mothurout.cpp

   1 /*
   2  *  mothurOut.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 2/25/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mothurout.h"
  11
  12
  13 /******************************************************/
  14 MothurOut* MothurOut::getInstance() {
  15         if( _uniqueInstance == 0) {
  16                 _uniqueInstance = new MothurOut();
  17         }
  18         return _uniqueInstance;
  19 }
  20 /*********************************************************************************************/
  21 void MothurOut::printCurrentFiles()  {
  22         try {
  23                 if (accnosfile != "")           {  mothurOut("accnos=" + accnosfile); mothurOutEndLine();                       }
  24                 if (columnfile != "")           {  mothurOut("column=" + columnfile); mothurOutEndLine();                       }
  25                 if (designfile != "")           {  mothurOut("design=" + designfile); mothurOutEndLine();                       }
  26                 if (fastafile != "")            {  mothurOut("fasta=" + fastafile); mothurOutEndLine();                         }
  27                 if (groupfile != "")            {  mothurOut("group=" + groupfile); mothurOutEndLine();                         }
  28                 if (listfile != "")                     {  mothurOut("list=" + listfile); mothurOutEndLine();                           }
  29                 if (namefile != "")                     {  mothurOut("name=" + namefile); mothurOutEndLine();                           }
  30                 if (oligosfile != "")           {  mothurOut("oligos=" + oligosfile); mothurOutEndLine();                       }
  31                 if (orderfile != "")            {  mothurOut("order=" + orderfile); mothurOutEndLine();                         }
  32                 if (ordergroupfile != "")       {  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();       }
  33                 if (phylipfile != "")           {  mothurOut("phylip=" + phylipfile); mothurOutEndLine();                       }
  34                 if (qualfile != "")                     {  mothurOut("qfile=" + qualfile); mothurOutEndLine();                          }
  35                 if (rabundfile != "")           {  mothurOut("rabund=" + rabundfile); mothurOutEndLine();                       }
  36                 if (relabundfile != "")         {  mothurOut("relabund=" + relabundfile); mothurOutEndLine();           }
  37                 if (sabundfile != "")           {  mothurOut("sabund=" + sabundfile); mothurOutEndLine();                       }
  38                 if (sfffile != "")                      {  mothurOut("sff=" + sfffile); mothurOutEndLine();                                     }
  39                 if (sharedfile != "")           {  mothurOut("shared=" + sharedfile); mothurOutEndLine();                       }
  40                 if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
  41                 if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
  42                 if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
  43                 if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
  44
  45         }
  46         catch(exception& e) {
  47                 errorOut(e, "MothurOut", "printCurrentFiles");
  48                 exit(1);
  49         }
  50 }
  51 /*********************************************************************************************/
  52 bool MothurOut::hasCurrentFiles()  {
  53         try {
  54                 bool hasCurrent = false;
  55
  56                 if (accnosfile != "")           {  return true;                 }
  57                 if (columnfile != "")           {  return true;                 }
  58                 if (designfile != "")           {  return true;                 }
  59                 if (fastafile != "")            {  return true;                 }
  60                 if (groupfile != "")            {  return true;                 }
  61                 if (listfile != "")                     {  return true;                 }
  62                 if (namefile != "")                     {  return true;                 }
  63                 if (oligosfile != "")           {  return true;                 }
  64                 if (orderfile != "")            {  return true;                 }
  65                 if (ordergroupfile != "")       {  return true;                 }
  66                 if (phylipfile != "")           {  return true;                 }
  67                 if (qualfile != "")                     {  return true;                 }
  68                 if (rabundfile != "")           {  return true;                 }
  69                 if (relabundfile != "")         {  return true;                 }
  70                 if (sabundfile != "")           {  return true;                 }
  71                 if (sfffile != "")                      {  return true;                 }
  72                 if (sharedfile != "")           {  return true;                 }
  73                 if (taxonomyfile != "")         {  return true;                 }
  74                 if (treefile != "")                     {  return true;                 }
  75                 if (flowfile != "")                     {  return true;                 }
  76                 if (processors != "1")          {  return true;                 }
  77
  78                 return hasCurrent;
  79
  80         }
  81         catch(exception& e) {
  82                 errorOut(e, "MothurOut", "hasCurrentFiles");
  83                 exit(1);
  84         }
  85 }
  86
  87 /*********************************************************************************************/
  88 void MothurOut::clearCurrentFiles()  {
  89         try {
  90                 phylipfile = "";
  91                 columnfile = "";
  92                 listfile = "";
  93                 rabundfile = "";
  94                 sabundfile = "";
  95                 namefile = "";
  96                 groupfile = "";
  97                 designfile = "";
  98                 orderfile = "";
  99                 treefile = "";
 100                 sharedfile = "";
 101                 ordergroupfile = "";
 102                 relabundfile = "";
 103                 fastafile = "";
 104                 qualfile = "";
 105                 sfffile = "";
 106                 oligosfile = "";
 107                 accnosfile = "";
 108                 taxonomyfile = "";
 109                 flowfile = "";
 110                 processors = "1";
 111         }
 112         catch(exception& e) {
 113                 errorOut(e, "MothurOut", "clearCurrentFiles");
 114                 exit(1);
 115         }
 116 }
 117 /*********************************************************************************************/
 118 void MothurOut::setFileName(string filename)  {
