifdef USE_MPI
 277                 int pid;
 278                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 279
 280                 if (pid == 0) { //only one process should output to screen
 281 #endif
 282
 283                         cout << endl;
 284                         out << endl;
 285                         outputFile << endl;
 286
 287 #ifdef USE_MPI
 288                 }
 289 #endif
 290         }
 291         catch(exception& e) {
 292                 errorOut(e, "MothurOut", "MothurOutEndLine");
 293                 exit(1);
 294         }
 295 }
 296 /*********************************************************************************************/
 297 void MothurOut::mothurOutJustToLog(string output) {
 298         try {
 299                 #ifdef USE_MPI
 300                         int pid;
 301                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 302
 303                         if (pid == 0) { //only one process should output to screen
 304                 #endif
 305
 306                 out << output;
 307
 308                 #ifdef USE_MPI
 309                         }
 310                 #endif
 311         }
 312         catch(exception& e) {
 313                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 314                 exit(1);
 315         }
 316 }
 317 /*********************************************************************************************/
 318 void MothurOut::errorOut(exception& e, string object, string function) {
 319         //double vm, rss;
 320         //mem_usage(vm, rss);
 321
 322         mothurOut("[ERROR]: ");
 323         mothurOut(toString(e.what()));
 324         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.");
 325         mothurOutEndLine();
 326 }
 327 /*********************************************************************************************/
 328 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 329 // process_mem_usage(double &, double &) - takes two doubles by reference,
 330 // attempts to read the system-dependent data for a process' virtual memory
 331 // size and resident set size, and return the results in KB.
 332 //
 333 // On failure, returns 0.0, 0.0
 334 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 335   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 336
 337            vm_usage     = 0.0;
 338            resident_set = 0.0;
 339
 340            // 'file' stat seems to give the most reliable results
 341            //
 342            ifstream stat_stream("/proc/self/stat",ios_base::in);
 343
 344            // dummy vars for leading entries in stat that we don't care about
 345            //
 346            string pid, comm, state, ppid, pgrp, session, tty_nr;
 347            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 348            string utime, stime, cutime, cstime, priority, nice;
 349            string O, itrealvalue, starttime;
 350
 351            // the two fields we want
 352            //
 353            unsigned long vsize;
 354            long rss;
 355
 356            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 357                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 358                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 359                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 360
 361            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 362            vm_usage     = vsize / 1024.0;
 363            resident_set = rss * page_size_kb;
 364
 365            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 366                 return 0;
 367
 368         #else
 369 /*              //windows memory usage
 370                 // Get the list of process identifiers.
 371                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 372
 373                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 374
 375                 // Calculate how many process identifiers were returned.
 376                 cProcesses = cbNeeded / sizeof(DWORD);
 377
 378                 // Print the memory usage for each process
 379                 for (int i = 0; i < cProcesses; i++ ) {
 380                         DWORD processID = aProcesses[i];
 381
 382                         PROCESS_MEMORY_COUNTERS pmc;
 383
 384                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 385
 386                         // Print the process identifier.
 387                         printf( "\nProcess ID: %u\n", processID);
 388
 389                         if (NULL != hProcess) {
 390
 391                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 392                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 393                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 394                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 395                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 396                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 397                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 398                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 399                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 400                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 401                                 }
 402                                 CloseHandle(hProcess);
 403                         }
 404                 }
 405 */
 406                         return 0;
 407
 408         #endif
 409 }
 410
 411
 412 /***********************************************************************/
 413 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 414         try {
 415                 fileName = getFullPathName(fileName);
 416
 417                 fileHandle.open(fileName.c_str(), ios::app);
 418                 if(!fileHandle) {
 419                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 420                         return 1;
 421                 }
 422                 else {
 423                         return 0;
 424                 }
 425         }
 426         catch(exception& e) {
 427                 errorOut(e, "MothurOut", "openOutputFileAppend");
 428                 exit(1);
 429         }
 430 }
 431 /***********************************************************************/
 432 void MothurOut::gobble(istream& f){
 433         try {
 434
 435                 char d;
 436                 while(isspace(d=f.get()))               { ;}
 437                 f.putback(d);
 438         }
 439         catch(exception& e) {
 440                 errorOut(e, "MothurOut", "gobble");
 441                 exit(1);
 442         }
 443 }
 444 /***********************************************************************/
 445 void MothurOut::gobble(istringstream& f){
 446         try {
 447                 char d;
 448                 while(isspace(d=f.get()))               {;}
 449                 f.putback(d);
 450         }
 451         catch(exception& e) {
 452                 errorOut(e, "MothurOut", "gobble");
 453                 exit(1);
 454         }
 455 }
 456
 457 /***********************************************************************/
 458
 459 string MothurOut::getline(istringstream& fileHandle) {
 460         try {
 461
 462                 string line = "";
 463
 464                 while (!fileHandle.eof())       {
 465                         //get next character
 466                         char c = fileHandle.get();
 467
 468                         //are you at the end of the line
 469                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 470                         else {          line += c;              }
 471                 }
 472
 473                 return line;
 474
 475         }
 476         catch(exception& e) {
 477                 errorOut(e, "MothurOut", "getline");
 478                 exit(1);
 479         }
 480 }
 481 /***********************************************************************/
 482
 483 string MothurOut::getline(ifstream& fileHandle) {
 484         try {
 485
 486                 string line = "";
 487
 488                 while (fileHandle)      {
 489                         //get next character
 490                         char c = fileHandle.get();
 491
 492                         //are you at the end of the line
 493                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }
 494                         else {          line += c;              }
 495                 }
 496
 497                 return line;
 498
 499         }
 500         catch(exception& e) {
 501                 errorOut(e, "MothurOut", "getline");
 502                 exit(1);
 503         }
 504 }
 505 /***********************************************************************/
 506
 507 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 508 #ifdef USE_COMPRESSION
 509 inline bool endsWith(string s, const char * suffix){
 510   size_t suffixLength = strlen(suffix);
 511   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 512 }
 513 #endif
 514 #endif
 515
 516 string MothurOut::getRootName(string longName){
 517         try {
 518
 519                 string rootName = longName;
 520
 521 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 522 #ifdef USE_COMPRESSION
 523     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 524       int pos = rootName.find_last_of('.');
 525       rootName = rootName.substr(0, pos);
 526       cerr << "shortening " << longName << " to " << rootName << "\n";
