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) || (__linux__) || (__unix__) || (__unix)
 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                 out << output;
 216         logger() << 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                 out << endl;
 238         logger() << 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
 261                         out << output;
 262                         outputFile << output;
 263             logger() << output;
 264
 265 #ifdef USE_MPI
 266                 }
 267 #endif
 268
 269         }
 270         catch(exception& e) {
 271                 errorOut(e, "MothurOut", "MothurOut");
 272                 exit(1);
 273         }
 274 }
 275 /*********************************************************************************************/
 276 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 277         try {
 278 #ifdef USE_MPI
 279                 int pid;
 280                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 281
 282                 if (pid == 0) { //only one process should output to screen
 283 #endif
 284
 285                         out << endl;
 286                         outputFile << endl;
 287             logger() << endl;
 288
 289 #ifdef USE_MPI
 290                 }
 291 #endif
 292         }
 293         catch(exception& e) {
 294                 errorOut(e, "MothurOut", "MothurOutEndLine");
 295                 exit(1);
 296         }
 297 }
 298 /*********************************************************************************************/
 299 void MothurOut::mothurOutJustToLog(string output) {
 300         try {
 301                 #ifdef USE_MPI
 302                         int pid;
 303                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 304
 305                         if (pid == 0) { //only one process should output to screen
 306                 #endif
 307
 308                 out << output;
 309
 310                 #ifdef USE_MPI
 311                         }
 312                 #endif
 313         }
 314         catch(exception& e) {
 315                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 316                 exit(1);
 317         }
 318 }
 319 /*********************************************************************************************/
 320 void MothurOut::errorOut(exception& e, string object, string function) {
 321         //double vm, rss;
 322         //mem_usage(vm, rss);
 323
 324         mothurOut("[ERROR]: ");
 325         mothurOut(toString(e.what()));
 326         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.");
 327         mothurOutEndLine();
 328 }
 329 /*********************************************************************************************/
 330 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 331 // process_mem_usage(double &, double &) - takes two doubles by reference,
 332 // attempts to read the system-dependent data for a process' virtual memory
 333 // size and resident set size, and return the results in KB.
 334 //
 335 // On failure, returns 0.0, 0.0
 336 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 337   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 338
 339            vm_usage     = 0.0;
 340            resident_set = 0.0;
 341
 342            // 'file' stat seems to give the most reliable results
 343            //
 344            ifstream stat_stream("/proc/self/stat",ios_base::in);
 345
 346            // dummy vars for leading entries in stat that we don't care about
 347            //
 348            string pid, comm, state, ppid, pgrp, session, tty_nr;
 349            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 350            string utime, stime, cutime, cstime, priority, nice;
 351            string O, itrealvalue, starttime;
 352
 353            // the two fields we want
 354            //
 355            unsigned long vsize;
 356            long rss;
 357
 358            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 359                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 360                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 361                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 362
 363            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 364            vm_usage     = vsize / 1024.0;
 365            resident_set = rss * page_size_kb;
 366
 367            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 368                 return 0;
 369
 370         #else
 371 /*              //windows memory usage
 372                 // Get the list of process identifiers.
 373                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 374
 375                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 376
 377                 // Calculate how many process identifiers were returned.
 378                 cProcesses = cbNeeded / sizeof(DWORD);
 379
 380                 // Print the memory usage for each process
 381                 for (int i = 0; i < cProcesses; i++ ) {
 382                         DWORD processID = aProcesses[i];
 383
 384                         PROCESS_MEMORY_COUNTERS pmc;
 385
 386                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 387
 388                         // Print the process identifier.
 389                         printf( "\nProcess ID: %u\n", processID);
 390
 391                         if (NULL != hProcess) {
 392
 393                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 394                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 395                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 396                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 397                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 398                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 399                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 400                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 401                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 402                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 403                                 }
 404                                 CloseHandle(hProcess);
 405                         }
 406                 }
 407 */
 408                         return 0;
 409
 410         #endif
 411 }
 412
 413
 414 /***********************************************************************/
 415 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 416         try {
 417                 fileName = getFullPathName(fileName);
 418
 419                 fileHandle.open(fileName.c_str(), ios::app);
 420                 if(!fileHandle) {
 421                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 422                         return 1;
 423                 }
 424                 else {
 425                         return 0;
 426                 }
 427         }
 428         catch(exception& e) {
 429                 errorOut(e, "MothurOut", "openOutputFileAppend");
 430                 exit(1);
 431         }
 432 }
 433 /***********************************************************************/
 434 void MothurOut::gobble(istream& f){
 435         try {
 436
 437                 char d;
 438                 while(isspace(d=f.get()))               { ;}
 439                 if(!f.eof()) { f.putback(d); }
 440         }
 441         catch(exception& e) {
 442                 errorOut(e, "MothurOut", "gobble");
 443                 exit(1);
 444         }
 445 }
 446 /***********************************************************************/
 447 void MothurOut::gobble(istringstream& f){
 448         try {
 449                 char d;
 450                 while(isspace(d=f.get()))               {;}
 451                 if(!f.eof()) { f.putback(d); }
 452         }
 453         catch(exception& e) {
 454                 errorOut(e, "MothurOut", "gobble");
 455                 exit(1);
 456         }
 457 }
 458
 459 /***********************************************************************/
 460
 461 string MothurOut::getline(istringstream& fileHandle) {
 462         try {
 463
 464                 string line = "";
 465
 466                 while (!fileHandle.eof())       {
 467                         //get next character
 468                         char c = fileHandle.get();
 469
 470                         //are you at the end of the line
 471                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 472                         else {          line += c;              }
 473                 }
 474
 475                 return line;
 476
 477         }
 478         catch(exception& e) {
 479                 errorOut(e, "MothurOut", "getline");
 480                 exit(1);
 481         }
 482 }
 483 /***********************************************************************/
 484
 485 string MothurOut::getline(ifstream& fileHandle) {
 486         try {
 487
 488                 string line = "";
 489
 490                 while (fileHandle)      {
 491                         //get next character
 492                         char c = fileHandle.get();
 493
 494                         //are you at the end of the line
 495                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }
 496                         else {          line += c;              }
 497                 }
 498
 499                 return line;
 500
 501         }
 502         catch(exception& e) {
 503                 errorOut(e, "MothurOut", "getline");
 504                 exit(1);
 505         }
 506 }
 507 /***********************************************************************/
 508
 509 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 510 #ifdef USE_COMPRESSION
 511 inline bool endsWith(string s, const char * suffix){
 512   size_t suffixLength = strlen(suffix);
 513   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 514 }
 515 #endif
 516 #endif
 517
 518 string MothurOut::getRootName(string longName){
 519         try {
 520
 521                 string rootName = longName;
 522
 523 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 524 #ifdef USE_COMPRESSION
 525     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 526       int pos = rootName.find_last_of('.');
 527       rootName = rootName.substr(0, pos);
 528       cerr << "shortening " << longName << " to " << rootName << "\n";