 119         try {
 120                 logFileName = filename;
 121
 122                 #ifdef USE_MPI
 123                         int pid;
 124                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 125
 126                         if (pid == 0) { //only one process should output to screen
 127                 #endif
 128
 129                 openOutputFile(filename, out);
 130
 131                 #ifdef USE_MPI
 132                         }
 133                 #endif
 134         }
 135         catch(exception& e) {
 136                 errorOut(e, "MothurOut", "setFileName");
 137                 exit(1);
 138         }
 139 }
 140 /*********************************************************************************************/
 141 void MothurOut::setDefaultPath(string pathname)  {
 142         try {
 143
 144                 //add / to name if needed
 145                 string lastChar = pathname.substr(pathname.length()-1);
 146                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 147                         if (lastChar != "/") { pathname += "/"; }
 148                 #else
 149                         if (lastChar != "\\") { pathname += "\\"; }
 150                 #endif
 151
 152                 defaultPath = pathname;
 153
 154         }
 155         catch(exception& e) {
 156                 errorOut(e, "MothurOut", "setDefaultPath");
 157                 exit(1);
 158         }
 159 }
 160 /*********************************************************************************************/
 161 void MothurOut::setOutputDir(string pathname)  {
 162         try {
 163                 outputDir = pathname;
 164         }
 165         catch(exception& e) {
 166                 errorOut(e, "MothurOut", "setOutputDir");
 167                 exit(1);
 168         }
 169 }
 170 /*********************************************************************************************/
 171 void MothurOut::closeLog()  {
 172         try {
 173
 174                 #ifdef USE_MPI
 175                         int pid;
 176                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 177
 178                         if (pid == 0) { //only one process should output to screen
 179                 #endif
 180
 181                 out.close();
 182
 183                 #ifdef USE_MPI
 184                         }
 185                 #endif
 186         }
 187         catch(exception& e) {
 188                 errorOut(e, "MothurOut", "closeLog");
 189                 exit(1);
 190         }
 191 }
 192
 193 /*********************************************************************************************/
 194 MothurOut::~MothurOut() {
 195         try {
 196                 _uniqueInstance = 0;
 197
 198         }
 199         catch(exception& e) {
 200                 errorOut(e, "MothurOut", "MothurOut");
 201                 exit(1);
 202         }
 203 }
 204 /*********************************************************************************************/
 205 void MothurOut::mothurOut(string output) {
 206         try {
 207
 208                 #ifdef USE_MPI
 209                         int pid;
 210                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 211
 212                         if (pid == 0) { //only one process should output to screen
 213                 #endif
 214
 215                 cout << output;
 216                 out << output;
 217
 218                 #ifdef USE_MPI
 219                         }
 220                 #endif
 221         }
 222         catch(exception& e) {
 223                 errorOut(e, "MothurOut", "MothurOut");
 224                 exit(1);
 225         }
 226 }
 227 /*********************************************************************************************/
 228 void MothurOut::mothurOutEndLine() {
 229         try {
 230                 #ifdef USE_MPI
 231                         int pid;
 232                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 233
 234                         if (pid == 0) { //only one process should output to screen
 235                 #endif
 236
 237                 cout << endl;
 238                 out << endl;
 239
 240                 #ifdef USE_MPI
 241                         }
 242                 #endif
 243         }
 244         catch(exception& e) {
 245                 errorOut(e, "MothurOut", "MothurOutEndLine");
 246                 exit(1);
 247         }
 248 }
 249 /*********************************************************************************************/
 250 void MothurOut::mothurOut(string output, ofstream& outputFile) {
 251         try {
 252
 253 #ifdef USE_MPI
 254                 int pid;
 255                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 256
 257                 if (pid == 0) { //only one process should output to screen
 258 #endif
 259
 260                         cout << output;
 261                         out << output;
 262                         outputFile << output;
 263
 264 #ifdef USE_MPI
 265                 }
 266 #endif
 267         }
 268         catch(exception& e) {
 269                 errorOut(e, "MothurOut", "MothurOut");
 270                 exit(1);
 271         }
 272 }
 273 /*********************************************************************************************/
 274 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 275         try {
 276 #ifdef USE_MPI
 277                 int pid;
 278                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 279
 280                 if (pid == 0) { //only one process should output to screen
 281 #endif
 282
 283                         cout << endl;
 284                         out << endl;
 285                         outputFile << endl;
 286
 287 #ifdef USE_MPI
 288                 }
 289 #endif
 290         }
 291         catch(exception& e) {
 292                 errorOut(e, "MothurOut", "MothurOutEndLine");
 293                 exit(1);
 294         }
 295 }
 296 /*********************************************************************************************/
 297 void MothurOut::mothurOutJustToLog(string output) {
 298         try {
 299                 #ifdef USE_MPI
 300                         int pid;
 301                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 302
 303                         if (pid == 0) { //only one process should output to screen
 304                 #endif
 305
 306                 out << output;
 307
 308                 #ifdef USE_MPI
 309                         }
 310                 #endif
 311         }
 312         catch(exception& e) {
 313                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 314                 exit(1);
 315         }
 316 }
 317 /*********************************************************************************************/
 318 void MothurOut::errorOut(exception& e, string object, string function) {