 527     }
 528 #endif
 529 #endif
 530                 if(rootName.find_last_of(".") != rootName.npos){
 531                         int pos = rootName.find_last_of('.')+1;
 532                         rootName = rootName.substr(0, pos);
 533                 }
 534
 535                 return rootName;
 536         }
 537         catch(exception& e) {
 538                 errorOut(e, "MothurOut", "getRootName");
 539                 exit(1);
 540         }
 541 }
 542 /***********************************************************************/
 543
 544 string MothurOut::getSimpleName(string longName){
 545         try {
 546                 string simpleName = longName;
 547
 548                 size_t found;
 549                 found=longName.find_last_of("/\\");
 550
 551                 if(found != longName.npos){
 552                         simpleName = longName.substr(found+1);
 553                 }
 554
 555                 return simpleName;
 556         }
 557         catch(exception& e) {
 558                 errorOut(e, "MothurOut", "getSimpleName");
 559                 exit(1);
 560         }
 561 }
 562
 563 /***********************************************************************/
 564
 565 string MothurOut::getPathName(string longName){
 566         try {
 567                 string rootPathName = longName;
 568
 569                 if(longName.find_last_of("/\\") != longName.npos){
 570                         int pos = longName.find_last_of("/\\")+1;
 571                         rootPathName = longName.substr(0, pos);
 572                 }
 573
 574                 return rootPathName;
 575         }
 576         catch(exception& e) {
 577                 errorOut(e, "MothurOut", "getPathName");
 578                 exit(1);
 579         }
 580
 581 }
 582 /***********************************************************************/
 583
 584 string MothurOut::hasPath(string longName){
 585         try {
 586                 string path = "";
 587
 588                 size_t found;
 589                 found=longName.find_last_of("~/\\");
 590
 591                 if(found != longName.npos){
 592                         path = longName.substr(0, found+1);
 593                 }
 594
 595                 return path;
 596         }
 597         catch(exception& e) {
 598                 errorOut(e, "MothurOut", "hasPath");
 599                 exit(1);
 600         }
 601 }
 602
 603 /***********************************************************************/
 604
 605 string MothurOut::getExtension(string longName){
 606         try {
 607                 string extension = longName;
 608
 609                 if(longName.find_last_of('.') != longName.npos){
 610                         int pos = longName.find_last_of('.');
 611                         extension = longName.substr(pos, longName.length());
 612                 }
 613
 614                 return extension;
 615         }
 616         catch(exception& e) {
 617                 errorOut(e, "MothurOut", "getExtension");
 618                 exit(1);
 619         }
 620 }
 621 /***********************************************************************/
 622 bool MothurOut::isBlank(string fileName){
 623         try {
 624
 625                 fileName = getFullPathName(fileName);
 626
 627                 ifstream fileHandle;
 628                 fileHandle.open(fileName.c_str());
 629                 if(!fileHandle) {
 630                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 631                         return false;
 632                 }else {
 633                         //check for blank file
 634                         gobble(fileHandle);
 635                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 636                         fileHandle.close();
 637                 }
 638                 return false;
 639         }
 640         catch(exception& e) {
 641                 errorOut(e, "MothurOut", "isBlank");
 642                 exit(1);
 643         }
 644 }
 645 /***********************************************************************/
 646
 647 string MothurOut::getFullPathName(string fileName){
 648         try{
 649
 650         string path = hasPath(fileName);
 651         string newFileName;
 652         int pos;
 653
 654         if (path == "") { return fileName; } //its a simple name
 655         else { //we need to complete the pathname
 656                 // ex. ../../../filename
 657                 // cwd = /user/work/desktop
 658
 659                 string cwd;
 660                 //get current working directory
 661                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 662
 663                         if (path.find("~") != -1) { //go to home directory
 664                                 string homeDir;
 665
 666                                 char *homepath = NULL;
 667                                 homepath = getenv ("HOME");
 668                                 if ( homepath != NULL) { homeDir = homepath; }
 669                                 else { homeDir = "";  }
 670
 671                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 672                                 return newFileName;
 673                         }else { //find path
 674                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 675                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 676
 677                                 //char* cwdpath = new char[1024];
 678                                 //size_t size;
 679                                 //cwdpath=getcwd(cwdpath,size);
 680                                 //cwd = cwdpath;
 681
 682                                 char *cwdpath = NULL;
 683                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 684                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 685                                 else { cwd = "";  }
 686
 687
 688                                 //rip off first '/'
 689                                 string simpleCWD;
 690                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 691
 692                                 //break apart the current working directory
 693                                 vector<string> dirs;
 694                                 while (simpleCWD.find_first_of('/') != string::npos) {
 695                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 696                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 697                                         dirs.push_back(dir);
 698                                 }
 699                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 700                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 701
 702
 703                                 int index = dirs.size()-1;
 704
 705                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 706                                         if (pos == 0) { break;  //you are at the end
 707                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 708                                                 path = path.substr(0, pos-1);
 709                                                 index--;
 710                                                 if (index == 0) {  break; }
 711                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 712                                                 path = path.substr(0, pos);
 713                                         }else if (pos == 1) { break;  //you are at the end
 714                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 715                                 }
 716
 717                                 for (int i = index; i >= 0; i--) {
 718                                         newFileName = dirs[i] +  "/" + newFileName;
 719                                 }
 720
 721                                 newFileName =  "/" +  newFileName;
 722                                 return newFileName;
 723                         }
 724                 #else
 725                         if (path.find("~") != string::npos) { //go to home directory
 726                                 string homeDir = getenv ("HOMEPATH");
 727                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 728                                 return newFileName;
 729                         }else { //find path
 730                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 731                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 732
 733                                 char *cwdpath = NULL;
 734                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 735                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 736                                 else { cwd = "";  }
 737
 738                                 //break apart the current working directory
 739                                 vector<string> dirs;
 740                                 while (cwd.find_first_of('\\') != -1) {
 741                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 742                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 743                                         dirs.push_back(dir);
 744
 745                                 }
 746                                 //get last one
 747                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 748
 749                                 int index = dirs.size()-1;
 750
