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 int MothurOut::getRandomIndex(int highest){
 566         try {
 567
 568                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 569
 570                 return random;
 571         }
 572         catch(exception& e) {
 573                 errorOut(e, "MothurOut", "getRandomIndex");
 574                 exit(1);
 575         }
 576
 577 }
 578 /**********************************************************************/
 579
 580 string MothurOut::getPathName(string longName){
 581         try {
 582                 string rootPathName = longName;
 583
 584                 if(longName.find_last_of("/\\") != longName.npos){
 585                         int pos = longName.find_last_of("/\\")+1;
 586                         rootPathName = longName.substr(0, pos);
 587                 }
 588
 589                 return rootPathName;
 590         }
 591         catch(exception& e) {
 592                 errorOut(e, "MothurOut", "getPathName");
 593                 exit(1);
 594         }
 595
 596 }
 597 /***********************************************************************/
 598
 599 string MothurOut::hasPath(string longName){
 600         try {
 601                 string path = "";
 602
 603                 size_t found;
 604                 found=longName.find_last_of("~/\\");
 605
 606                 if(found != longName.npos){
 607                         path = longName.substr(0, found+1);
 608                 }
 609
 610                 return path;
 611         }
 612         catch(exception& e) {
 613                 errorOut(e, "MothurOut", "hasPath");
 614                 exit(1);
 615         }
 616 }
 617
 618 /***********************************************************************/
 619
 620 string MothurOut::getExtension(string longName){
 621         try {
 622                 string extension = longName;
 623
 624                 if(longName.find_last_of('.') != longName.npos){
 625                         int pos = longName.find_last_of('.');
 626                         extension = longName.substr(pos, longName.length());
 627                 }
 628
 629                 return extension;
 630         }
 631         catch(exception& e) {
 632                 errorOut(e, "MothurOut", "getExtension");
 633                 exit(1);
 634         }
 635 }
 636 /***********************************************************************/
 637 bool MothurOut::isBlank(string fileName){
 638         try {
 639
 640                 fileName = getFullPathName(fileName);
 641
 642                 ifstream fileHandle;
 643                 fileHandle.open(fileName.c_str());
 644                 if(!fileHandle) {
 645                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 646                         return false;
 647                 }else {
 648                         //check for blank file
 649                         gobble(fileHandle);
 650                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 651                         fileHandle.close();
 652                 }
 653                 return false;
 654         }
 655         catch(exception& e) {
 656                 errorOut(e, "MothurOut", "isBlank");
 657                 exit(1);
 658         }
 659 }
 660 /***********************************************************************/
 661
 662 string MothurOut::getFullPathName(string fileName){
 663         try{
 664
 665         string path = hasPath(fileName);
 666         string newFileName;
 667         int pos;
 668
 669         if (path == "") { return fileName; } //its a simple name
 670         else { //we need to complete the pathname
 671                 // ex. ../../../filename
 672                 // cwd = /user/work/desktop
 673
 674                 string cwd;
 675                 //get current working directory
 676                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 677
 678                         if (path.find("~") != -1) { //go to home directory
 679                                 string homeDir;
 680
 681                                 char *homepath = NULL;
 682                                 homepath = getenv ("HOME");
 683                                 if ( homepath != NULL) { homeDir = homepath; }
 684                                 else { homeDir = "";  }
 685
 686                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 687                                 return newFileName;
 688                         }else { //find path
 689                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 690                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 691
 692                                 //char* cwdpath = new char[1024];
 693                                 //size_t size;
 694                                 //cwdpath=getcwd(cwdpath,size);
 695                                 //cwd = cwdpath;
 696
 697                                 char *cwdpath = NULL;
 698                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 699                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 700                                 else { cwd = "";  }
 701
 702
 703                                 //rip off first '/'
 704                                 string simpleCWD;
 705                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 706
 707                                 //break apart the current working directory
 708                                 vector<string> dirs;
 709                                 while (simpleCWD.find_first_of('/') != string::npos) {
 710                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 711                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 712                                         dirs.push_back(dir);
 713                                 }
 714                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 715                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 716
 717
 718                                 int index = dirs.size()-1;
 719
 720                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 721                                         if (pos == 0) { break;  //you are at the end
 722                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 723                                                 path = path.substr(0, pos-1);
 724                                                 index--;
 725                                                 if (index == 0) {  break; }
 726                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 727                                                 path = path.substr(0, pos);
 728                                         }else if (pos == 1) { break;  //you are at the end
 729                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 730                                 }
 731
 732                                 for (int i = index; i >= 0; i--) {
 733                                         newFileName = dirs[i] +  "/" + newFileName;
 734                                 }
 735
 736                                 newFileName =  "/" +  newFileName;