 319         //double vm, rss;
 320         //mem_usage(vm, rss);
 321
 322         mothurOut("[ERROR]: ");
 323         mothurOut(toString(e.what()));
 324         mothurOut(" has occurred in the " + object + " class function " + function + ". Please contact Pat Schloss at mothur.bugs@gmail.com, and be sure to include the mothur.logFile with your inquiry.");
 325         mothurOutEndLine();
 326 }
 327 /*********************************************************************************************/
 328 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 329 // process_mem_usage(double &, double &) - takes two doubles by reference,
 330 // attempts to read the system-dependent data for a process' virtual memory
 331 // size and resident set size, and return the results in KB.
 332 //
 333 // On failure, returns 0.0, 0.0
 334 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 335   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 336
 337            vm_usage     = 0.0;
 338            resident_set = 0.0;
 339
 340            // 'file' stat seems to give the most reliable results
 341            //
 342            ifstream stat_stream("/proc/self/stat",ios_base::in);
 343
 344            // dummy vars for leading entries in stat that we don't care about
 345            //
 346            string pid, comm, state, ppid, pgrp, session, tty_nr;
 347            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 348            string utime, stime, cutime, cstime, priority, nice;
 349            string O, itrealvalue, starttime;
 350
 351            // the two fields we want
 352            //
 353            unsigned long vsize;
 354            long rss;
 355
 356            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 357                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 358                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 359                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 360
 361            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 362            vm_usage     = vsize / 1024.0;
 363            resident_set = rss * page_size_kb;
 364
 365            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 366                 return 0;
 367
 368         #else
 369 /*              //windows memory usage
 370                 // Get the list of process identifiers.
 371                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 372
 373                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 374
 375                 // Calculate how many process identifiers were returned.
 376                 cProcesses = cbNeeded / sizeof(DWORD);
 377
 378                 // Print the memory usage for each process
 379                 for (int i = 0; i < cProcesses; i++ ) {
 380                         DWORD processID = aProcesses[i];
 381
 382                         PROCESS_MEMORY_COUNTERS pmc;
 383
 384                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 385
 386                         // Print the process identifier.
 387                         printf( "\nProcess ID: %u\n", processID);
 388
 389                         if (NULL != hProcess) {
 390
 391                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 392                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 393                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 394                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 395                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 396                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 397                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 398                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 399                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 400                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 401                                 }
 402                                 CloseHandle(hProcess);
 403                         }
 404                 }
 405 */
 406                         return 0;
 407
 408         #endif
 409 }
 410
 411
 412 /***********************************************************************/
 413 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 414         try {
 415                 fileName = getFullPathName(fileName);
 416
 417                 fileHandle.open(fileName.c_str(), ios::app);
 418                 if(!fileHandle) {
 419                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 420                         return 1;
 421                 }
 422                 else {
 423                         return 0;
 424                 }
 425         }
 426         catch(exception& e) {
 427                 errorOut(e, "MothurOut", "openOutputFileAppend");
 428                 exit(1);
 429         }
 430 }
 431 /***********************************************************************/
 432 void MothurOut::gobble(istream& f){
 433         try {
 434
 435                 char d;
 436                 while(isspace(d=f.get()))               { ;}
 437                 if(!f.eof()) { f.putback(d); }
 438         }
 439         catch(exception& e) {
 440                 errorOut(e, "MothurOut", "gobble");
 441                 exit(1);
 442         }
 443 }
 444 /***********************************************************************/
 445 void MothurOut::gobble(istringstream& f){
 446         try {
 447                 char d;
 448                 while(isspace(d=f.get()))               {;}
 449                 if(!f.eof()) { f.putback(d); }
 450         }
 451         catch(exception& e) {
 452                 errorOut(e, "MothurOut", "gobble");
 453                 exit(1);
 454         }
 455 }
 456
 457 /***********************************************************************/
 458
 459 string MothurOut::getline(istringstream& fileHandle) {
 460         try {
 461
 462                 string line = "";
 463
 464                 while (!fileHandle.eof())       {
 465                         //get next character
 466                         char c = fileHandle.get();
 467
 468                         //are you at the end of the line
 469                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 470                         else {          line += c;              }
 471                 }
 472
 473                 return line;
 474
 475         }
 476         catch(exception& e) {
 477                 errorOut(e, "MothurOut", "getline");
 478                 exit(1);
 479         }
 480 }
 481 /***********************************************************************/
 482
 483 string MothurOut::getline(ifstream& fileHandle) {
 484         try {
 485
 486                 string line = "";
 487
 488                 while (fileHandle)      {
 489                         //get next character
 490                         char c = fileHandle.get();
 491