 529     }
 530 #endif
 531 #endif
 532                 if(rootName.find_last_of(".") != rootName.npos){
 533                         int pos = rootName.find_last_of('.')+1;
 534                         rootName = rootName.substr(0, pos);
 535                 }
 536
 537                 return rootName;
 538         }
 539         catch(exception& e) {
 540                 errorOut(e, "MothurOut", "getRootName");
 541                 exit(1);
 542         }
 543 }
 544 /***********************************************************************/
 545
 546 string MothurOut::getSimpleName(string longName){
 547         try {
 548                 string simpleName = longName;
 549
 550                 size_t found;
 551                 found=longName.find_last_of("/\\");
 552
 553                 if(found != longName.npos){
 554                         simpleName = longName.substr(found+1);
 555                 }
 556
 557                 return simpleName;
 558         }
 559         catch(exception& e) {
 560                 errorOut(e, "MothurOut", "getSimpleName");
 561                 exit(1);
 562         }
 563 }
 564
 565 /***********************************************************************/
 566
 567 int MothurOut::getRandomIndex(int highest){
 568         try {
 569
 570                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 571
 572                 return random;
 573         }
 574         catch(exception& e) {
 575                 errorOut(e, "MothurOut", "getRandomIndex");
 576                 exit(1);
 577         }
 578
 579 }
 580 /**********************************************************************/
 581
 582 string MothurOut::getPathName(string longName){
 583         try {
 584                 string rootPathName = longName;
 585
 586                 if(longName.find_last_of("/\\") != longName.npos){
 587                         int pos = longName.find_last_of("/\\")+1;
 588                         rootPathName = longName.substr(0, pos);
 589                 }
 590
 591                 return rootPathName;
 592         }
 593         catch(exception& e) {
 594                 errorOut(e, "MothurOut", "getPathName");
 595                 exit(1);
 596         }
 597
 598 }
 599 /***********************************************************************/
 600
 601 bool MothurOut::dirCheck(string& dirName){
 602         try {
 603
 604         string tag = "";
 605         #ifdef USE_MPI
 606             int pid;
 607             MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 608
 609             tag = toString(pid);
 610         #endif
 611
 612         //add / to name if needed
 613         string lastChar = dirName.substr(dirName.length()-1);
 614         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 615         if (lastChar != "/") { dirName += "/"; }
 616         #else
 617         if (lastChar != "\\") { dirName += "\\"; }
 618         #endif
 619
 620         //test to make sure directory exists
 621         dirName = getFullPathName(dirName);
 622         string outTemp = dirName + tag + "temp";
 623         ofstream out;
 624         out.open(outTemp.c_str(), ios::trunc);
 625         if(!out) {
 626             mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine();
 627         }else{
 628             out.close();
 629             mothurRemove(outTemp);
 630             return true;
 631         }
 632
 633         return false;
 634     }
 635         catch(exception& e) {
 636                 errorOut(e, "MothurOut", "dirCheck");
 637                 exit(1);
 638         }
 639
 640 }
 641 /***********************************************************************/
 642
 643 string MothurOut::hasPath(string longName){
 644         try {
 645                 string path = "";
 646
 647                 size_t found;
 648                 found=longName.find_last_of("~/\\");
 649
 650                 if(found != longName.npos){
 651                         path = longName.substr(0, found+1);
 652                 }
 653
 654                 return path;
 655         }
 656         catch(exception& e) {
 657                 errorOut(e, "MothurOut", "hasPath");
 658                 exit(1);
 659         }
 660 }
 661
 662 /***********************************************************************/
 663
 664 string MothurOut::getExtension(string longName){
 665         try {
 666                 string extension = "";
 667
 668                 if(longName.find_last_of('.') != longName.npos){
 669                         int pos = longName.find_last_of('.');
 670                         extension = longName.substr(pos, longName.length());
 671                 }
 672
 673                 return extension;
 674         }
 675         catch(exception& e) {
 676                 errorOut(e, "MothurOut", "getExtension");
 677                 exit(1);
 678         }
 679 }
 680 /***********************************************************************/
 681 bool MothurOut::isBlank(string fileName){
 682         try {
 683
 684                 fileName = getFullPathName(fileName);
 685
 686                 ifstream fileHandle;
 687                 fileHandle.open(fileName.c_str());
 688                 if(!fileHandle) {
 689                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 690                         return false;
 691                 }else {
 692                         //check for blank file
 693                         gobble(fileHandle);
 694                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 695                         fileHandle.close();
 696                 }
 697                 return false;
 698         }
 699         catch(exception& e) {
 700                 errorOut(e, "MothurOut", "isBlank");
 701                 exit(1);
 702         }
 703 }
 704 /***********************************************************************/
 705
 706 string MothurOut::getFullPathName(string fileName){
 707         try{
 708
 709         string path = hasPath(fileName);
 710         string newFileName;
 711         int pos;
 712
 713         if (path == "") { return fileName; } //its a simple name
 714         else { //we need to complete the pathname
 715                 // ex. ../../../filename
 716                 // cwd = /user/work/desktop
 717
 718                 string cwd;
 719                 //get current working directory
 720                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 721
 722                         if (path.find("~") != -1) { //go to home directory
 723                                 string homeDir;
 724
 725                                 char *homepath = NULL;
 726                                 homepath = getenv ("HOME");
 727                                 if ( homepath != NULL) { homeDir = homepath; }
 728                                 else { homeDir = "";  }
 729
 730                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 731                                 return newFileName;
 732                         }else { //find path
 733                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 734                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 735
 736                                 //char* cwdpath = new char[1024];
 737                                 //size_t size;
 738                                 //cwdpath=getcwd(cwdpath,size);
 739                                 //cwd = cwdpath;
 740
 741                                 char *cwdpath = NULL;
 742                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 743                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 744                                 else { cwd = "";  }
 745
 746
 747                                 //rip off first '/'
 748                                 string simpleCWD;
 749                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 750
 751                                 //break apart the current working directory
 752                                 vector<string> dirs;
 753                                 while (simpleCWD.find_first_of('/') != string::npos) {
 754                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 755                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 756                                         dirs.push_back(dir);
 757                                 }
 758                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 759                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 760
 761
 762                                 int index = dirs.size()-1;
 763
 764                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 765                                         if (pos == 0) { break;  //you are at the end
 766                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 767                                                 path = path.substr(0, pos-1);
 768                                                 index--;
 769                                                 if (index == 0) {  break; }
 770                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 771                                                 path = path.substr(0, pos);
 772                                         }else if (pos == 1) { break;  //you are at the end
 773                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 774                                 }
 775
 776                                 for (int i = index; i >= 0; i--) {
 777                                         newFileName = dirs[i] +  "/" + newFileName;
 778                                 }
 779
 780                                 newFileName =  "/" +  newFileName;
 781                                 return newFileName;
 782                         }
 783                 #else
 784                         if (path.find("~") != string::npos) { //go to home directory
 785                                 string homeDir = getenv ("HOMEPATH");
 786                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 787                                 return newFileName;
 788                         }else { //find path
 789                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 790                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 791
 792                                 char *cwdpath = NULL;