 737                                 return newFileName;
 738                         }
 739                 #else
 740                         if (path.find("~") != string::npos) { //go to home directory
 741                                 string homeDir = getenv ("HOMEPATH");
 742                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 743                                 return newFileName;
 744                         }else { //find path
 745                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 746                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 747
 748                                 char *cwdpath = NULL;
 749                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 750                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 751                                 else { cwd = "";  }
 752
 753                                 //break apart the current working directory
 754                                 vector<string> dirs;
 755                                 while (cwd.find_first_of('\\') != -1) {
 756                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 757                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 758                                         dirs.push_back(dir);
 759
 760                                 }
 761                                 //get last one
 762                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 763
 764                                 int index = dirs.size()-1;
 765
 766                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 767                                         if (pos == 0) { break;  //you are at the end
 768                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 769                                                 path = path.substr(0, pos-1);
 770                                                 index--;
 771                                                 if (index == 0) {  break; }
 772                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 773                                                 path = path.substr(0, pos);
 774                                         }else if (pos == 1) { break;  //you are at the end
 775                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 776                                 }
 777
 778                                 for (int i = index; i >= 0; i--) {
 779                                         newFileName = dirs[i] +  "\\" + newFileName;
 780                                 }
 781
 782                                 return newFileName;
 783                         }
 784
 785                 #endif
 786         }
 787         }
 788         catch(exception& e) {
 789                 errorOut(e, "MothurOut", "getFullPathName");
 790                 exit(1);
 791         }
 792 }
 793 /***********************************************************************/
 794
 795 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 796         try {
 797                         //get full path name
 798                         string completeFileName = getFullPathName(fileName);
 799 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 800 #ifdef USE_COMPRESSION
 801       // check for gzipped or bzipped file
 802       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 803         string tempName = string(tmpnam(0));
 804         mkfifo(tempName.c_str(), 0666);
 805         int fork_result = fork();
 806         if (fork_result < 0) {
 807           cerr << "Error forking.\n";
 808           exit(1);
 809         } else if (fork_result == 0) {
 810           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 811           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 812           system(command.c_str());
 813           cerr << "Done decompressing " << completeFileName << "\n";
 814           remove(tempName.c_str());
 815           exit(EXIT_SUCCESS);
 816         } else {
 817           cerr << "waiting on child process " << fork_result << "\n";
 818           completeFileName = tempName;
 819         }
 820       }
 821 #endif
 822 #endif
 823                         fileHandle.open(completeFileName.c_str());
 824                         if(!fileHandle) {
 825                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 826                                 return 1;
 827                         }else {
 828                                 //check for blank file
 829                                 gobble(fileHandle);
 830                                 return 0;
 831                         }
 832         }
 833         catch(exception& e) {
 834                 errorOut(e, "MothurOut", "openInputFile - no Error");
 835                 exit(1);
 836         }
 837 }
 838 /***********************************************************************/
 839
 840 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 841         try {
 842
 843                 //get full path name
 844                 string completeFileName = getFullPathName(fileName);
 845 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 846 #ifdef USE_COMPRESSION
 847   // check for gzipped or bzipped file
 848   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 849     string tempName = string(tmpnam(0));
 850     mkfifo(tempName.c_str(), 0666);
 851     int fork_result = fork();
 852     if (fork_result < 0) {
 853       cerr << "Error forking.\n";
 854       exit(1);
 855     } else if (fork_result == 0) {
 856       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 857       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 858       system(command.c_str());
 859       cerr << "Done decompressing " << completeFileName << "\n";
 860       remove(tempName.c_str());
 861       exit(EXIT_SUCCESS);
 862     } else {
 863       cerr << "waiting on child process " << fork_result << "\n";
 864       completeFileName = tempName;
 865     }
 866   }
 867 #endif
 868 #endif
 869
 870                 fileHandle.open(completeFileName.c_str());
 871                 if(!fileHandle) {
 872                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 873                         return 1;
 874                 }
 875                 else {
 876                         //check for blank file
 877                         gobble(fileHandle);
 878                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 879
 880                         return 0;
 881                 }
 882         }
 883         catch(exception& e) {
 884                 errorOut(e, "MothurOut", "openInputFile");
 885                 exit(1);
 886         }
 887 }
 888 /***********************************************************************/
 889
 890 int MothurOut::renameFile(string oldName, string newName){
 891         try {
 892                 ifstream inTest;
 893                 int exist = openInputFile(newName, inTest, "");
 894
 895         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 896                 if (exist == 0) { //you could open it so you want to delete it
 897                         inTest.close();
 898                         string command = "rm " + newName;