 751                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 752                                         if (pos == 0) { break;  //you are at the end
 753                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 754                                                 path = path.substr(0, pos-1);
 755                                                 index--;
 756                                                 if (index == 0) {  break; }
 757                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 758                                                 path = path.substr(0, pos);
 759                                         }else if (pos == 1) { break;  //you are at the end
 760                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 761                                 }
 762
 763                                 for (int i = index; i >= 0; i--) {
 764                                         newFileName = dirs[i] +  "\\" + newFileName;
 765                                 }
 766
 767                                 return newFileName;
 768                         }
 769
 770                 #endif
 771         }
 772         }
 773         catch(exception& e) {
 774                 errorOut(e, "MothurOut", "getFullPathName");
 775                 exit(1);
 776         }
 777 }
 778 /***********************************************************************/
 779
 780 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 781         try {
 782                         //get full path name
 783                         string completeFileName = getFullPathName(fileName);
 784 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 785 #ifdef USE_COMPRESSION
 786       // check for gzipped or bzipped file
 787       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 788         string tempName = string(tmpnam(0));
 789         mkfifo(tempName.c_str(), 0666);
 790         int fork_result = fork();
 791         if (fork_result < 0) {
 792           cerr << "Error forking.\n";
 793           exit(1);
 794         } else if (fork_result == 0) {
 795           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 796           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 797           system(command.c_str());
 798           cerr << "Done decompressing " << completeFileName << "\n";
 799           remove(tempName.c_str());
 800           exit(EXIT_SUCCESS);
 801         } else {
 802           cerr << "waiting on child process " << fork_result << "\n";
 803           completeFileName = tempName;
 804         }
 805       }
 806 #endif
 807 #endif
 808                         fileHandle.open(completeFileName.c_str());
 809                         if(!fileHandle) {
 810                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 811                                 return 1;
 812                         }else {
 813                                 //check for blank file
 814                                 gobble(fileHandle);
 815                                 return 0;
 816                         }
 817         }
 818         catch(exception& e) {
 819                 errorOut(e, "MothurOut", "openInputFile - no Error");
 820                 exit(1);
 821         }
 822 }
 823 /***********************************************************************/
 824
 825 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 826         try {
 827
 828                 //get full path name
 829                 string completeFileName = getFullPathName(fileName);
 830 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 831 #ifdef USE_COMPRESSION
 832   // check for gzipped or bzipped file
 833   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 834     string tempName = string(tmpnam(0));
 835     mkfifo(tempName.c_str(), 0666);
 836     int fork_result = fork();
 837     if (fork_result < 0) {
 838       cerr << "Error forking.\n";
 839       exit(1);
 840     } else if (fork_result == 0) {
 841       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 842       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 843       system(command.c_str());
 844       cerr << "Done decompressing " << completeFileName << "\n";
 845       remove(tempName.c_str());
 846       exit(EXIT_SUCCESS);
 847     } else {
 848       cerr << "waiting on child process " << fork_result << "\n";
 849       completeFileName = tempName;
 850     }
 851   }
 852 #endif
 853 #endif
 854
 855                 fileHandle.open(completeFileName.c_str());
 856                 if(!fileHandle) {
 857                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 858                         return 1;
 859                 }
 860                 else {
 861                         //check for blank file
 862                         gobble(fileHandle);
 863                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 864
 865                         return 0;
 866                 }
 867         }
 868         catch(exception& e) {
 869                 errorOut(e, "MothurOut", "openInputFile");
 870                 exit(1);
 871         }
 872 }
 873 /***********************************************************************/
 874
 875 int MothurOut::renameFile(string oldName, string newName){
 876         try {
 877                 ifstream inTest;
 878                 int exist = openInputFile(newName, inTest, "");
 879
 880         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 881                 if (exist == 0) { //you could open it so you want to delete it
 882                         inTest.close();
 883                         string command = "rm " + newName;
 884                         system(command.c_str());
 885                 }
 886
 887                 string command = "mv " + oldName + " " + newName;
 888                 system(command.c_str());
 889         #else
 890                 remove(newName.c_str());
 891                 int renameOk = rename(oldName.c_str(), newName.c_str());
 892         #endif
 893                 return 0;
 894
 895         }
 896         catch(exception& e) {
 897                 errorOut(e, "MothurOut", "renameFile");
 898                 exit(1);
 899         }
 900 }
 901
 902 /***********************************************************************/
 903
 904 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 905         try {
 906
 907                 string completeFileName = getFullPathName(fileName);
 908 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 909 #ifdef USE_COMPRESSION
 910     // check for gzipped file
 911     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 912       string tempName = string(tmpnam(0));
 913       mkfifo(tempName.c_str(), 0666);
 914       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 915       int fork_result = fork();
 916       if (fork_result < 0) {
 917         cerr << "Error forking.\n";
 918         exit(1);
 919       } else if (fork_result == 0) {
 920         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 921         system(command.c_str());
 922         exit(0);
 923       } else {
 924         completeFileName = tempName;
 925       }
 926     }
 927 #endif
 928 #endif
 929                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 930                 if(!fileHandle) {
 931                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 932                         return 1;
 933                 }
 934                 else {
 935                         return 0;
 936                 }
 937         }
 938         catch(exception& e) {
 939                 errorOut(e, "MothurOut", "openOutputFile");
 940                 exit(1);
 941         }
 942
 943 }
 944
 945 /**************************************************************************************************/
 946 void MothurOut::appendFiles(string temp, string filename) {
 947         try{
 948                 ofstream output;
 949                 ifstream input;
 950
 951                 //open output file in append mode
 952                 openOutputFileAppend(filename, output);
 953                 int ableToOpen = openInputFile(temp, input, "no error");
 954                 //int ableToOpen = openInputFile(temp, input);
 955
 956                 if (ableToOpen == 0) { //you opened it
 957                         while(char c = input.get()){
 958                                 if(input.eof())         {       break;                  }
 959                                 else                            {       output << c;    }
 960                         }
 961                         input.close();
 962                 }
 963
 964                 output.close();
 965         }
 966         catch(exception& e) {
 967                 errorOut(e, "MothurOut", "appendFiles");
 968                 exit(1);
 969         }
 970 }
 971
 972 /**************************************************************************************************/
 973 string MothurOut::sortFile(string distFile, string outputDir){
 974         try {
 975
 976                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 977                 string outfile = getRootName(distFile) + "sorted.dist";
 978
 979
 980                 //if you can, use the unix sort since its been optimized for years
 981                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 982                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 983                         system(command.c_str());
 984                 #else //you are stuck with my best attempt...