 793                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 794                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 795                                 else { cwd = "";  }
 796
 797                                 //break apart the current working directory
 798                                 vector<string> dirs;
 799                                 while (cwd.find_first_of('\\') != -1) {
 800                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 801                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 802                                         dirs.push_back(dir);
 803
 804                                 }
 805                                 //get last one
 806                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 807
 808                                 int index = dirs.size()-1;
 809
 810                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 811                                         if (pos == 0) { break;  //you are at the end
 812                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 813                                                 path = path.substr(0, pos-1);
 814                                                 index--;
 815                                                 if (index == 0) {  break; }
 816                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 817                                                 path = path.substr(0, pos);
 818                                         }else if (pos == 1) { break;  //you are at the end
 819                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 820                                 }
 821
 822                                 for (int i = index; i >= 0; i--) {
 823                                         newFileName = dirs[i] +  "\\" + newFileName;
 824                                 }
 825
 826                                 return newFileName;
 827                         }
 828
 829                 #endif
 830         }
 831         }
 832         catch(exception& e) {
 833                 errorOut(e, "MothurOut", "getFullPathName");
 834                 exit(1);
 835         }
 836 }
 837 /***********************************************************************/
 838
 839 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 840         try {
 841                         //get full path name
 842                         string completeFileName = getFullPathName(fileName);
 843 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 844 #ifdef USE_COMPRESSION
 845       // check for gzipped or bzipped file
 846       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 847         string tempName = string(tmpnam(0));
 848         mkfifo(tempName.c_str(), 0666);
 849         int fork_result = fork();
 850         if (fork_result < 0) {
 851           cerr << "Error forking.\n";
 852           exit(1);
 853         } else if (fork_result == 0) {
 854           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 855           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 856           system(command.c_str());
 857           cerr << "Done decompressing " << completeFileName << "\n";
 858           mothurRemove(tempName);
 859           exit(EXIT_SUCCESS);
 860         } else {
 861           cerr << "waiting on child process " << fork_result << "\n";
 862           completeFileName = tempName;
 863         }
 864       }
 865 #endif
 866 #endif
 867                         fileHandle.open(completeFileName.c_str());
 868                         if(!fileHandle) {
 869                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 870                                 return 1;
 871                         }else {
 872                                 //check for blank file
 873                                 gobble(fileHandle);
 874                                 return 0;
 875                         }
 876         }
 877         catch(exception& e) {
 878                 errorOut(e, "MothurOut", "openInputFile - no Error");
 879                 exit(1);
 880         }
 881 }
 882 /***********************************************************************/
 883
 884 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 885         try {
 886
 887                 //get full path name
 888                 string completeFileName = getFullPathName(fileName);
 889 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 890 #ifdef USE_COMPRESSION
 891   // check for gzipped or bzipped file
 892   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 893     string tempName = string(tmpnam(0));
 894     mkfifo(tempName.c_str(), 0666);
 895     int fork_result = fork();
 896     if (fork_result < 0) {
 897       cerr << "Error forking.\n";
 898       exit(1);
 899     } else if (fork_result == 0) {
 900       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 901       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 902       system(command.c_str());
 903       cerr << "Done decompressing " << completeFileName << "\n";
 904       mothurRemove(tempName);
 905       exit(EXIT_SUCCESS);
 906     } else {
 907       cerr << "waiting on child process " << fork_result << "\n";
 908       completeFileName = tempName;
 909     }
 910   }
 911 #endif
 912 #endif
 913
 914                 fileHandle.open(completeFileName.c_str());
 915                 if(!fileHandle) {
 916                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 917                         return 1;
 918                 }
 919                 else {
 920                         //check for blank file
 921                         gobble(fileHandle);
 922                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 923
 924                         return 0;
 925                 }
 926         }
 927         catch(exception& e) {
 928                 errorOut(e, "MothurOut", "openInputFile");
 929                 exit(1);
 930         }
 931 }
 932 /***********************************************************************/
 933
 934 int MothurOut::renameFile(string oldName, string newName){
 935         try {
 936                 ifstream inTest;
 937                 int exist = openInputFile(newName, inTest, "");
 938                 inTest.close();
 939
 940         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 941                 if (exist == 0) { //you could open it so you want to delete it
 942                         string command = "rm " + newName;
 943                         system(command.c_str());
 944                 }
 945
 946                 string command = "mv " + oldName + " " + newName;
 947                 system(command.c_str());
 948         #else
 949                 mothurRemove(newName);
 950                 int renameOk = rename(oldName.c_str(), newName.c_str());
 951         #endif
 952                 return 0;
 953
 954         }
 955         catch(exception& e) {
 956                 errorOut(e, "MothurOut", "renameFile");
 957                 exit(1);
 958         }
 959 }
 960
 961 /***********************************************************************/
 962
 963 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 964         try {
 965
 966                 string completeFileName = getFullPathName(fileName);
 967 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 968 #ifdef USE_COMPRESSION
 969     // check for gzipped file
 970     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 971       string tempName = string(tmpnam(0));
 972       mkfifo(tempName.c_str(), 0666);
 973       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 974       int fork_result = fork();
 975       if (fork_result < 0) {
 976         cerr << "Error forking.\n";
 977         exit(1);
 978       } else if (fork_result == 0) {
 979         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 980         system(command.c_str());
 981         exit(0);
 982       } else {
 983         completeFileName = tempName;
 984       }
 985     }
 986 #endif
 987 #endif
 988                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 989                 if(!fileHandle) {
 990                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 991                         return 1;
 992                 }
 993                 else {
 994                         return 0;
 995                 }
 996         }
 997         catch(exception& e) {
 998                 errorOut(e, "MothurOut", "openOutputFile");
 999                 exit(1);
1000         }
1001
1002 }
1003
1004 /**************************************************************************************************/
1005 int MothurOut::appendFiles(string temp, string filename) {
1006         try{
1007                 ofstream output;
1008                 ifstream input;
1009
1010                 //open output file in append mode
1011                 openOutputFileAppend(filename, output);
1012                 int ableToOpen = openInputFile(temp, input, "no error");
1013                 //int ableToOpen = openInputFile(temp, input);
1014
1015                 int numLines = 0;
1016                 if (ableToOpen == 0) { //you opened it
1017                         while(char c = input.get()){
1018                                 if(input.eof())         {       break;                  }
1019                                 else                            {       output << c;    if (c == '\n') {numLines++;} }
1020                         }
1021                         input.close();
1022                 }
1023
1024                 output.close();
1025
1026                 return numLines;
1027         }
1028         catch(exception& e) {
1029                 errorOut(e, "MothurOut", "appendFiles");
1030                 exit(1);
1031         }
1032 }
1033
1034 /**************************************************************************************************/
1035 string MothurOut::sortFile(string distFile, string outputDir){
1036         try {
1037
1038                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
1039                 string outfile = getRootName(distFile) + "sorted.dist";
1040
1041
1042                 //if you can, use the unix sort since its been optimized for years
1043                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1044                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
1045                         system(command.c_str());
1046                 #else //you are stuck with my best attempt...