 899                         system(command.c_str());
 900                 }
 901
 902                 string command = "mv " + oldName + " " + newName;
 903                 system(command.c_str());
 904         #else
 905                 remove(newName.c_str());
 906                 int renameOk = rename(oldName.c_str(), newName.c_str());
 907         #endif
 908                 return 0;
 909
 910         }
 911         catch(exception& e) {
 912                 errorOut(e, "MothurOut", "renameFile");
 913                 exit(1);
 914         }
 915 }
 916
 917 /***********************************************************************/
 918
 919 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 920         try {
 921
 922                 string completeFileName = getFullPathName(fileName);
 923 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 924 #ifdef USE_COMPRESSION
 925     // check for gzipped file
 926     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 927       string tempName = string(tmpnam(0));
 928       mkfifo(tempName.c_str(), 0666);
 929       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 930       int fork_result = fork();
 931       if (fork_result < 0) {
 932         cerr << "Error forking.\n";
 933         exit(1);
 934       } else if (fork_result == 0) {
 935         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 936         system(command.c_str());
 937         exit(0);
 938       } else {
 939         completeFileName = tempName;
 940       }
 941     }
 942 #endif
 943 #endif
 944                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 945                 if(!fileHandle) {
 946                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 947                         return 1;
 948                 }
 949                 else {
 950                         return 0;
 951                 }
 952         }
 953         catch(exception& e) {
 954                 errorOut(e, "MothurOut", "openOutputFile");
 955                 exit(1);
 956         }
 957
 958 }
 959
 960 /**************************************************************************************************/
 961 void MothurOut::appendFiles(string temp, string filename) {
 962         try{
 963                 ofstream output;
 964                 ifstream input;
 965
 966                 //open output file in append mode
 967                 openOutputFileAppend(filename, output);
 968                 int ableToOpen = openInputFile(temp, input, "no error");
 969                 //int ableToOpen = openInputFile(temp, input);
 970
 971                 if (ableToOpen == 0) { //you opened it
 972                         while(char c = input.get()){
 973                                 if(input.eof())         {       break;                  }
 974                                 else                            {       output << c;    }
 975                         }
 976                         input.close();
 977                 }
 978
 979                 output.close();
 980         }
 981         catch(exception& e) {
 982                 errorOut(e, "MothurOut", "appendFiles");
 983                 exit(1);
 984         }
 985 }
 986
 987 /**************************************************************************************************/
 988 string MothurOut::sortFile(string distFile, string outputDir){
 989         try {
 990
 991                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 992                 string outfile = getRootName(distFile) + "sorted.dist";
 993
 994
 995                 //if you can, use the unix sort since its been optimized for years
 996                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 997                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 998                         system(command.c_str());
 999                 #else //you are stuck with my best attempt...
1000                         //windows sort does not have a way to specify a column, only a character in the line
1001                         //since we cannot assume that the distance will always be at the the same character location on each line
1002                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1003
1004                         //read in file line by file and put distance first
1005                         string tempDistFile = distFile + ".temp";
1006                         ifstream input;
1007                         ofstream output;
1008                         openInputFile(distFile, input);
1009                         openOutputFile(tempDistFile, output);
1010
1011                         string firstName, secondName;
1012                         float dist;
1013                         while (input) {
1014                                 input >> firstName >> secondName >> dist;
1015                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1016                                 gobble(input);
1017                         }
1018                         input.close();
1019                         output.close();
1020
1021
1022                         //sort using windows sort
1023                         string tempOutfile = outfile + ".temp";
1024                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1025                         system(command.c_str());
1026
1027                         //read in sorted file and put distance at end again
1028                         ifstream input2;
1029                         openInputFile(tempOutfile, input2);
1030                         openOutputFile(outfile, output);
1031
1032                         while (input2) {
1033                                 input2 >> dist >> firstName >> secondName;
1034                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1035                                 gobble(input2);
1036                         }
1037                         input2.close();
1038                         output.close();
1039
1040                         //remove temp files
1041                         remove(tempDistFile.c_str());
1042                         remove(tempOutfile.c_str());
1043                 #endif
1044
1045                 return outfile;
1046         }
1047         catch(exception& e) {
1048                 errorOut(e, "MothurOut", "sortFile");
1049                 exit(1);
1050         }
1051 }
1052 /**************************************************************************************************/
1053 vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
1054         try {
1055                         vector<unsigned long int> positions;
1056                         ifstream inFASTA;
1057                         openInputFile(filename, inFASTA);
1058
1059                         string input;
1060                         while(!inFASTA.eof()){
1061                                 input = getline(inFASTA);
1062                                 if (input.length() != 0) {
1063                                         if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
1064                                 }
1065                                 gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1066                         }