 492                         //are you at the end of the line
 493                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }
 494                         else {          line += c;              }
 495                 }
 496
 497                 return line;
 498
 499         }
 500         catch(exception& e) {
 501                 errorOut(e, "MothurOut", "getline");
 502                 exit(1);
 503         }
 504 }
 505 /***********************************************************************/
 506
 507 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 508 #ifdef USE_COMPRESSION
 509 inline bool endsWith(string s, const char * suffix){
 510   size_t suffixLength = strlen(suffix);
 511   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 512 }
 513 #endif
 514 #endif
 515
 516 string MothurOut::getRootName(string longName){
 517         try {
 518
 519                 string rootName = longName;
 520
 521 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 522 #ifdef USE_COMPRESSION
 523     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 524       int pos = rootName.find_last_of('.');
 525       rootName = rootName.substr(0, pos);
 526       cerr << "shortening " << longName << " to " << rootName << "\n";
 527     }
 528 #endif
 529 #endif
 530                 if(rootName.find_last_of(".") != rootName.npos){
 531                         int pos = rootName.find_last_of('.')+1;
 532                         rootName = rootName.substr(0, pos);
 533                 }
 534
 535                 return rootName;
 536         }
 537         catch(exception& e) {
 538                 errorOut(e, "MothurOut", "getRootName");
 539                 exit(1);
 540         }
 541 }
 542 /***********************************************************************/
 543
 544 string MothurOut::getSimpleName(string longName){
 545         try {
 546                 string simpleName = longName;
 547
 548                 size_t found;
 549                 found=longName.find_last_of("/\\");
 550
 551                 if(found != longName.npos){
 552                         simpleName = longName.substr(found+1);
 553                 }
 554
 555                 return simpleName;
 556         }
 557         catch(exception& e) {
 558                 errorOut(e, "MothurOut", "getSimpleName");
 559                 exit(1);
 560         }
 561 }
 562
 563 /***********************************************************************/
 564
 565 int MothurOut::getRandomIndex(int highest){
 566         try {
 567
 568                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 569
 570                 return random;
 571         }
 572         catch(exception& e) {
 573                 errorOut(e, "MothurOut", "getRandomIndex");
 574                 exit(1);
 575         }
 576
 577 }
 578 /**********************************************************************/
 579
 580 string MothurOut::getPathName(string longName){
 581         try {
 582                 string rootPathName = longName;
 583
 584                 if(longName.find_last_of("/\\") != longName.npos){
 585                         int pos = longName.find_last_of("/\\")+1;
 586                         rootPathName = longName.substr(0, pos);
 587                 }
 588
 589                 return rootPathName;
 590         }
 591         catch(exception& e) {
 592                 errorOut(e, "MothurOut", "getPathName");
 593                 exit(1);
 594         }
 595
 596 }
 597 /***********************************************************************/
 598
 599 string MothurOut::hasPath(string longName){
 600         try {
 601                 string path = "";
 602
 603                 size_t found;
 604                 found=longName.find_last_of("~/\\");
 605
 606                 if(found != longName.npos){
 607                         path = longName.substr(0, found+1);
 608                 }
 609
 610                 return path;
 611         }
 612         catch(exception& e) {
 613                 errorOut(e, "MothurOut", "hasPath");
 614                 exit(1);
 615         }
 616 }
 617
 618 /***********************************************************************/
 619
 620 string MothurOut::getExtension(string longName){
 621         try {
 622                 string extension = longName;
 623
 624                 if(longName.find_last_of('.') != longName.npos){
 625                         int pos = longName.find_last_of('.');
 626                         extension = longName.substr(pos, longName.length());
 627                 }
 628
 629                 return extension;
 630         }
 631         catch(exception& e) {
 632                 errorOut(e, "MothurOut", "getExtension");
 633                 exit(1);
 634         }
 635 }
 636 /***********************************************************************/
 637 bool MothurOut::isBlank(string fileName){
 638         try {
 639
 640                 fileName = getFullPathName(fileName);
 641
 642                 ifstream fileHandle;
 643                 fileHandle.open(fileName.c_str());
 644                 if(!fileHandle) {
 645                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 646                         return false;
 647                 }else {
 648                         //check for blank file
 649                         gobble(fileHandle);
 650                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 651                         fileHandle.close();
 652                 }
 653                 return false;
 654         }
 655         catch(exception& e) {
 656                 errorOut(e, "MothurOut", "isBlank");
 657                 exit(1);
 658         }
 659 }
 660 /***********************************************************************/
 661
 662 string MothurOut::getFullPathName(string fileName){
 663         try{
 664
 665         string path = hasPath(fileName);
 666         string newFileName;
 667         int pos;
 668
 669         if (path == "") { return fileName; } //its a simple name
 670         else { //we need to complete the pathname
 671                 // ex. ../../../filename
 672                 // cwd = /user/work/desktop
 673
 674                 string cwd;
 675                 //get current working directory
 676                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 677
 678                         if (path.find("~") != -1) { //go to home directory
 679                                 string homeDir;
 680
 681                                 char *homepath = NULL;
 682                                 homepath = getenv ("HOME");
 683                                 if ( homepath != NULL) { homeDir = homepath; }
 684                                 else { homeDir = "";  }
 685
 686                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 687                                 return newFileName;
 688                         }else { //find path