1047                         //windows sort does not have a way to specify a column, only a character in the line
1048                         //since we cannot assume that the distance will always be at the the same character location on each line
1049                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1050
1051                         //read in file line by file and put distance first
1052                         string tempDistFile = distFile + ".temp";
1053                         ifstream input;
1054                         ofstream output;
1055                         openInputFile(distFile, input);
1056                         openOutputFile(tempDistFile, output);
1057
1058                         string firstName, secondName;
1059                         float dist;
1060                         while (input) {
1061                                 input >> firstName >> secondName >> dist;
1062                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1063                                 gobble(input);
1064                         }
1065                         input.close();
1066                         output.close();
1067
1068
1069                         //sort using windows sort
1070                         string tempOutfile = outfile + ".temp";
1071                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1072                         system(command.c_str());
1073
1074                         //read in sorted file and put distance at end again
1075                         ifstream input2;
1076                         openInputFile(tempOutfile, input2);
1077                         openOutputFile(outfile, output);
1078
1079                         while (input2) {
1080                                 input2 >> dist >> firstName >> secondName;
1081                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1082                                 gobble(input2);
1083                         }
1084                         input2.close();
1085                         output.close();
1086
1087                         //remove temp files
1088                         mothurRemove(tempDistFile);
1089                         mothurRemove(tempOutfile);
1090                 #endif
1091
1092                 return outfile;
1093         }
1094         catch(exception& e) {
1095                 errorOut(e, "MothurOut", "sortFile");
1096                 exit(1);
1097         }
1098 }
1099 /**************************************************************************************************/
1100 vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
1101         try {
1102                         vector<unsigned long long> positions;
1103                         ifstream inFASTA;
1104                         //openInputFile(filename, inFASTA);
1105                         inFASTA.open(filename.c_str(), ios::binary);
1106
1107                         string input;
1108                         unsigned long long count = 0;
1109                         while(!inFASTA.eof()){
1110                                 //input = getline(inFASTA);
1111                                 //cout << input << '\t' << inFASTA.tellg() << endl;
1112                                 //if (input.length() != 0) {
1113                                 //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
1114                                 //}
1115                                 //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1116                                 char c = inFASTA.get(); count++;
1117                                 if (c == '>') {
1118                                         positions.push_back(count-1);
1119                                         //cout << count << endl;
1120                                 }
1121                         }
1122                         inFASTA.close();
1123
1124                         num = positions.size();
1125
1126                         /*FILE * pFile;
1127                         long size;
1128
1129                         //get num bytes in file
1130                         pFile = fopen (filename.c_str(),"rb");
1131                         if (pFile==NULL) perror ("Error opening file");
1132                         else{
1133                                 fseek (pFile, 0, SEEK_END);
1134                                 size=ftell (pFile);
1135                                 fclose (pFile);
1136                         }*/
1137
1138                         unsigned long long size = positions[(positions.size()-1)];
1139                         ifstream in;
1140                         openInputFile(filename, in);
1141
1142                         in.seekg(size);
1143
1144                         while(in.get()){
1145                                 if(in.eof())            {       break;  }
1146                                 else                            {       size++; }
1147                         }
1148                         in.close();
1149
1150                         positions.push_back(size);
1151                         positions[0] = 0;
1152
1153                         return positions;
1154         }
1155         catch(exception& e) {
1156                 errorOut(e, "MothurOut", "setFilePosFasta");
1157                 exit(1);
1158         }
1159 }
1160 /**************************************************************************************************/
1161 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
1162         try {
1163                         filename = getFullPathName(filename);
1164
1165                         vector<unsigned long long> positions;
1166                         ifstream in;
1167                         //openInputFile(filename, in);
1168                         in.open(filename.c_str(), ios::binary);
1169
1170                         string input;
1171                         unsigned long long count = 0;
1172                         positions.push_back(0);
1173
1174                         while(!in.eof()){
1175                                 //unsigned long long lastpos = in.tellg();
1176                                 //input = getline(in);
1177                                 //if (input.length() != 0) {
1178                                         //unsigned long long pos = in.tellg();
1179                                         //if (pos != -1) { positions.push_back(pos - input.length() - 1);       }
1180                                         //else {  positions.push_back(lastpos);  }
1181                                 //}
1182                                 //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
1183
1184
1185                                 //getline counting reads
1186                                 char d = in.get(); count++;
1187                                 while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
1188                                         //get next character
1189                                         d = in.get();
1190                                         count++;
1191                                 }
1192
1193                                 if (!in.eof()) {
1194                                         d=in.get(); count++;
1195                                         while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
1196                                 }
1197                                 positions.push_back(count-1);
1198                                 //cout << count-1 << endl;
1199                         }
1200                         in.close();
1201
1202                         num = positions.size()-1;
1203
1204                         FILE * pFile;
1205                         unsigned long long size;
1206
1207                         //get num bytes in file
1208                         pFile = fopen (filename.c_str(),"rb");
1209                         if (pFile==NULL) perror ("Error opening file");
1210                         else{
1211                                 fseek (pFile, 0, SEEK_END);
1212                                 size=ftell (pFile);
1213                                 fclose (pFile);
1214                         }
1215
1216                         positions[(positions.size()-1)] = size;
1217
1218                         return positions;
1219         }
1220         catch(exception& e) {
1221                 errorOut(e, "MothurOut", "setFilePosEachLine");
1222                 exit(1);
1223         }
1224 }
1225 /**************************************************************************************************/
1226
1227 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
1228         try{
1229                 vector<unsigned long long> filePos;
1230                 filePos.push_back(0);
1231
1232                 FILE * pFile;
1233                 unsigned long long size;
1234
1235                 filename = getFullPathName(filename);
1236
1237                 //get num bytes in file
1238                 pFile = fopen (filename.c_str(),"rb");
1239                 if (pFile==NULL) perror ("Error opening file");
1240                 else{
1241                         fseek (pFile, 0, SEEK_END);
1242                         size=ftell (pFile);
1243                         fclose (pFile);
1244                 }
1245
1246         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1247