1067                         inFASTA.close();
1068
1069                         num = positions.size();
1070
1071                         /*FILE * pFile;
1072                         long size;
1073
1074                         //get num bytes in file
1075                         pFile = fopen (filename.c_str(),"rb");
1076                         if (pFile==NULL) perror ("Error opening file");
1077                         else{
1078                                 fseek (pFile, 0, SEEK_END);
1079                                 size=ftell (pFile);
1080                                 fclose (pFile);
1081                         }*/
1082
1083                         unsigned long int size = positions[(positions.size()-1)];
1084                         ifstream in;
1085                         openInputFile(filename, in);
1086
1087                         in.seekg(size);
1088
1089                         while(in.get()){
1090                                 if(in.eof())            {       break;  }
1091                                 else                            {       size++; }
1092                         }
1093                         in.close();
1094
1095                         positions.push_back(size);
1096
1097                         return positions;
1098         }
1099         catch(exception& e) {
1100                 errorOut(e, "MothurOut", "setFilePosFasta");
1101                 exit(1);
1102         }
1103 }
1104 /**************************************************************************************************/
1105 vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
1106         try {
1107                         filename = getFullPathName(filename);
1108
1109                         vector<unsigned long int> positions;
1110                         ifstream in;
1111                         openInputFile(filename, in);
1112
1113                         string input;
1114                         while(!in.eof()){
1115                                 unsigned long int lastpos = in.tellg();
1116                                 input = getline(in);
1117                                 if (input.length() != 0) {
1118                                         unsigned long int pos = in.tellg();
1119                                         if (pos != -1) { positions.push_back(pos - input.length() - 1); }
1120                                         else {  positions.push_back(lastpos);  }
1121                                 }
1122                                 gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
1123                         }
1124                         in.close();
1125
1126                         num = positions.size();
1127
1128                         FILE * pFile;
1129                         unsigned long int size;
1130
1131                         //get num bytes in file
1132                         pFile = fopen (filename.c_str(),"rb");
1133                         if (pFile==NULL) perror ("Error opening file");
1134                         else{
1135                                 fseek (pFile, 0, SEEK_END);
1136                                 size=ftell (pFile);
1137                                 fclose (pFile);
1138                         }
1139
1140                         positions.push_back(size);
1141
1142                         return positions;
1143         }
1144         catch(exception& e) {
1145                 errorOut(e, "MothurOut", "setFilePosEachLine");
1146                 exit(1);
1147         }
1148 }
1149 /**************************************************************************************************/
1150
1151 vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
1152         try{
1153
1154                 vector<unsigned long int> filePos;
1155                 filePos.push_back(0);
1156
1157                 FILE * pFile;
1158                 unsigned long int size;
1159
1160                 filename = getFullPathName(filename);
1161
1162                 //get num bytes in file
1163                 pFile = fopen (filename.c_str(),"rb");
1164                 if (pFile==NULL) perror ("Error opening file");
1165                 else{
1166                         fseek (pFile, 0, SEEK_END);
1167                         size=ftell (pFile);
1168                         fclose (pFile);
1169                 }
1170
1171                 //estimate file breaks
1172                 unsigned long int chunkSize = 0;
1173                 chunkSize = size / proc;
1174
1175                 //file to small to divide by processors
1176                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1177
1178                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1179                 for (int i = 0; i < proc; i++) {
1180                         unsigned long int spot = (i+1) * chunkSize;
1181
1182                         ifstream in;
1183                         openInputFile(filename, in);
1184                         in.seekg(spot);
1185
1186                         //look for next '>'
1187                         unsigned long int newSpot = spot;
1188                         while (!in.eof()) {
1189                            char c = in.get();
1190                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1191                         }
1192
1193                         //there was not another sequence before the end of the file
1194                         unsigned long int sanityPos = in.tellg();
1195
1196                         if (sanityPos == -1) {  break;  }
1197                         else {  filePos.push_back(newSpot);  }
1198
1199                         in.close();
1200                 }
1201
1202                 //save end pos
1203                 filePos.push_back(size);
1204
1205                 //sanity check filePos
1206                 for (int i = 0; i < (filePos.size()-1); i++) {
1207                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1208                 }
1209
1210                 proc = (filePos.size() - 1);
1211
1212                 return filePos;
1213         }
1214         catch(exception& e) {
1215                 errorOut(e, "MothurOut", "divideFile");
1216                 exit(1);
1217         }
1218 }
1219 /**************************************************************************************************/
1220 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1221         try{
1222
1223                 vector<unsigned long int> filePos = divideFile(filename, proc);
1224
1225                 for (int i = 0; i < (filePos.size()-1); i++) {
1226
1227                         //read file chunk
1228                         ifstream in;
1229                         openInputFile(filename, in);
1230                         in.seekg(filePos[i]);
1231                         unsigned long int size = filePos[(i+1)] - filePos[i];
1232                         char* chunk = new char[size];
1233                         in.read(chunk, size);
1234                         in.close();
1235
1236                         //open new file
1237                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1238                         ofstream out;
1239                         openOutputFile(fileChunkName, out);
1240