 689                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 690                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 691
 692                                 //char* cwdpath = new char[1024];
 693                                 //size_t size;
 694                                 //cwdpath=getcwd(cwdpath,size);
 695                                 //cwd = cwdpath;
 696
 697                                 char *cwdpath = NULL;
 698                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 699                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 700                                 else { cwd = "";  }
 701
 702
 703                                 //rip off first '/'
 704                                 string simpleCWD;
 705                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 706
 707                                 //break apart the current working directory
 708                                 vector<string> dirs;
 709                                 while (simpleCWD.find_first_of('/') != string::npos) {
 710                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 711                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 712                                         dirs.push_back(dir);
 713                                 }
 714                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 715                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 716
 717
 718                                 int index = dirs.size()-1;
 719
 720                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 721                                         if (pos == 0) { break;  //you are at the end
 722                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 723                                                 path = path.substr(0, pos-1);
 724                                                 index--;
 725                                                 if (index == 0) {  break; }
 726                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 727                                                 path = path.substr(0, pos);
 728                                         }else if (pos == 1) { break;  //you are at the end
 729                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 730                                 }
 731
 732                                 for (int i = index; i >= 0; i--) {
 733                                         newFileName = dirs[i] +  "/" + newFileName;
 734                                 }
 735
 736                                 newFileName =  "/" +  newFileName;
 737                                 return newFileName;
 738                         }
 739                 #else
 740                         if (path.find("~") != string::npos) { //go to home directory
 741                                 string homeDir = getenv ("HOMEPATH");
 742                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 743                                 return newFileName;
 744                         }else { //find path
 745                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 746                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 747
 748                                 char *cwdpath = NULL;
 749                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 750                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 751                                 else { cwd = "";  }
 752
 753                                 //break apart the current working directory
 754                                 vector<string> dirs;
 755                                 while (cwd.find_first_of('\\') != -1) {
 756                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 757                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 758                                         dirs.push_back(dir);
 759
 760                                 }
 761                                 //get last one
 762                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 763
 764                                 int index = dirs.size()-1;
 765
 766                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 767                                         if (pos == 0) { break;  //you are at the end
 768                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 769                                                 path = path.substr(0, pos-1);
 770                                                 index--;
 771                                                 if (index == 0) {  break; }
 772                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 773                                                 path = path.substr(0, pos);
 774                                         }else if (pos == 1) { break;  //you are at the end
 775                                         }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 776                                 }
 777
 778                                 for (int i = index; i >= 0; i--) {
 779                                         newFileName = dirs[i] +  "\\" + newFileName;
 780                                 }
 781
 782                                 return newFileName;
 783                         }
 784
 785                 #endif
 786         }
 787         }
 788         catch(exception& e) {
 789                 errorOut(e, "MothurOut", "getFullPathName");
 790                 exit(1);
 791         }
 792 }
 793 /***********************************************************************/
 794
 795 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 796         try {
 797                         //get full path name
 798                         string completeFileName = getFullPathName(fileName);
 799 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 800 #ifdef USE_COMPRESSION
 801       // check for gzipped or bzipped file
 802       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 803         string tempName = string(tmpnam(0));
 804         mkfifo(tempName.c_str(), 0666);
 805         int fork_result = fork();
 806         if (fork_result < 0) {
 807           cerr << "Error forking.\n";
 808           exit(1);
 809         } else if (fork_result == 0) {
 810           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 811           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 812           system(command.c_str());
 813           cerr << "Done decompressing " << completeFileName << "\n";
 814           mothurRemove(tempName);
 815           exit(EXIT_SUCCESS);
 816         } else {
 817           cerr << "waiting on child process " << fork_result << "\n";
 818           completeFileName = tempName;
 819         }
 820       }
 821 #endif
 822 #endif
 823                         fileHandle.open(completeFileName.c_str());
 824                         if(!fileHandle) {