 985                         //windows sort does not have a way to specify a column, only a character in the line
 986                         //since we cannot assume that the distance will always be at the the same character location on each line
 987                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 988
 989                         //read in file line by file and put distance first
 990                         string tempDistFile = distFile + ".temp";
 991                         ifstream input;
 992                         ofstream output;
 993                         openInputFile(distFile, input);
 994                         openOutputFile(tempDistFile, output);
 995
 996                         string firstName, secondName;
 997                         float dist;
 998                         while (input) {
 999                                 input >> firstName >> secondName >> dist;
1000                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1001                                 gobble(input);
1002                         }
1003                         input.close();
1004                         output.close();
1005
1006
1007                         //sort using windows sort
1008                         string tempOutfile = outfile + ".temp";
1009                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1010                         system(command.c_str());
1011
1012                         //read in sorted file and put distance at end again
1013                         ifstream input2;
1014                         openInputFile(tempOutfile, input2);
1015                         openOutputFile(outfile, output);
1016
1017                         while (input2) {
1018                                 input2 >> dist >> firstName >> secondName;
1019                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1020                                 gobble(input2);
1021                         }
1022                         input2.close();
1023                         output.close();
1024
1025                         //remove temp files
1026                         remove(tempDistFile.c_str());
1027                         remove(tempOutfile.c_str());
1028                 #endif
1029
1030                 return outfile;
1031         }
1032         catch(exception& e) {
1033                 errorOut(e, "MothurOut", "sortFile");
1034                 exit(1);
1035         }
1036 }
1037 /**************************************************************************************************/
1038 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
1039         try {
1040                         vector<unsigned long int> positions;
1041                         ifstream inFASTA;
1042                         openInputFile(filename, inFASTA);
1043
1044                         string input;
1045                         while(!inFASTA.eof()){
1046                                 input = getline(inFASTA);
1047                                 if (input.length() != 0) {
1048                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
1049                                 }
1050                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1051                         }
1052                         inFASTA.close();
1053
1054                         num = positions.size();
1055
1056                         /*FILE * pFile;
1057                         long size;
1058
1059                         //get num bytes in file
1060                         pFile = fopen (filename.c_str(),"rb");
1061                         if (pFile==NULL) perror ("Error opening file");
1062                         else{
1063                                 fseek (pFile, 0, SEEK_END);
1064                                 size=ftell (pFile);
1065                                 fclose (pFile);
1066                         }*/
1067
1068                         unsigned long int size = positions[(positions.size()-1)];
1069                         ifstream in;
1070                         openInputFile(filename, in);
1071
1072                         in.seekg(size);
1073
1074                         while(in.get()){
1075                                 if(in.eof())            {       break;  }
1076                                 else                            {       size++; }
1077                         }
1078                         in.close();
1079
1080                         positions.push_back(size);
1081
1082                         return positions;
1083         }
1084         catch(exception& e) {
1085                 errorOut(e, "MothurOut", "setFilePosFasta");
1086                 exit(1);
1087         }
1088 }
1089 /**************************************************************************************************/
1090 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
1091         try {
1092                         filename = getFullPathName(filename);
1093
1094                         vector<unsigned long int> positions;
1095                         ifstream in;
1096                         openInputFile(filename, in);
1097
1098                         string input;
1099                         while(!in.eof()){
1100                                 unsigned long int lastpos = in.tellg();
1101                                 input = getline(in);
1102                                 if (input.length() != 0) {
1103                                         unsigned long int pos = in.tellg();
1104                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
1105                                         else {  positions.push_back(lastpos);  }
1106                                 }
1107                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
1108                         }
1109                         in.close();
1110
1111                         num = positions.size();
1112
1113                         FILE * pFile;
1114                         unsigned long int size;
1115
1116                         //get num bytes in file
1117                         pFile = fopen (filename.c_str(),"rb");
1118                         if (pFile==NULL) perror ("Error opening file");
1119                         else{
1120                                 fseek (pFile, 0, SEEK_END);
1121                                 size=ftell (pFile);
1122                                 fclose (pFile);
1123                         }
1124
1125                         positions.push_back(size);
1126
1127                         return positions;
1128         }
1129         catch(exception& e) {
1130                 errorOut(e, "MothurOut", "setFilePosEachLine");
1131                 exit(1);
1132         }
1133 }
1134 /**************************************************************************************************/
1135
1136 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
1137         try{
1138
1139                 vector<unsigned long int> filePos;
1140                 filePos.push_back(0);
1141
1142                 FILE * pFile;
1143                 unsigned long int size;
1144
1145                 filename = getFullPathName(filename);
1146
1147                 //get num bytes in file
1148                 pFile = fopen (filename.c_str(),"rb");
1149                 if (pFile==NULL) perror ("Error opening file");
1150                 else{
1151                         fseek (pFile, 0, SEEK_END);
1152                         size=ftell (pFile);
1153                         fclose (pFile);
