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