 825                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 826                                 return 1;
 827                         }else {
 828                                 //check for blank file
 829                                 gobble(fileHandle);
 830                                 return 0;
 831                         }
 832         }
 833         catch(exception& e) {
 834                 errorOut(e, "MothurOut", "openInputFile - no Error");
 835                 exit(1);
 836         }
 837 }
 838 /***********************************************************************/
 839
 840 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
 841         try {
 842
 843                 //get full path name
 844                 string completeFileName = getFullPathName(fileName);
 845 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 846 #ifdef USE_COMPRESSION
 847   // check for gzipped or bzipped file
 848   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 849     string tempName = string(tmpnam(0));
 850     mkfifo(tempName.c_str(), 0666);
 851     int fork_result = fork();
 852     if (fork_result < 0) {
 853       cerr << "Error forking.\n";
 854       exit(1);
 855     } else if (fork_result == 0) {
 856       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 857       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 858       system(command.c_str());
 859       cerr << "Done decompressing " << completeFileName << "\n";
 860       mothurRemove(tempName);
 861       exit(EXIT_SUCCESS);
 862     } else {
 863       cerr << "waiting on child process " << fork_result << "\n";
 864       completeFileName = tempName;
 865     }
 866   }
 867 #endif
 868 #endif
 869
 870                 fileHandle.open(completeFileName.c_str());
 871                 if(!fileHandle) {
 872                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 873                         return 1;
 874                 }
 875                 else {
 876                         //check for blank file
 877                         gobble(fileHandle);
 878                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
 879
 880                         return 0;
 881                 }
 882         }
 883         catch(exception& e) {
 884                 errorOut(e, "MothurOut", "openInputFile");
 885                 exit(1);
 886         }
 887 }
 888 /***********************************************************************/
 889
 890 int MothurOut::renameFile(string oldName, string newName){
 891         try {
 892                 ifstream inTest;
 893                 int exist = openInputFile(newName, inTest, "");
 894                 inTest.close();
 895
 896         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 897                 if (exist == 0) { //you could open it so you want to delete it
 898                         string command = "rm " + newName;
 899                         system(command.c_str());
 900                 }
 901
 902                 string command = "mv " + oldName + " " + newName;
 903                 system(command.c_str());
 904         #else
 905                 mothurRemove(newName);
 906                 int renameOk = rename(oldName.c_str(), newName.c_str());
 907         #endif
 908                 return 0;
 909
 910         }
 911         catch(exception& e) {
 912                 errorOut(e, "MothurOut", "renameFile");
 913                 exit(1);
 914         }
 915 }
 916
 917 /***********************************************************************/
 918
 919 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
 920         try {
 921
 922                 string completeFileName = getFullPathName(fileName);
 923 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 924 #ifdef USE_COMPRESSION
 925     // check for gzipped file
 926     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 927       string tempName = string(tmpnam(0));
 928       mkfifo(tempName.c_str(), 0666);
 929       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 930       int fork_result = fork();
 931       if (fork_result < 0) {
 932         cerr << "Error forking.\n";
 933         exit(1);
 934       } else if (fork_result == 0) {
 935         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
 936         system(command.c_str());
 937         exit(0);
 938       } else {
 939         completeFileName = tempName;
 940       }
 941     }
 942 #endif
 943 #endif
 944                 fileHandle.open(completeFileName.c_str(), ios::trunc);
 945                 if(!fileHandle) {
 946                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 947                         return 1;
 948                 }
 949                 else {
 950                         return 0;
 951                 }
 952         }
 953         catch(exception& e) {
 954                 errorOut(e, "MothurOut", "openOutputFile");
 955                 exit(1);
 956         }
 957
 958 }
 959
 960 /**************************************************************************************************/
 961 int MothurOut::appendFiles(string temp, string filename) {
 962         try{
 963                 ofstream output;
 964                 ifstream input;
 965
 966                 //open output file in append mode
 967                 openOutputFileAppend(filename, output);
 968                 int ableToOpen = openInputFile(temp, input, "no error");
 969                 //int ableToOpen = openInputFile(temp, input);
 970
 971                 int numLines = 0;
 972                 if (ableToOpen == 0) { //you opened it
 973                         while(char c = input.get()){
 974                                 if(input.eof())         {       break;                  }
 975                                 else                            {       output << c;    if (c == '\n') {numLines++;} }
 976                         }
 977                         input.close();
 978                 }
 979
 980                 output.close();
 981
 982                 return numLines;
 983         }
 984         catch(exception& e) {
 985                 errorOut(e, "MothurOut", "appendFiles");
 986                 exit(1);
 987         }
 988 }
 989
 990 /**************************************************************************************************/
 991 string MothurOut::sortFile(string distFile, string outputDir){
 992         try {
 993
 994                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
 995                 string outfile = getRootName(distFile) + "sorted.dist";
 996
 997
 998                 //if you can, use the unix sort since its been optimized for years
 999                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1000                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
1001                         system(command.c_str());
1002                 #else //you are stuck with my best attempt...