1154                 }
1155
1156                 //estimate file breaks
1157                 unsigned long int chunkSize = 0;
1158                 chunkSize = size / proc;
1159
1160                 //file to small to divide by processors
1161                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1162
1163                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1164                 for (int i = 0; i < proc; i++) {
1165                         unsigned long int spot = (i+1) * chunkSize;
1166
1167                         ifstream in;
1168                         openInputFile(filename, in);
1169                         in.seekg(spot);
1170
1171                         //look for next '>'
1172                         unsigned long int newSpot = spot;
1173                         while (!in.eof()) {
1174                            char c = in.get();
1175                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1176                         }
1177
1178                         //there was not another sequence before the end of the file
1179                         unsigned long int sanityPos = in.tellg();
1180
1181                         if (sanityPos == -1) {  break;  }
1182                         else {  filePos.push_back(newSpot);  }
1183
1184                         in.close();
1185                 }
1186
1187                 //save end pos
1188                 filePos.push_back(size);
1189
1190                 //sanity check filePos
1191                 for (int i = 0; i < (filePos.size()-1); i++) {
1192                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1193                 }
1194
1195                 proc = (filePos.size() - 1);
1196
1197                 return filePos;
1198         }
1199         catch(exception& e) {
1200                 errorOut(e, "MothurOut", "divideFile");
1201                 exit(1);
1202         }
1203 }
1204 /**************************************************************************************************/
1205 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1206         try{
1207
1208                 vector<unsigned long int> filePos = divideFile(filename, proc);
1209
1210                 for (int i = 0; i < (filePos.size()-1); i++) {
1211
1212                         //read file chunk
1213                         ifstream in;
1214                         openInputFile(filename, in);
1215                         in.seekg(filePos[i]);
1216                         unsigned long int size = filePos[(i+1)] - filePos[i];
1217                         char* chunk = new char[size];
1218                         in.read(chunk, size);
1219                         in.close();
1220
1221                         //open new file
1222                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1223                         ofstream out;
1224                         openOutputFile(fileChunkName, out);
1225
1226                         out << chunk << endl;
1227                         out.close();
1228                         delete[] chunk;
1229
1230                         //save name
1231                         files.push_back(fileChunkName);
1232                 }
1233
1234                 return 0;
1235         }
1236         catch(exception& e) {
1237                 errorOut(e, "MothurOut", "divideFile");
1238                 exit(1);
1239         }
1240 }
1241 /***********************************************************************/
1242
1243 bool MothurOut::isTrue(string f){
1244         try {
1245
1246                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1247
1248                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1249                 else {  return false;  }
1250         }
1251         catch(exception& e) {
1252                 errorOut(e, "MothurOut", "isTrue");
1253                 exit(1);
1254         }
1255 }
1256
1257 /***********************************************************************/
1258
1259 float MothurOut::roundDist(float dist, int precision){
1260         try {
1261                 return int(dist * precision + 0.5)/float(precision);
1262         }
1263         catch(exception& e) {
1264                 errorOut(e, "MothurOut", "roundDist");
1265                 exit(1);
1266         }
1267 }
1268 /***********************************************************************/
1269
1270 float MothurOut::ceilDist(float dist, int precision){
1271         try {
1272                 return int(ceil(dist * precision))/float(precision);
1273         }
1274         catch(exception& e) {
1275                 errorOut(e, "MothurOut", "ceilDist");
1276                 exit(1);
1277         }
1278 }
1279 /**********************************************************************************************************************/
1280 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1281         try {
1282
1283                 //open input file
1284                 ifstream in;
1285                 openInputFile(namefile, in);
1286
1287                 while (!in.eof()) {
1288                         if (control_pressed) { break; }
1289
1290                         string firstCol, secondCol;
1291                         in >> firstCol >> secondCol; gobble(in);
1292
1293                         nameMap[firstCol] = secondCol;
1294                 }
1295                 in.close();
1296
1297                 return 0;
1298
1299         }
1300         catch(exception& e) {
1301                 errorOut(e, "MothurOut", "readNames");
1302                 exit(1);
1303         }
1304 }
1305
1306 /**********************************************************************************************************************/
1307 map<string, int> MothurOut::readNames(string namefile) {
1308         try {
1309
1310                 map<string, int> nameMap;
1311
1312                 //open input file
1313                 ifstream in;
1314                 openInputFile(namefile, in);
1315
1316                 while (!in.eof()) {
1317                         if (control_pressed) { break; }
1318
1319                         string firstCol, secondCol;
1320                         in >> firstCol >> secondCol; gobble(in);
1321
1322                         int num = getNumNames(secondCol);
1323
1324                         nameMap[firstCol] = num;
1325                 }
1326                 in.close();
1327
1328                 return nameMap;
1329
1330         }
1331         catch(exception& e) {
1332                 errorOut(e, "MothurOut", "readNames");
1333                 exit(1);
1334         }
1335 }
1336 /**********************************************************************************************************************/
1337 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1338         try {
1339                 int error = 0;
1340
1341                 //open input file
1342                 ifstream in;
1343                 openInputFile(namefile, in);
1344
1345                 while (!in.eof()) {
1346                         if (control_pressed) { break; }
1347
1348                         string firstCol, secondCol;
1349                         in >> firstCol >> secondCol; gobble(in);
1350
1351                         int num = getNumNames(secondCol);
1352
1353                         map<string, string>::iterator it = fastamap.find(firstCol);
1354                         if (it == fastamap.end()) {
1355                                 error = 1;