1248                 //estimate file breaks
1249                 unsigned long long chunkSize = 0;
1250                 chunkSize = size / proc;
1251
1252                 //file to small to divide by processors
1253                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1254
1255                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1256                 for (int i = 0; i < proc; i++) {
1257                         unsigned long long spot = (i+1) * chunkSize;
1258
1259                         ifstream in;
1260                         openInputFile(filename, in);
1261                         in.seekg(spot);
1262
1263                         //look for next '>'
1264                         unsigned long long newSpot = spot;
1265                         while (!in.eof()) {
1266                            char c = in.get();
1267
1268                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1269                            else if (int(c) == -1) { break; }
1270
1271                         }
1272
1273                         //there was not another sequence before the end of the file
1274                         unsigned long long sanityPos = in.tellg();
1275
1276                         if (sanityPos == -1) {  break;  }
1277                         else {  filePos.push_back(newSpot);  }
1278
1279                         in.close();
1280                 }
1281
1282                 //save end pos
1283                 filePos.push_back(size);
1284
1285                 //sanity check filePos
1286                 for (int i = 0; i < (filePos.size()-1); i++) {
1287                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1288                 }
1289
1290                 proc = (filePos.size() - 1);
1291 #else
1292                 mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
1293                 proc=1;
1294                 filePos.push_back(size);
1295 #endif
1296                 return filePos;
1297         }
1298         catch(exception& e) {
1299                 errorOut(e, "MothurOut", "divideFile");
1300                 exit(1);
1301         }
1302 }
1303 /**************************************************************************************************/
1304 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1305         try{
1306
1307                 vector<unsigned long long> filePos = divideFile(filename, proc);
1308
1309                 for (int i = 0; i < (filePos.size()-1); i++) {
1310
1311                         //read file chunk
1312                         ifstream in;
1313                         openInputFile(filename, in);
1314                         in.seekg(filePos[i]);
1315                         unsigned long long size = filePos[(i+1)] - filePos[i];
1316                         char* chunk = new char[size];
1317                         in.read(chunk, size);
1318                         in.close();
1319
1320                         //open new file
1321                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1322                         ofstream out;
1323                         openOutputFile(fileChunkName, out);
1324
1325                         out << chunk << endl;
1326                         out.close();
1327                         delete[] chunk;
1328
1329                         //save name
1330                         files.push_back(fileChunkName);
1331                 }
1332
1333                 return 0;
1334         }
1335         catch(exception& e) {
1336                 errorOut(e, "MothurOut", "divideFile");
1337                 exit(1);
1338         }
1339 }
1340 /***********************************************************************/
1341
1342 bool MothurOut::isTrue(string f){
1343         try {
1344
1345                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1346
1347                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1348                 else {  return false;  }
1349         }
1350         catch(exception& e) {
1351                 errorOut(e, "MothurOut", "isTrue");
1352                 exit(1);
1353         }
1354 }
1355
1356 /***********************************************************************/
1357
1358 float MothurOut::roundDist(float dist, int precision){
1359         try {
1360                 return int(dist * precision + 0.5)/float(precision);
1361         }
1362         catch(exception& e) {
1363                 errorOut(e, "MothurOut", "roundDist");
1364                 exit(1);
1365         }
1366 }
1367 /***********************************************************************/
1368
1369 float MothurOut::ceilDist(float dist, int precision){
1370         try {
1371                 return int(ceil(dist * precision))/float(precision);
1372         }
1373         catch(exception& e) {
1374                 errorOut(e, "MothurOut", "ceilDist");
1375                 exit(1);
1376         }
1377 }
1378 /**********************************************************************************************************************/
1379 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1380         try {
1381
1382                 //open input file
1383                 ifstream in;
1384                 openInputFile(namefile, in);
1385
1386                 while (!in.eof()) {
1387                         if (control_pressed) { break; }
1388
1389                         string firstCol, secondCol;
1390                         in >> firstCol >> secondCol; gobble(in);
1391
1392                         nameMap[firstCol] = secondCol;
1393                 }
1394                 in.close();
1395
1396                 return nameMap.size();
1397
1398         }
1399         catch(exception& e) {
1400                 errorOut(e, "MothurOut", "readNames");
1401                 exit(1);
1402         }
1403 }
1404 /**********************************************************************************************************************/
1405 int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
1406         try {
1407
1408                 //open input file
1409                 ifstream in;
1410                 openInputFile(namefile, in);
1411
1412                 while (!in.eof()) {
1413                         if (control_pressed) { break; }
1414
1415                         string firstCol, secondCol;
1416                         in >> firstCol >> secondCol; gobble(in);
1417
1418                         vector<string> temp;
1419                         splitAtComma(secondCol, temp);
1420
1421                         nameMap[firstCol] = temp;
1422                 }
1423                 in.close();
1424
1425                 return nameMap.size();
1426
1427         }
1428         catch(exception& e) {
1429                 errorOut(e, "MothurOut", "readNames");
1430                 exit(1);
1431         }
1432 }
1433 /**********************************************************************************************************************/
1434 map<string, int> MothurOut::readNames(string namefile) {
1435         try {
1436
1437                 map<string, int> nameMap;
1438
1439                 //open input file
1440                 ifstream in;
1441                 openInputFile(namefile, in);
1442
1443                 while (!in.eof()) {
1444                         if (control_pressed) { break; }
1445
1446                         string firstCol, secondCol;
1447                         in >> firstCol >> secondCol; gobble(in);
1448
1449                         int num = getNumNames(secondCol);
1450
1451                         nameMap[firstCol] = num;
1452                 }
1453                 in.close();
1454
1455                 return nameMap;
1456
1457         }
1458         catch(exception& e) {
1459                 errorOut(e, "MothurOut", "readNames");
1460                 exit(1);
1461         }
1462 }
1463 /**********************************************************************************************************************/
1464 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1465         try {
1466                 int error = 0;
1467
1468                 //open input file
1469                 ifstream in;
1470                 openInputFile(namefile, in);
1471
1472                 while (!in.eof()) {
1473                         if (control_pressed) { break; }
1474
1475                         string firstCol, secondCol;
1476                         in >> firstCol >> secondCol; gobble(in);
1477
1478                         int num = getNumNames(secondCol);
1479
1480                         map<string, string>::iterator it = fastamap.find(firstCol);
1481                         if (it == fastamap.end()) {
1482                                 error = 1;
1483                                 mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1484                         }else {
1485                                 seqPriorityNode temp(num, it->second, firstCol);
1486                                 nameVector.push_back(temp);
1487                         }
1488                 }
1489                 in.close();
1490
1491                 return error;
1492
1493         }
1494         catch(exception& e) {
1495                 errorOut(e, "MothurOut", "readNames");
1496                 exit(1);
1497         }
1498 }
1499
1500 /***********************************************************************/