1241                         out << chunk << endl;
1242                         out.close();
1243                         delete[] chunk;
1244
1245                         //save name
1246                         files.push_back(fileChunkName);
1247                 }
1248
1249                 return 0;
1250         }
1251         catch(exception& e) {
1252                 errorOut(e, "MothurOut", "divideFile");
1253                 exit(1);
1254         }
1255 }
1256 /***********************************************************************/
1257
1258 bool MothurOut::isTrue(string f){
1259         try {
1260
1261                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1262
1263                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1264                 else {  return false;  }
1265         }
1266         catch(exception& e) {
1267                 errorOut(e, "MothurOut", "isTrue");
1268                 exit(1);
1269         }
1270 }
1271
1272 /***********************************************************************/
1273
1274 float MothurOut::roundDist(float dist, int precision){
1275         try {
1276                 return int(dist * precision + 0.5)/float(precision);
1277         }
1278         catch(exception& e) {
1279                 errorOut(e, "MothurOut", "roundDist");
1280                 exit(1);
1281         }
1282 }
1283 /***********************************************************************/
1284
1285 float MothurOut::ceilDist(float dist, int precision){
1286         try {
1287                 return int(ceil(dist * precision))/float(precision);
1288         }
1289         catch(exception& e) {
1290                 errorOut(e, "MothurOut", "ceilDist");
1291                 exit(1);
1292         }
1293 }
1294 /**********************************************************************************************************************/
1295 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1296         try {
1297
1298                 //open input file
1299                 ifstream in;
1300                 openInputFile(namefile, in);
1301
1302                 while (!in.eof()) {
1303                         if (control_pressed) { break; }
1304
1305                         string firstCol, secondCol;
1306                         in >> firstCol >> secondCol; gobble(in);
1307
1308                         nameMap[firstCol] = secondCol;
1309                 }
1310                 in.close();
1311
1312                 return 0;
1313
1314         }
1315         catch(exception& e) {
1316                 errorOut(e, "MothurOut", "readNames");
1317                 exit(1);
1318         }
1319 }
1320
1321 /**********************************************************************************************************************/
1322 map<string, int> MothurOut::readNames(string namefile) {
1323         try {
1324
1325                 map<string, int> nameMap;
1326
1327                 //open input file
1328                 ifstream in;
1329                 openInputFile(namefile, in);
1330
1331                 while (!in.eof()) {
1332                         if (control_pressed) { break; }
1333
1334                         string firstCol, secondCol;
1335                         in >> firstCol >> secondCol; gobble(in);
1336
1337                         int num = getNumNames(secondCol);
1338
1339                         nameMap[firstCol] = num;
1340                 }
1341                 in.close();
1342
1343                 return nameMap;
1344
1345         }
1346         catch(exception& e) {
1347                 errorOut(e, "MothurOut", "readNames");
1348                 exit(1);
1349         }
1350 }
1351 /**********************************************************************************************************************/
1352 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1353         try {
1354                 int error = 0;
1355
1356                 //open input file
1357                 ifstream in;
1358                 openInputFile(namefile, in);
1359
1360                 while (!in.eof()) {
1361                         if (control_pressed) { break; }
1362
1363                         string firstCol, secondCol;
1364                         in >> firstCol >> secondCol; gobble(in);
1365
1366                         int num = getNumNames(secondCol);
1367
1368                         map<string, string>::iterator it = fastamap.find(firstCol);
1369                         if (it == fastamap.end()) {
1370                                 error = 1;
1371                                 mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1372                         }else {
1373                                 seqPriorityNode temp(num, it->second, firstCol);
1374                                 nameVector.push_back(temp);
1375                         }
1376                 }
1377                 in.close();
1378
1379                 return error;
1380
1381         }
1382         catch(exception& e) {
1383                 errorOut(e, "MothurOut", "readNames");
1384                 exit(1);
1385         }
1386 }
1387
1388 /***********************************************************************/
1389
1390 int MothurOut::getNumNames(string names){
1391         try {
1392                 int count = 0;
1393
1394                 if(names != ""){
1395                         count = 1;
1396                         for(int i=0;i<names.size();i++){
1397                                 if(names[i] == ','){
1398                                         count++;
1399                                 }
1400                         }
1401                 }
1402
1403                 return count;
1404         }
1405         catch(exception& e) {
1406                 errorOut(e, "MothurOut", "getNumNames");
1407                 exit(1);
1408         }
1409 }
1410
1411 /**************************************************************************************************/
1412
1413 vector<vector<double> > MothurOut::binomial(int maxOrder){
1414         try {
1415         vector<vector<double> > binomial(maxOrder+1);
1416
1417     for(int i=0;i<=maxOrder;i++){
1418                 binomial[i].resize(maxOrder+1);
1419                 binomial[i][0]=1;
1420                 binomial[0][i]=0;
1421     }
1422     binomial[0][0]=1;
1423
1424     binomial[1][0]=1;
1425     binomial[1][1]=1;
1426
1427     for(int i=2;i<=maxOrder;i++){
1428                 binomial[1][i]=0;
1429     }
1430
1431     for(int i=2;i<=maxOrder;i++){
1432                 for(int j=1;j<=maxOrder;j++){
1433                         if(i==j){       binomial[i][j]=1;                                                                       }
1434                         if(j>i) {       binomial[i][j]=0;                                                                       }
1435                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1436                 }
1437     }
1438
1439         return binomial;
1440
1441         }
1442         catch(exception& e) {
1443                 errorOut(e, "MothurOut", "binomial");
1444                 exit(1);
1445         }
1446 }
1447 /**************************************************************************************************/