1356                                 mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1357                         }else {
1358                                 seqPriorityNode temp(num, it->second, firstCol);
1359                                 nameVector.push_back(temp);
1360                         }
1361                 }
1362                 in.close();
1363
1364                 return error;
1365
1366         }
1367         catch(exception& e) {
1368                 errorOut(e, "MothurOut", "readNames");
1369                 exit(1);
1370         }
1371 }
1372
1373 /***********************************************************************/
1374
1375 int MothurOut::getNumNames(string names){
1376         try {
1377                 int count = 0;
1378
1379                 if(names != ""){
1380                         count = 1;
1381                         for(int i=0;i<names.size();i++){
1382                                 if(names[i] == ','){
1383                                         count++;
1384                                 }
1385                         }
1386                 }
1387
1388                 return count;
1389         }
1390         catch(exception& e) {
1391                 errorOut(e, "MothurOut", "getNumNames");
1392                 exit(1);
1393         }
1394 }
1395
1396 /**************************************************************************************************/
1397
1398 vector<vector<double> > MothurOut::binomial(int maxOrder){
1399         try {
1400         vector<vector<double> > binomial(maxOrder+1);
1401
1402     for(int i=0;i<=maxOrder;i++){
1403                 binomial[i].resize(maxOrder+1);
1404                 binomial[i][0]=1;
1405                 binomial[0][i]=0;
1406     }
1407     binomial[0][0]=1;
1408
1409     binomial[1][0]=1;
1410     binomial[1][1]=1;
1411
1412     for(int i=2;i<=maxOrder;i++){
1413                 binomial[1][i]=0;
1414     }
1415
1416     for(int i=2;i<=maxOrder;i++){
1417                 for(int j=1;j<=maxOrder;j++){
1418                         if(i==j){       binomial[i][j]=1;                                                                       }
1419                         if(j>i) {       binomial[i][j]=0;                                                                       }
1420                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1421                 }
1422     }
1423
1424         return binomial;
1425
1426         }
1427         catch(exception& e) {
1428                 errorOut(e, "MothurOut", "binomial");
1429                 exit(1);
1430         }
1431 }
1432 /**************************************************************************************************/
1433 unsigned int MothurOut::fromBase36(string base36){
1434         try {
1435                 unsigned int num = 0;
1436
1437                 map<char, int> converts;
1438                 converts['A'] = 0;
1439                 converts['a'] = 0;
1440                 converts['B'] = 1;
1441                 converts['b'] = 1;
1442                 converts['C'] = 2;
1443                 converts['c'] = 2;
1444                 converts['D'] = 3;
1445                 converts['d'] = 3;
1446                 converts['E'] = 4;
1447                 converts['e'] = 4;
1448                 converts['F'] = 5;
1449                 converts['f'] = 5;
1450                 converts['G'] = 6;
1451                 converts['g'] = 6;
1452                 converts['H'] = 7;
1453                 converts['h'] = 7;
1454                 converts['I'] = 8;
1455                 converts['i'] = 8;
1456                 converts['J'] = 9;
1457                 converts['j'] = 9;
1458                 converts['K'] = 10;
1459                 converts['k'] = 10;
1460                 converts['L'] = 11;
1461                 converts['l'] = 11;
1462                 converts['M'] = 12;
1463                 converts['m'] = 12;
1464                 converts['N'] = 13;
1465                 converts['n'] = 13;
1466                 converts['O'] = 14;
1467                 converts['o'] = 14;
1468                 converts['P'] = 15;
1469                 converts['p'] = 15;
1470                 converts['Q'] = 16;
1471                 converts['q'] = 16;
1472                 converts['R'] = 17;
1473                 converts['r'] = 17;
1474                 converts['S'] = 18;
1475                 converts['s'] = 18;
1476                 converts['T'] = 19;
1477                 converts['t'] = 19;
1478                 converts['U'] = 20;
1479                 converts['u'] = 20;
1480                 converts['V'] = 21;
1481                 converts['v'] = 21;
1482                 converts['W'] = 22;
1483                 converts['w'] = 22;
1484                 converts['X'] = 23;
1485                 converts['x'] = 23;
1486                 converts['Y'] = 24;
1487                 converts['y'] = 24;
1488                 converts['Z'] = 25;
1489                 converts['z'] = 25;
1490                 converts['0'] = 26;
1491                 converts['1'] = 27;
1492                 converts['2'] = 28;
1493                 converts['3'] = 29;
1494                 converts['4'] = 30;
1495                 converts['5'] = 31;
1496                 converts['6'] = 32;
1497                 converts['7'] = 33;
1498                 converts['8'] = 34;
1499                 converts['9'] = 35;
1500
1501                 int i = 0;
1502                 while (i < base36.length()) {
1503                         char c = base36[i];
1504                         num = 36 * num + converts[c];
1505                         i++;
1506                 }
1507
1508                 return num;
1509
1510         }
1511         catch(exception& e) {
1512                 errorOut(e, "MothurOut", "fromBase36");
1513                 exit(1);
1514         }
1515 }
1516 /***********************************************************************/
1517
1518 int MothurOut::factorial(int num){
1519         try {
1520                 int total = 1;
1521
1522                 for (int i = 1; i <= num; i++) {
1523                         total *= i;
1524                 }
1525
1526                 return total;
1527         }
1528         catch(exception& e) {
1529                 errorOut(e, "MothurOut", "factorial");
1530                 exit(1);
1531         }
1532 }
1533 /***********************************************************************/
1534
1535 int MothurOut::getNumSeqs(ifstream& file){
1536         try {
1537                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1538                 file.seekg(0);
1539                 return numSeqs;
1540         }
1541         catch(exception& e) {
1542                 errorOut(e, "MothurOut", "getNumSeqs");
1543                 exit(1);
1544         }
1545 }
1546 /***********************************************************************/
1547 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1548         try {
1549                 string input;
1550                 numSeqs = 0;
1551                 while(!file.eof()){
1552                         input = getline(file);
1553                         if (input.length() != 0) {
1554                                 if(input[0] == '>'){ numSeqs++; }
1555                         }
1556                 }
1557         }
1558         catch(exception& e) {
1559                 errorOut(e, "MothurOut", "getNumSeqs");
1560                 exit(1);
1561         }
1562 }
1563 /***********************************************************************/