1003                         //windows sort does not have a way to specify a column, only a character in the line
1004                         //since we cannot assume that the distance will always be at the the same character location on each line
1005                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1006
1007                         //read in file line by file and put distance first
1008                         string tempDistFile = distFile + ".temp";
1009                         ifstream input;
1010                         ofstream output;
1011                         openInputFile(distFile, input);
1012                         openOutputFile(tempDistFile, output);
1013
1014                         string firstName, secondName;
1015                         float dist;
1016                         while (input) {
1017                                 input >> firstName >> secondName >> dist;
1018                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1019                                 gobble(input);
1020                         }
1021                         input.close();
1022                         output.close();
1023
1024
1025                         //sort using windows sort
1026                         string tempOutfile = outfile + ".temp";
1027                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1028                         system(command.c_str());
1029
1030                         //read in sorted file and put distance at end again
1031                         ifstream input2;
1032                         openInputFile(tempOutfile, input2);
1033                         openOutputFile(outfile, output);
1034
1035                         while (input2) {
1036                                 input2 >> dist >> firstName >> secondName;
1037                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1038                                 gobble(input2);
1039                         }
1040                         input2.close();
1041                         output.close();
1042
1043                         //remove temp files
1044                         mothurRemove(tempDistFile);
1045                         mothurRemove(tempOutfile);
1046                 #endif
1047
1048                 return outfile;
1049         }
1050         catch(exception& e) {
1051                 errorOut(e, "MothurOut", "sortFile");
1052                 exit(1);
1053         }
1054 }
1055 /**************************************************************************************************/
1056 vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
1057         try {
1058                         vector<unsigned long long> positions;
1059                         ifstream inFASTA;
1060                         //openInputFile(filename, inFASTA);
1061                         inFASTA.open(filename.c_str(), ios::binary);
1062
1063                         string input;
1064                         unsigned long long count = 0;
1065                         while(!inFASTA.eof()){
1066                                 //input = getline(inFASTA);
1067                                 //cout << input << '\t' << inFASTA.tellg() << endl;
1068                                 //if (input.length() != 0) {
1069                                 //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
1070                                 //}
1071                                 //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1072                                 char c = inFASTA.get(); count++;
1073                                 if (c == '>') {
1074                                         positions.push_back(count-1);
1075                                         //cout << count << endl;
1076                                 }
1077                         }
1078                         inFASTA.close();
1079
1080                         num = positions.size();
1081
1082                         /*FILE * pFile;
1083                         long size;
1084
1085                         //get num bytes in file
1086                         pFile = fopen (filename.c_str(),"rb");
1087                         if (pFile==NULL) perror ("Error opening file");
1088                         else{
1089                                 fseek (pFile, 0, SEEK_END);
1090                                 size=ftell (pFile);
1091                                 fclose (pFile);
1092                         }*/
1093
1094                         unsigned long long size = positions[(positions.size()-1)];
1095                         ifstream in;
1096                         openInputFile(filename, in);
1097
1098                         in.seekg(size);
1099
1100                         while(in.get()){
1101                                 if(in.eof())            {       break;  }
1102                                 else                            {       size++; }
1103                         }
1104                         in.close();
1105
1106                         positions.push_back(size);
1107                         positions[0] = 0;
1108
1109                         return positions;
1110         }
1111         catch(exception& e) {
1112                 errorOut(e, "MothurOut", "setFilePosFasta");
1113                 exit(1);
1114         }
1115 }
1116 /**************************************************************************************************/
1117 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
1118         try {
1119                         filename = getFullPathName(filename);
1120
1121                         vector<unsigned long long> positions;
1122                         ifstream in;
1123                         //openInputFile(filename, in);
1124                         in.open(filename.c_str(), ios::binary);
1125
1126                         string input;
1127                         unsigned long long count = 0;
1128                         positions.push_back(0);
1129
1130                         while(!in.eof()){
1131                                 //unsigned long long lastpos = in.tellg();
1132                                 //input = getline(in);
1133                                 //if (input.length() != 0) {
1134                                         //unsigned long long pos = in.tellg();
1135                                         //if (pos != -1) { positions.push_back(pos - input.length() - 1);       }
1136                                         //else {  positions.push_back(lastpos);  }
1137                                 //}
1138                                 //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
1139
1140
1141                                 //getline counting reads
1142                                 char d = in.get(); count++;
1143                                 while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
1144                                         //get next character