1448 unsigned int MothurOut::fromBase36(string base36){
1449         try {
1450                 unsigned int num = 0;
1451
1452                 map<char, int> converts;
1453                 converts['A'] = 0;
1454                 converts['a'] = 0;
1455                 converts['B'] = 1;
1456                 converts['b'] = 1;
1457                 converts['C'] = 2;
1458                 converts['c'] = 2;
1459                 converts['D'] = 3;
1460                 converts['d'] = 3;
1461                 converts['E'] = 4;
1462                 converts['e'] = 4;
1463                 converts['F'] = 5;
1464                 converts['f'] = 5;
1465                 converts['G'] = 6;
1466                 converts['g'] = 6;
1467                 converts['H'] = 7;
1468                 converts['h'] = 7;
1469                 converts['I'] = 8;
1470                 converts['i'] = 8;
1471                 converts['J'] = 9;
1472                 converts['j'] = 9;
1473                 converts['K'] = 10;
1474                 converts['k'] = 10;
1475                 converts['L'] = 11;
1476                 converts['l'] = 11;
1477                 converts['M'] = 12;
1478                 converts['m'] = 12;
1479                 converts['N'] = 13;
1480                 converts['n'] = 13;
1481                 converts['O'] = 14;
1482                 converts['o'] = 14;
1483                 converts['P'] = 15;
1484                 converts['p'] = 15;
1485                 converts['Q'] = 16;
1486                 converts['q'] = 16;
1487                 converts['R'] = 17;
1488                 converts['r'] = 17;
1489                 converts['S'] = 18;
1490                 converts['s'] = 18;
1491                 converts['T'] = 19;
1492                 converts['t'] = 19;
1493                 converts['U'] = 20;
1494                 converts['u'] = 20;
1495                 converts['V'] = 21;
1496                 converts['v'] = 21;
1497                 converts['W'] = 22;
1498                 converts['w'] = 22;
1499                 converts['X'] = 23;
1500                 converts['x'] = 23;
1501                 converts['Y'] = 24;
1502                 converts['y'] = 24;
1503                 converts['Z'] = 25;
1504                 converts['z'] = 25;
1505                 converts['0'] = 26;
1506                 converts['1'] = 27;
1507                 converts['2'] = 28;
1508                 converts['3'] = 29;
1509                 converts['4'] = 30;
1510                 converts['5'] = 31;
1511                 converts['6'] = 32;
1512                 converts['7'] = 33;
1513                 converts['8'] = 34;
1514                 converts['9'] = 35;
1515
1516                 int i = 0;
1517                 while (i < base36.length()) {
1518                         char c = base36[i];
1519                         num = 36 * num + converts[c];
1520                         i++;
1521                 }
1522
1523                 return num;
1524
1525         }
1526         catch(exception& e) {
1527                 errorOut(e, "MothurOut", "fromBase36");
1528                 exit(1);
1529         }
1530 }
1531 /***********************************************************************/
1532
1533 int MothurOut::factorial(int num){
1534         try {
1535                 int total = 1;
1536
1537                 for (int i = 1; i <= num; i++) {
1538                         total *= i;
1539                 }
1540
1541                 return total;
1542         }
1543         catch(exception& e) {
1544                 errorOut(e, "MothurOut", "factorial");
1545                 exit(1);
1546         }
1547 }
1548 /***********************************************************************/
1549
1550 int MothurOut::getNumSeqs(ifstream& file){
1551         try {
1552                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1553                 file.seekg(0);
1554                 return numSeqs;
1555         }
1556         catch(exception& e) {
1557                 errorOut(e, "MothurOut", "getNumSeqs");
1558                 exit(1);
1559         }
1560 }
1561 /***********************************************************************/
1562 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1563         try {
1564                 string input;
1565                 numSeqs = 0;
1566                 while(!file.eof()){
1567                         input = getline(file);
1568                         if (input.length() != 0) {
1569                                 if(input[0] == '>'){ numSeqs++; }
1570                         }
1571                 }
1572         }
1573         catch(exception& e) {
1574                 errorOut(e, "MothurOut", "getNumSeqs");
1575                 exit(1);
1576         }
1577 }
1578 /***********************************************************************/
1579
1580 //This function parses the estimator options and puts them in a vector
1581 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1582         try {
1583                 string individual = "";
1584                 int estimLength = estim.size();
1585                 for(int i=0;i<estimLength;i++){
1586                         if(estim[i] == symbol){
1587                                 container.push_back(individual);
1588                                 individual = "";
1589                         }
1590                         else{
1591                                 individual += estim[i];
1592                         }
1593                 }
1594                 container.push_back(individual);
1595
1596         }
1597         catch(exception& e) {
1598                 errorOut(e, "MothurOut", "splitAtChar");
1599                 exit(1);
1600         }
1601 }
1602
1603 /***********************************************************************/
1604
1605 //This function parses the estimator options and puts them in a vector
1606 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1607         try {
1608                 string individual = "";
1609                 int estimLength = estim.size();
1610                 for(int i=0;i<estimLength;i++){
1611                         if(estim[i] == '-'){
1612                                 container.push_back(individual);
1613                                 individual = "";
1614                         }
1615                         else{
1616                                 individual += estim[i];
1617                         }
1618                 }
1619                 container.push_back(individual);
1620
1621
1622         /*      string individual;
1623
1624                 while (estim.find_first_of('-') != -1) {
1625                         individual = estim.substr(0,estim.find_first_of('-'));
1626                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1627                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1628                                 container.push_back(individual);
1629                         }
1630                 }
1631                 //get last one
1632                 container.push_back(estim); */
1633         }
1634         catch(exception& e) {
1635                 errorOut(e, "MothurOut", "splitAtDash");