1564
1565 //This function parses the estimator options and puts them in a vector
1566 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1567         try {
1568                 string individual = "";
1569                 int estimLength = estim.size();
1570                 for(int i=0;i<estimLength;i++){
1571                         if(estim[i] == symbol){
1572                                 container.push_back(individual);
1573                                 individual = "";
1574                         }
1575                         else{
1576                                 individual += estim[i];
1577                         }
1578                 }
1579                 container.push_back(individual);
1580
1581         }
1582         catch(exception& e) {
1583                 errorOut(e, "MothurOut", "splitAtChar");
1584                 exit(1);
1585         }
1586 }
1587
1588 /***********************************************************************/
1589
1590 //This function parses the estimator options and puts them in a vector
1591 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1592         try {
1593                 string individual = "";
1594                 int estimLength = estim.size();
1595                 for(int i=0;i<estimLength;i++){
1596                         if(estim[i] == '-'){
1597                                 container.push_back(individual);
1598                                 individual = "";
1599                         }
1600                         else{
1601                                 individual += estim[i];
1602                         }
1603                 }
1604                 container.push_back(individual);
1605
1606
1607         /*      string individual;
1608
1609                 while (estim.find_first_of('-') != -1) {
1610                         individual = estim.substr(0,estim.find_first_of('-'));
1611                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1612                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1613                                 container.push_back(individual);
1614                         }
1615                 }
1616                 //get last one
1617                 container.push_back(estim); */
1618         }
1619         catch(exception& e) {
1620                 errorOut(e, "MothurOut", "splitAtDash");
1621                 exit(1);
1622         }
1623 }
1624
1625 /***********************************************************************/
1626 //This function parses the label options and puts them in a set
1627 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1628         try {
1629                 string individual = "";
1630                 int estimLength = estim.size();
1631                 for(int i=0;i<estimLength;i++){
1632                         if(estim[i] == '-'){
1633                                 container.insert(individual);
1634                                 individual = "";
1635                         }
1636                         else{
1637                                 individual += estim[i];
1638                         }
1639                 }
1640                 container.insert(individual);
1641
1642         //      string individual;
1643
1644         //      while (estim.find_first_of('-') != -1) {
1645         //              individual = estim.substr(0,estim.find_first_of('-'));
1646         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1647         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1648         //                      container.insert(individual);
1649         //              }
1650         //      }
1651                 //get last one
1652         //      container.insert(estim);
1653
1654         }
1655         catch(exception& e) {
1656                 errorOut(e, "MothurOut", "splitAtDash");
1657                 exit(1);
1658         }
1659 }
1660 /***********************************************************************/
1661 //This function parses the line options and puts them in a set
1662 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1663         try {
1664                 string individual;
1665                 int lineNum;
1666
1667                 while (estim.find_first_of('-') != -1) {
1668                         individual = estim.substr(0,estim.find_first_of('-'));
1669                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1670                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1671                                 convert(individual, lineNum); //convert the string to int
1672                                 container.insert(lineNum);
1673                         }
1674                 }
1675                 //get last one
1676                 convert(estim, lineNum); //convert the string to int
1677                 container.insert(lineNum);
1678         }
1679         catch(exception& e) {
1680                 errorOut(e, "MothurOut", "splitAtDash");
1681                 exit(1);
1682         }
1683 }
1684 /***********************************************************************/
1685 //This function parses the a string and puts peices in a vector
1686 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1687         try {
1688                 string individual = "";
1689                 int estimLength = estim.size();
1690                 for(int i=0;i<estimLength;i++){
1691                         if(estim[i] == ','){
1692                                 container.push_back(individual);
1693                                 individual = "";
1694                         }
1695                         else{
1696                                 individual += estim[i];
1697                         }
1698                 }
1699                 container.push_back(individual);
1700
1701
1702
1703
1704 //              string individual;
1705 //
1706 //              while (estim.find_first_of(',') != -1) {
1707 //                      individual = estim.substr(0,estim.find_first_of(','));
1708 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1709 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1710 //                              container.push_back(individual);
1711 //                      }
1712 //              }
1713 //              //get last one
1714 //              container.push_back(estim);
1715         }
1716         catch(exception& e) {
1717                 errorOut(e, "MothurOut", "splitAtComma");
1718                 exit(1);
1719         }
1720 }
1721 /***********************************************************************/
1722
1723 //This function splits up the various option parameters
1724 void MothurOut::splitAtComma(string& prefix, string& suffix){
1725         try {
1726                 prefix = suffix.substr(0,suffix.find_first_of(','));
1727                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1728                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1729                         string space = " ";
1730                         while(suffix.at(0) == ' ')
1731                                 suffix = suffix.substr(1, suffix.length());
1732                 }
1733
1734         }
1735         catch(exception& e) {
1736                 errorOut(e, "MothurOut", "splitAtComma");
1737                 exit(1);
1738         }
1739 }
1740 /***********************************************************************/
1741
1742 //This function separates the key value from the option value i.e. dist=96_...