1501
1502 int MothurOut::getNumNames(string names){
1503         try {
1504                 int count = 0;
1505
1506                 if(names != ""){
1507                         count = 1;
1508                         for(int i=0;i<names.size();i++){
1509                                 if(names[i] == ','){
1510                                         count++;
1511                                 }
1512                         }
1513                 }
1514
1515                 return count;
1516         }
1517         catch(exception& e) {
1518                 errorOut(e, "MothurOut", "getNumNames");
1519                 exit(1);
1520         }
1521 }
1522 /***********************************************************************/
1523
1524 int MothurOut::getNumChar(string line, char c){
1525         try {
1526                 int count = 0;
1527
1528                 if(line != ""){
1529                         for(int i=0;i<line.size();i++){
1530                                 if(line[i] == c){
1531                                         count++;
1532                                 }
1533                         }
1534                 }
1535
1536                 return count;
1537         }
1538         catch(exception& e) {
1539                 errorOut(e, "MothurOut", "getNumChar");
1540                 exit(1);
1541         }
1542 }
1543 /***********************************************************************/
1544 int MothurOut::mothurRemove(string filename){
1545         try {
1546                 filename = getFullPathName(filename);
1547                 int error = remove(filename.c_str());
1548                 //if (error != 0) {
1549                 //      if (errno != ENOENT) { //ENOENT == file does not exist
1550                 //              string message = "Error deleting file " + filename;
1551                 //              perror(message.c_str());
1552                 //      }
1553                 //}
1554                 return error;
1555         }
1556         catch(exception& e) {
1557                 errorOut(e, "MothurOut", "mothurRemove");
1558                 exit(1);
1559         }
1560 }
1561 /***********************************************************************/
1562 bool MothurOut::mothurConvert(string item, int& num){
1563         try {
1564                 bool error = false;
1565
1566                 if (isNumeric1(item)) {
1567                         convert(item, num);
1568                 }else {
1569                         num = 0;
1570                         error = true;
1571                         mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
1572                         commandInputsConvertError = true;
1573                 }
1574
1575                 return error;
1576         }
1577         catch(exception& e) {
1578                 errorOut(e, "MothurOut", "mothurConvert");
1579                 exit(1);
1580         }
1581 }
1582 /***********************************************************************/
1583 bool MothurOut::isNumeric1(string stringToCheck){
1584         try {
1585                 bool numeric = false;
1586
1587                 if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
1588
1589                 return numeric;
1590         }
1591         catch(exception& e) {
1592                 errorOut(e, "MothurOut", "isNumeric1");
1593                 exit(1);
1594         }
1595
1596 }
1597 /***********************************************************************/
1598 bool MothurOut::mothurConvert(string item, float& num){
1599         try {
1600                 bool error = false;
1601
1602                 if (isNumeric1(item)) {
1603                         convert(item, num);
1604                 }else {
1605                         num = 0;
1606                         error = true;
1607                         mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
1608                         commandInputsConvertError = true;
1609                 }
1610
1611                 return error;
1612         }
1613         catch(exception& e) {
1614                 errorOut(e, "MothurOut", "mothurConvert");
1615                 exit(1);
1616         }
1617 }
1618 /***********************************************************************/
1619 bool MothurOut::mothurConvert(string item, double& num){
1620         try {
1621                 bool error = false;
1622
1623                 if (isNumeric1(item)) {
1624                         convert(item, num);
1625                 }else {
1626                         num = 0;
1627                         error = true;
1628                         mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
1629                         commandInputsConvertError = true;
1630                 }
1631
1632                 return error;
1633         }
1634         catch(exception& e) {
1635                 errorOut(e, "MothurOut", "mothurConvert");
1636                 exit(1);
1637         }
1638 }
1639 /**************************************************************************************************/
1640
1641 vector<vector<double> > MothurOut::binomial(int maxOrder){
1642         try {
1643         vector<vector<double> > binomial(maxOrder+1);
1644
1645     for(int i=0;i<=maxOrder;i++){
1646                 binomial[i].resize(maxOrder+1);
1647                 binomial[i][0]=1;
1648                 binomial[0][i]=0;
1649     }
1650     binomial[0][0]=1;
1651
1652     binomial[1][0]=1;
1653     binomial[1][1]=1;
1654
1655     for(int i=2;i<=maxOrder;i++){
1656                 binomial[1][i]=0;
1657     }
1658
1659     for(int i=2;i<=maxOrder;i++){
1660                 for(int j=1;j<=maxOrder;j++){
1661                         if(i==j){       binomial[i][j]=1;                                                                       }
1662                         if(j>i) {       binomial[i][j]=0;                                                                       }
1663                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1664                 }
1665     }
1666
1667         return binomial;
1668
1669         }
1670         catch(exception& e) {
1671                 errorOut(e, "MothurOut", "binomial");
1672                 exit(1);
1673         }
1674 }
1675 /**************************************************************************************************/
1676 unsigned int MothurOut::fromBase36(string base36){
1677         try {
1678                 unsigned int num = 0;
1679
1680                 map<char, int> converts;
1681                 converts['A'] = 0;
1682                 converts['a'] = 0;
1683                 converts['B'] = 1;
1684                 converts['b'] = 1;
1685                 converts['C'] = 2;
1686                 converts['c'] = 2;
1687                 converts['D'] = 3;
1688                 converts['d'] = 3;
1689                 converts['E'] = 4;
1690                 converts['e'] = 4;
1691                 converts['F'] = 5;
1692                 converts['f'] = 5;
1693                 converts['G'] = 6;
1694                 converts['g'] = 6;
1695                 converts['H'] = 7;
1696                 converts['h'] = 7;
1697                 converts['I'] = 8;
1698                 converts['i'] = 8;
1699                 converts['J'] = 9;
1700                 converts['j'] = 9;
1701                 converts['K'] = 10;
1702                 converts['k'] = 10;
1703                 converts['L'] = 11;
1704                 converts['l'] = 11;
1705                 converts['M'] = 12;
1706                 converts['m'] = 12;
1707                 converts['N'] = 13;
1708                 converts['n'] = 13;
1709                 converts['O'] = 14;
1710                 converts['o'] = 14;
1711                 converts['P'] = 15;
1712                 converts['p'] = 15;
1713                 converts['Q'] = 16;
1714                 converts['q'] = 16;
1715                 converts['R'] = 17;
1716                 converts['r'] = 17;
1717                 converts['S'] = 18;
1718                 converts['s'] = 18;
1719                 converts['T'] = 19;
1720                 converts['t'] = 19;
1721                 converts['U'] = 20;
1722                 converts['u'] = 20;
1723                 converts['V'] = 21;
1724                 converts['v'] = 21;
1725                 converts['W'] = 22;
1726                 converts['w'] = 22;
1727                 converts['X'] = 23;
1728                 converts['x'] = 23;
1729                 converts['Y'] = 24;
1730                 converts['y'] = 24;
1731                 converts['Z'] = 25;
1732                 converts['z'] = 25;
1733                 converts['0'] = 26;
1734                 converts['1'] = 27;
1735                 converts['2'] = 28;
1736                 converts['3'] = 29;
1737                 converts['4'] = 30;
1738                 converts['5'] = 31;
1739                 converts['6'] = 32;
1740                 converts['7'] = 33;
1741                 converts['8'] = 34;
1742                 converts['9'] = 35;
1743
1744                 int i = 0;
1745                 while (i < base36.length()) {
1746                         char c = base36[i];
1747                         num = 36 * num + converts[c];
1748                         i++;
1749                 }
1750
1751                 return num;