1636                 exit(1);
1637         }
1638 }
1639
1640 /***********************************************************************/
1641 //This function parses the label options and puts them in a set
1642 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1643         try {
1644                 string individual = "";
1645                 int estimLength = estim.size();
1646                 for(int i=0;i<estimLength;i++){
1647                         if(estim[i] == '-'){
1648                                 container.insert(individual);
1649                                 individual = "";
1650                         }
1651                         else{
1652                                 individual += estim[i];
1653                         }
1654                 }
1655                 container.insert(individual);
1656
1657         //      string individual;
1658
1659         //      while (estim.find_first_of('-') != -1) {
1660         //              individual = estim.substr(0,estim.find_first_of('-'));
1661         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1662         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1663         //                      container.insert(individual);
1664         //              }
1665         //      }
1666                 //get last one
1667         //      container.insert(estim);
1668
1669         }
1670         catch(exception& e) {
1671                 errorOut(e, "MothurOut", "splitAtDash");
1672                 exit(1);
1673         }
1674 }
1675 /***********************************************************************/
1676 //This function parses the line options and puts them in a set
1677 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1678         try {
1679                 string individual;
1680                 int lineNum;
1681
1682                 while (estim.find_first_of('-') != -1) {
1683                         individual = estim.substr(0,estim.find_first_of('-'));
1684                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1685                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1686                                 convert(individual, lineNum); //convert the string to int
1687                                 container.insert(lineNum);
1688                         }
1689                 }
1690                 //get last one
1691                 convert(estim, lineNum); //convert the string to int
1692                 container.insert(lineNum);
1693         }
1694         catch(exception& e) {
1695                 errorOut(e, "MothurOut", "splitAtDash");
1696                 exit(1);
1697         }
1698 }
1699 /***********************************************************************/
1700 //This function parses the a string and puts peices in a vector
1701 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1702         try {
1703                 string individual = "";
1704                 int estimLength = estim.size();
1705                 for(int i=0;i<estimLength;i++){
1706                         if(estim[i] == ','){
1707                                 container.push_back(individual);
1708                                 individual = "";
1709                         }
1710                         else{
1711                                 individual += estim[i];
1712                         }
1713                 }
1714                 container.push_back(individual);
1715
1716
1717
1718
1719 //              string individual;
1720 //
1721 //              while (estim.find_first_of(',') != -1) {
1722 //                      individual = estim.substr(0,estim.find_first_of(','));
1723 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1724 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1725 //                              container.push_back(individual);
1726 //                      }
1727 //              }
1728 //              //get last one
1729 //              container.push_back(estim);
1730         }
1731         catch(exception& e) {
1732                 errorOut(e, "MothurOut", "splitAtComma");
1733                 exit(1);
1734         }
1735 }
1736 /***********************************************************************/
1737
1738 //This function splits up the various option parameters
1739 void MothurOut::splitAtComma(string& prefix, string& suffix){
1740         try {
1741                 prefix = suffix.substr(0,suffix.find_first_of(','));
1742                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1743                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1744                         string space = " ";
1745                         while(suffix.at(0) == ' ')
1746                                 suffix = suffix.substr(1, suffix.length());
1747                 }
1748
1749         }
1750         catch(exception& e) {
1751                 errorOut(e, "MothurOut", "splitAtComma");
1752                 exit(1);
1753         }
1754 }
1755 /***********************************************************************/
1756
1757 //This function separates the key value from the option value i.e. dist=96_...
1758 void MothurOut::splitAtEquals(string& key, string& value){
1759         try {
1760                 if(value.find_first_of('=') != -1){
1761                         key = value.substr(0,value.find_first_of('='));
1762                         if ((value.find_first_of('=')+1) <= value.length()) {
1763                                 value = value.substr(value.find_first_of('=')+1, value.length());
1764                         }
1765                 }else{
1766                         key = value;
1767                         value = 1;
1768                 }
1769         }
1770         catch(exception& e) {
1771                 errorOut(e, "MothurOut", "splitAtEquals");
1772                 exit(1);
1773         }
1774 }
1775
1776 /**************************************************************************************************/
1777
1778 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1779         try {
1780                 for (int i = 0; i < Groups.size(); i++) {
1781                         if (groupname == Groups[i]) { return true; }
1782                 }
1783                 return false;
1784         }
1785         catch(exception& e) {
1786                 errorOut(e, "MothurOut", "inUsersGroups");
1787                 exit(1);
1788         }
1789 }
1790 /**************************************************************************************************/
1791 //returns true if any of the strings in first vector are in second vector
1792 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1793         try {
1794
1795                 for (int i = 0; i < groupnames.size(); i++) {
1796                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1797                 }
1798                 return false;
1799         }
1800         catch(exception& e) {
1801                 errorOut(e, "MothurOut", "inUsersGroups");
1802                 exit(1);
1803         }
1804 }
1805 /***********************************************************************/
1806 //this function determines if the user has given us labels that are smaller than the given label.