1743 void MothurOut::splitAtEquals(string& key, string& value){
1744         try {
1745                 if(value.find_first_of('=') != -1){
1746                         key = value.substr(0,value.find_first_of('='));
1747                         if ((value.find_first_of('=')+1) <= value.length()) {
1748                                 value = value.substr(value.find_first_of('=')+1, value.length());
1749                         }
1750                 }else{
1751                         key = value;
1752                         value = 1;
1753                 }
1754         }
1755         catch(exception& e) {
1756                 errorOut(e, "MothurOut", "splitAtEquals");
1757                 exit(1);
1758         }
1759 }
1760
1761 /**************************************************************************************************/
1762
1763 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1764         try {
1765                 for (int i = 0; i < Groups.size(); i++) {
1766                         if (groupname == Groups[i]) { return true; }
1767                 }
1768                 return false;
1769         }
1770         catch(exception& e) {
1771                 errorOut(e, "MothurOut", "inUsersGroups");
1772                 exit(1);
1773         }
1774 }
1775 /**************************************************************************************************/
1776 //returns true if any of the strings in first vector are in second vector
1777 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1778         try {
1779
1780                 for (int i = 0; i < groupnames.size(); i++) {
1781                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1782                 }
1783                 return false;
1784         }
1785         catch(exception& e) {
1786                 errorOut(e, "MothurOut", "inUsersGroups");
1787                 exit(1);
1788         }
1789 }
1790 /***********************************************************************/
1791 //this function determines if the user has given us labels that are smaller than the given label.
1792 //if so then it returns true so that the calling function can run the previous valid distance.
1793 //it's a "smart" distance function.  It also checks for invalid labels.
1794 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1795         try {
1796
1797                 set<string>::iterator it;
1798                 vector<float> orderFloat;
1799                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1800                 map<string, float>::iterator it2;
1801                 float labelFloat;
1802                 bool smaller = false;
1803
1804                 //unique is the smallest line
1805                 if (label == "unique") {  return false;  }
1806                 else {
1807                         if (convertTestFloat(label, labelFloat)) {
1808                                 convert(label, labelFloat);
1809                         }else { //cant convert
1810                                 return false;
1811                         }
1812                 }
1813
1814                 //go through users set and make them floats
1815                 for(it = userLabels.begin(); it != userLabels.end();) {
1816
1817                         float temp;
1818                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1819                                 convert(*it, temp);
1820                                 orderFloat.push_back(temp);
1821                                 userMap[*it] = temp;
1822                                 it++;
1823                         }else if (*it == "unique") {
1824                                 orderFloat.push_back(-1.0);
1825                                 userMap["unique"] = -1.0;
1826                                 it++;
1827                         }else {
1828                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1829                                 userLabels.erase(it++);
1830                         }
1831                 }
1832
1833                 //sort order
1834                 sort(orderFloat.begin(), orderFloat.end());
1835
1836                 /*************************************************/
1837                 //is this label bigger than any of the users labels
1838                 /*************************************************/
1839
1840                 //loop through order until you find a label greater than label
1841                 for (int i = 0; i < orderFloat.size(); i++) {
1842                         if (orderFloat[i] < labelFloat) {
1843                                 smaller = true;
1844                                 if (orderFloat[i] == -1) {
1845                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1846                                         userLabels.erase("unique");
1847                                 }
1848                                 else {
1849                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1850                                         string s = "";
1851                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1852                                                 if (it2->second == orderFloat[i]) {
1853                                                         s = it2->first;
1854                                                         //remove small labels
1855                                                         userLabels.erase(s);
1856                                                         break;
1857                                                 }
1858                                         }
1859                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1860                                 }
1861                         //since they are sorted once you find a bigger one stop looking
1862                         }else { break; }
1863                 }
1864
1865                 return smaller;
1866
1867         }
1868         catch(exception& e) {
1869                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1870                 exit(1);
1871         }
1872 }
1873
1874 /**************************************************************************************************/
1875 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1876         try {
1877
1878                 bool good = true;
1879
1880                 string line = getline(file);
1881
1882                 //before we added this check
1883                 if (line[0] != '#') {  good = false;  }
1884                 else {
1885                         //rip off #
1886                         line = line.substr(1);
1887
1888                         vector<string> versionVector;
1889                         splitAtChar(version, versionVector, '.');
1890
1891                         //check file version
1892                         vector<string> linesVector;
1893                         splitAtChar(line, linesVector, '.');
1894
1895                         if (versionVector.size() != linesVector.size()) { good = false; }
1896                         else {
1897                                 for (int j = 0; j < versionVector.size(); j++) {
1898                                         int num1, num2;
1899                                         convert(versionVector[j], num1);
1900                                         convert(linesVector[j], num2);
1901
1902                                         //if mothurs version is newer than this files version, then we want to remake it
1903                                         if (num1 > num2) {  good = false; break;  }
1904                                 }
1905                         }
1906
1907                 }
1908
1909                 if (!good) {  file.close();  }
1910                 else { file.seekg(0);  }
1911
1912                 return good;
1913         }
1914         catch(exception& e) {
1915                 errorOut(e, "MothurOut", "checkReleaseVersion");
1916                 exit(1);
1917         }
1918 }
1919 /**************************************************************************************************/
1920 bool MothurOut::isContainingOnlyDigits(string input) {
1921         try{
1922
1923                 //are you a digit in ascii code
1924                 for (int i = 0;i < input.length(); i++){
1925                         if( input[i]>47 && input[i]<58){}
1926                         else { return false; }
1927                 }
1928
1929                 return true;
1930         }
1931         catch(exception& e) {
1932                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
1933                 exit(1);
1934         }
1935 }
1936 /**************************************************************************************************/
1937
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