1752
1753         }
1754         catch(exception& e) {
1755                 errorOut(e, "MothurOut", "fromBase36");
1756                 exit(1);
1757         }
1758 }
1759 /***********************************************************************/
1760
1761 int MothurOut::factorial(int num){
1762         try {
1763                 int total = 1;
1764
1765                 for (int i = 1; i <= num; i++) {
1766                         total *= i;
1767                 }
1768
1769                 return total;
1770         }
1771         catch(exception& e) {
1772                 errorOut(e, "MothurOut", "factorial");
1773                 exit(1);
1774         }
1775 }
1776 /***********************************************************************/
1777
1778 int MothurOut::getNumSeqs(ifstream& file){
1779         try {
1780                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1781                 file.seekg(0);
1782                 return numSeqs;
1783         }
1784         catch(exception& e) {
1785                 errorOut(e, "MothurOut", "getNumSeqs");
1786                 exit(1);
1787         }
1788 }
1789 /***********************************************************************/
1790 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1791         try {
1792                 string input;
1793                 numSeqs = 0;
1794                 while(!file.eof()){
1795                         input = getline(file);
1796                         if (input.length() != 0) {
1797                                 if(input[0] == '>'){ numSeqs++; }
1798                         }
1799                 }
1800         }
1801         catch(exception& e) {
1802                 errorOut(e, "MothurOut", "getNumSeqs");
1803                 exit(1);
1804         }
1805 }
1806 /***********************************************************************/
1807
1808 //This function parses the estimator options and puts them in a vector
1809 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1810         try {
1811                 string individual = "";
1812                 int estimLength = estim.size();
1813                 for(int i=0;i<estimLength;i++){
1814                         if(estim[i] == symbol){
1815                                 container.push_back(individual);
1816                                 individual = "";
1817                         }
1818                         else{
1819                                 individual += estim[i];
1820                         }
1821                 }
1822                 container.push_back(individual);
1823
1824         }
1825         catch(exception& e) {
1826                 errorOut(e, "MothurOut", "splitAtChar");
1827                 exit(1);
1828         }
1829 }
1830
1831 /***********************************************************************/
1832
1833 //This function parses the estimator options and puts them in a vector
1834 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1835         try {
1836                 string individual = "";
1837                 int estimLength = estim.size();
1838                 for(int i=0;i<estimLength;i++){
1839                         if(estim[i] == '-'){
1840                                 container.push_back(individual);
1841                                 individual = "";
1842                         }
1843                         else{
1844                                 individual += estim[i];
1845                         }
1846                 }
1847                 container.push_back(individual);
1848
1849
1850         /*      string individual;
1851
1852                 while (estim.find_first_of('-') != -1) {
1853                         individual = estim.substr(0,estim.find_first_of('-'));
1854                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1855                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1856                                 container.push_back(individual);
1857                         }
1858                 }
1859                 //get last one
1860                 container.push_back(estim); */
1861         }
1862         catch(exception& e) {
1863                 errorOut(e, "MothurOut", "splitAtDash");
1864                 exit(1);
1865         }
1866 }
1867
1868 /***********************************************************************/
1869 //This function parses the label options and puts them in a set
1870 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1871         try {
1872                 string individual = "";
1873                 int estimLength = estim.size();
1874                 for(int i=0;i<estimLength;i++){
1875                         if(estim[i] == '-'){
1876                                 container.insert(individual);
1877                                 individual = "";
1878                         }
1879                         else{
1880                                 individual += estim[i];
1881                         }
1882                 }
1883                 container.insert(individual);
1884
1885         //      string individual;
1886
1887         //      while (estim.find_first_of('-') != -1) {
1888         //              individual = estim.substr(0,estim.find_first_of('-'));
1889         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1890         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1891         //                      container.insert(individual);
1892         //              }
1893         //      }
1894                 //get last one
1895         //      container.insert(estim);
1896
1897         }
1898         catch(exception& e) {
1899                 errorOut(e, "MothurOut", "splitAtDash");
1900                 exit(1);
1901         }
1902 }
1903 /***********************************************************************/
1904 //This function parses the line options and puts them in a set
1905 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1906         try {
1907                 string individual;
1908                 int lineNum;
1909
1910                 while (estim.find_first_of('-') != -1) {
1911                         individual = estim.substr(0,estim.find_first_of('-'));
1912                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1913                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1914                                 convert(individual, lineNum); //convert the string to int
1915                                 container.insert(lineNum);
1916                         }
1917                 }
1918                 //get last one
1919                 convert(estim, lineNum); //convert the string to int
1920                 container.insert(lineNum);
1921         }
1922         catch(exception& e) {
1923                 errorOut(e, "MothurOut", "splitAtDash");
1924                 exit(1);
1925         }
1926 }
1927 /***********************************************************************/
1928 //This function parses the a string and puts peices in a vector
1929 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1930         try {
1931                 string individual = "";
1932                 int estimLength = estim.size();
1933                 for(int i=0;i<estimLength;i++){
1934                         if(estim[i] == ','){
1935                                 container.push_back(individual);
1936                                 individual = "";
1937                         }
1938                         else{
1939                                 individual += estim[i];
1940                         }
1941                 }
1942                 container.push_back(individual);
1943
1944
1945
1946
1947 //              string individual;
1948 //
1949 //              while (estim.find_first_of(',') != -1) {
1950 //                      individual = estim.substr(0,estim.find_first_of(','));
1951 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1952 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1953 //                              container.push_back(individual);
1954 //                      }
1955 //              }
1956 //              //get last one
1957 //              container.push_back(estim);
1958         }
1959         catch(exception& e) {
1960                 errorOut(e, "MothurOut", "splitAtComma");
1961                 exit(1);
1962         }
1963 }
1964 /***********************************************************************/
1965
1966 //This function splits up the various option parameters
1967 void MothurOut::splitAtComma(string& prefix, string& suffix){
1968         try {
1969                 prefix = suffix.substr(0,suffix.find_first_of(','));
1970                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1971                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1972                         string space = " ";
1973                         while(suffix.at(0) == ' ')
1974                                 suffix = suffix.substr(1, suffix.length());
1975                 }
1976
1977         }
1978         catch(exception& e) {
1979                 errorOut(e, "MothurOut", "splitAtComma");
1980                 exit(1);
1981         }
1982 }
1983 /***********************************************************************/
1984
1985 //This function separates the key value from the option value i.e. dist=96_...