1807 //if so then it returns true so that the calling function can run the previous valid distance.
1808 //it's a "smart" distance function.  It also checks for invalid labels.
1809 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1810         try {
1811
1812                 set<string>::iterator it;
1813                 vector<float> orderFloat;
1814                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1815                 map<string, float>::iterator it2;
1816                 float labelFloat;
1817                 bool smaller = false;
1818
1819                 //unique is the smallest line
1820                 if (label == "unique") {  return false;  }
1821                 else {
1822                         if (convertTestFloat(label, labelFloat)) {
1823                                 convert(label, labelFloat);
1824                         }else { //cant convert
1825                                 return false;
1826                         }
1827                 }
1828
1829                 //go through users set and make them floats
1830                 for(it = userLabels.begin(); it != userLabels.end();) {
1831
1832                         float temp;
1833                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1834                                 convert(*it, temp);
1835                                 orderFloat.push_back(temp);
1836                                 userMap[*it] = temp;
1837                                 it++;
1838                         }else if (*it == "unique") {
1839                                 orderFloat.push_back(-1.0);
1840                                 userMap["unique"] = -1.0;
1841                                 it++;
1842                         }else {
1843                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1844                                 userLabels.erase(it++);
1845                         }
1846                 }
1847
1848                 //sort order
1849                 sort(orderFloat.begin(), orderFloat.end());
1850
1851                 /*************************************************/
1852                 //is this label bigger than any of the users labels
1853                 /*************************************************/
1854
1855                 //loop through order until you find a label greater than label
1856                 for (int i = 0; i < orderFloat.size(); i++) {
1857                         if (orderFloat[i] < labelFloat) {
1858                                 smaller = true;
1859                                 if (orderFloat[i] == -1) {
1860                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1861                                         userLabels.erase("unique");
1862                                 }
1863                                 else {
1864                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1865                                         string s = "";
1866                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1867                                                 if (it2->second == orderFloat[i]) {
1868                                                         s = it2->first;
1869                                                         //remove small labels
1870                                                         userLabels.erase(s);
1871                                                         break;
1872                                                 }
1873                                         }
1874                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1875                                 }
1876                         //since they are sorted once you find a bigger one stop looking
1877                         }else { break; }
1878                 }
1879
1880                 return smaller;
1881
1882         }
1883         catch(exception& e) {
1884                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1885                 exit(1);
1886         }
1887 }
1888
1889 /**************************************************************************************************/
1890 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1891         try {
1892
1893                 bool good = true;
1894
1895                 string line = getline(file);
1896
1897                 //before we added this check
1898                 if (line[0] != '#') {  good = false;  }
1899                 else {
1900                         //rip off #
1901                         line = line.substr(1);
1902
1903                         vector<string> versionVector;
1904                         splitAtChar(version, versionVector, '.');
1905
1906                         //check file version
1907                         vector<string> linesVector;
1908                         splitAtChar(line, linesVector, '.');
1909
1910                         if (versionVector.size() != linesVector.size()) { good = false; }
1911                         else {
1912                                 for (int j = 0; j < versionVector.size(); j++) {
1913                                         int num1, num2;
1914                                         convert(versionVector[j], num1);
1915                                         convert(linesVector[j], num2);
1916
1917                                         //if mothurs version is newer than this files version, then we want to remake it
1918                                         if (num1 > num2) {  good = false; break;  }
1919                                 }
1920                         }
1921
1922                 }
1923
1924                 if (!good) {  file.close();  }
1925                 else { file.seekg(0);  }
1926
1927                 return good;
1928         }
1929         catch(exception& e) {
1930                 errorOut(e, "MothurOut", "checkReleaseVersion");
1931                 exit(1);
1932         }
1933 }
1934 /**************************************************************************************************/
1935 bool MothurOut::isContainingOnlyDigits(string input) {
1936         try{
1937
1938                 //are you a digit in ascii code
1939                 for (int i = 0;i < input.length(); i++){
1940                         if( input[i]>47 && input[i]<58){}
1941                         else { return false; }
1942                 }
1943
1944                 return true;
1945         }
1946         catch(exception& e) {
1947                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
1948                 exit(1);
1949         }
1950 }
1951 /**************************************************************************************************/
1952
1953
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1956