1986 void MothurOut::splitAtEquals(string& key, string& value){
1987         try {
1988                 if(value.find_first_of('=') != -1){
1989                         key = value.substr(0,value.find_first_of('='));
1990                         if ((value.find_first_of('=')+1) <= value.length()) {
1991                                 value = value.substr(value.find_first_of('=')+1, value.length());
1992                         }
1993                 }else{
1994                         key = value;
1995                         value = 1;
1996                 }
1997         }
1998         catch(exception& e) {
1999                 errorOut(e, "MothurOut", "splitAtEquals");
2000                 exit(1);
2001         }
2002 }
2003
2004 /**************************************************************************************************/
2005
2006 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
2007         try {
2008                 for (int i = 0; i < Groups.size(); i++) {
2009                         if (groupname == Groups[i]) { return true; }
2010                 }
2011                 return false;
2012         }
2013         catch(exception& e) {
2014                 errorOut(e, "MothurOut", "inUsersGroups");
2015                 exit(1);
2016         }
2017 }
2018 /**************************************************************************************************/
2019 //returns true if any of the strings in first vector are in second vector
2020 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
2021         try {
2022
2023                 for (int i = 0; i < groupnames.size(); i++) {
2024                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
2025                 }
2026                 return false;
2027         }
2028         catch(exception& e) {
2029                 errorOut(e, "MothurOut", "inUsersGroups");
2030                 exit(1);
2031         }
2032 }
2033 /***********************************************************************/
2034 //this function determines if the user has given us labels that are smaller than the given label.
2035 //if so then it returns true so that the calling function can run the previous valid distance.
2036 //it's a "smart" distance function.  It also checks for invalid labels.
2037 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
2038         try {
2039
2040                 set<string>::iterator it;
2041                 vector<float> orderFloat;
2042                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
2043                 map<string, float>::iterator it2;
2044                 float labelFloat;
2045                 bool smaller = false;
2046
2047                 //unique is the smallest line
2048                 if (label == "unique") {  return false;  }
2049                 else {
2050                         if (convertTestFloat(label, labelFloat)) {
2051                                 convert(label, labelFloat);
2052                         }else { //cant convert
2053                                 return false;
2054                         }
2055                 }
2056
2057                 //go through users set and make them floats
2058                 for(it = userLabels.begin(); it != userLabels.end();) {
2059
2060                         float temp;
2061                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
2062                                 convert(*it, temp);
2063                                 orderFloat.push_back(temp);
2064                                 userMap[*it] = temp;
2065                                 it++;
2066                         }else if (*it == "unique") {
2067                                 orderFloat.push_back(-1.0);
2068                                 userMap["unique"] = -1.0;
2069                                 it++;
2070                         }else {
2071                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
2072                                 userLabels.erase(it++);
2073                         }
2074                 }
2075
2076                 //sort order
2077                 sort(orderFloat.begin(), orderFloat.end());
2078
2079                 /*************************************************/
2080                 //is this label bigger than any of the users labels
2081                 /*************************************************/
2082
2083                 //loop through order until you find a label greater than label
2084                 for (int i = 0; i < orderFloat.size(); i++) {
2085                         if (orderFloat[i] < labelFloat) {
2086                                 smaller = true;
2087                                 if (orderFloat[i] == -1) {
2088                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
2089                                         userLabels.erase("unique");
2090                                 }
2091                                 else {
2092                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
2093                                         string s = "";
2094                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
2095                                                 if (it2->second == orderFloat[i]) {
2096                                                         s = it2->first;
2097                                                         //remove small labels
2098                                                         userLabels.erase(s);
2099                                                         break;
2100                                                 }
2101                                         }
2102                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
2103                                 }
2104                         //since they are sorted once you find a bigger one stop looking
2105                         }else { break; }
2106                 }
2107
2108                 return smaller;
2109
2110         }
2111         catch(exception& e) {
2112                 errorOut(e, "MothurOut", "anyLabelsToProcess");
2113                 exit(1);
2114         }
2115 }
2116
2117 /**************************************************************************************************/
2118 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
2119         try {
2120
2121                 bool good = true;
2122
2123                 string line = getline(file);
2124
2125                 //before we added this check
2126                 if (line[0] != '#') {  good = false;  }
2127                 else {
2128                         //rip off #
2129                         line = line.substr(1);
2130
2131                         vector<string> versionVector;
2132                         splitAtChar(version, versionVector, '.');
2133
2134                         //check file version
2135                         vector<string> linesVector;
2136                         splitAtChar(line, linesVector, '.');
2137
2138                         if (versionVector.size() != linesVector.size()) { good = false; }
2139                         else {
2140                                 for (int j = 0; j < versionVector.size(); j++) {
2141                                         int num1, num2;
2142                                         convert(versionVector[j], num1);
2143                                         convert(linesVector[j], num2);
2144
2145                                         //if mothurs version is newer than this files version, then we want to remake it
2146                                         if (num1 > num2) {  good = false; break;  }
2147                                 }
2148                         }
2149
2150                 }
2151
2152                 if (!good) {  file.close();  }
2153                 else { file.seekg(0);  }
2154
2155                 return good;
2156         }
2157         catch(exception& e) {
2158                 errorOut(e, "MothurOut", "checkReleaseVersion");
2159                 exit(1);
2160         }
2161 }
2162 /**************************************************************************************************/
2163 bool MothurOut::isContainingOnlyDigits(string input) {
2164         try{
2165
2166                 //are you a digit in ascii code
2167                 for (int i = 0;i < input.length(); i++){
2168                         if( input[i]>47 && input[i]<58){}
2169                         else { return false; }
2170                 }
2171
2172                 return true;
2173         }
2174         catch(exception& e) {
2175                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
2176                 exit(1);
2177         }
2178 }
2179 /**************************************************************************************************/
2180 int MothurOut::removeConfidences(string& tax) {
2181         try {
2182
2183                 string taxon;
2184                 string newTax = "";
2185
2186                 while (tax.find_first_of(';') != -1) {
2187
2188                         if (control_pressed) { return 0; }
2189
2190                         //get taxon
2191                         taxon = tax.substr(0,tax.find_first_of(';'));
2192
2193                         int pos = taxon.find_last_of('(');
2194                         if (pos != -1) {
2195                                 //is it a number?
2196                                 int pos2 = taxon.find_last_of(')');
2197                                 if (pos2 != -1) {
2198                                         string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
2199                                         if (isNumeric1(confidenceScore)) {
2200                                                 taxon = taxon.substr(0, pos); //rip off confidence
2201                                         }
2202                                 }
2203                         }
2204                         taxon += ";";
2205
2206                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
2207                         newTax += taxon;
2208                 }
2209
2210                 tax = newTax;
2211
2212                 return 0;
2213         }
2214         catch(exception& e) {
2215                 errorOut(e, "MothurOut", "removeConfidences");
2216                 exit(1);
2217         }
2218 }
2219 /**************************************************************************************************/
2220
2221
2222
2223
2224