1145                                         d = in.get();
1146                                         count++;
1147                                 }
1148
1149                                 if (!in.eof()) {
1150                                         d=in.get(); count++;
1151                                         while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
1152                                 }
1153                                 positions.push_back(count-1);
1154                                 cout << count-1 << endl;
1155                         }
1156                         in.close();
1157
1158                         num = positions.size()-1;
1159
1160                         FILE * pFile;
1161                         unsigned long long size;
1162
1163                         //get num bytes in file
1164                         pFile = fopen (filename.c_str(),"rb");
1165                         if (pFile==NULL) perror ("Error opening file");
1166                         else{
1167                                 fseek (pFile, 0, SEEK_END);
1168                                 size=ftell (pFile);
1169                                 fclose (pFile);
1170                         }
1171
1172                         positions[(positions.size()-1)] = size;
1173
1174                         return positions;
1175         }
1176         catch(exception& e) {
1177                 errorOut(e, "MothurOut", "setFilePosEachLine");
1178                 exit(1);
1179         }
1180 }
1181 /**************************************************************************************************/
1182
1183 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
1184         try{
1185
1186                 vector<unsigned long long> filePos;
1187                 filePos.push_back(0);
1188
1189                 FILE * pFile;
1190                 unsigned long long size;
1191
1192                 filename = getFullPathName(filename);
1193
1194                 //get num bytes in file
1195                 pFile = fopen (filename.c_str(),"rb");
1196                 if (pFile==NULL) perror ("Error opening file");
1197                 else{
1198                         fseek (pFile, 0, SEEK_END);
1199                         size=ftell (pFile);
1200                         fclose (pFile);
1201                 }
1202
1203                 //estimate file breaks
1204                 unsigned long long chunkSize = 0;
1205                 chunkSize = size / proc;
1206
1207                 //file to small to divide by processors
1208                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1209
1210                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1211                 for (int i = 0; i < proc; i++) {
1212                         unsigned long long spot = (i+1) * chunkSize;
1213
1214                         ifstream in;
1215                         openInputFile(filename, in);
1216                         in.seekg(spot);
1217
1218                         //look for next '>'
1219                         unsigned long long newSpot = spot;
1220                         while (!in.eof()) {
1221                            char c = in.get();
1222                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1223                         }
1224
1225                         //there was not another sequence before the end of the file
1226                         unsigned long long sanityPos = in.tellg();
1227
1228                         if (sanityPos == -1) {  break;  }
1229                         else {  filePos.push_back(newSpot);  }
1230
1231                         in.close();
1232                 }
1233
1234                 //save end pos
1235                 filePos.push_back(size);
1236
1237                 //sanity check filePos
1238                 for (int i = 0; i < (filePos.size()-1); i++) {
1239                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1240                 }
1241
1242                 proc = (filePos.size() - 1);
1243
1244                 return filePos;
1245         }
1246         catch(exception& e) {
1247                 errorOut(e, "MothurOut", "divideFile");
1248                 exit(1);
1249         }
1250 }
1251 /**************************************************************************************************/
1252 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1253         try{
1254
1255                 vector<unsigned long long> filePos = divideFile(filename, proc);
1256
1257                 for (int i = 0; i < (filePos.size()-1); i++) {
1258
1259                         //read file chunk
1260                         ifstream in;
1261                         openInputFile(filename, in);
1262                         in.seekg(filePos[i]);
1263                         unsigned long long size = filePos[(i+1)] - filePos[i];
1264                         char* chunk = new char[size];
1265                         in.read(chunk, size);
1266                         in.close();
1267
1268                         //open new file
1269                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1270                         ofstream out;
1271                         openOutputFile(fileChunkName, out);
1272
1273                         out << chunk << endl;
1274                         out.close();
1275                         delete[] chunk;
1276
1277                         //save name
1278                         files.push_back(fileChunkName);
1279                 }
1280
1281                 return 0;
1282         }
1283         catch(exception& e) {
1284                 errorOut(e, "MothurOut", "divideFile");
1285                 exit(1);
1286         }
1287 }
1288 /***********************************************************************/
1289
1290 bool MothurOut::isTrue(string f){
1291         try {
1292
1293                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1294
1295                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1296                 else {  return false;  }
1297         }
1298         catch(exception& e) {
1299                 errorOut(e, "MothurOut", "isTrue");
1300                 exit(1);
1301         }
1302 }
1303
1304 /***********************************************************************/
1305
1306 float MothurOut::roundDist(float dist, int precision){
1307         try {
1308                 return int(dist * precision + 0.5)/float(precision);
1309         }
1310         catch(exception& e) {
1311                 errorOut(e, "MothurOut", "roundDist");
1312                 exit(1);
1313         }
1314 }
1315 /***********************************************************************/
1316
1317 float MothurOut::ceilDist(float dist, int precision){
1318         try {
1319                 return int(ceil(dist * precision))/float(precision);
1320         }
1321         catch(exception& e) {
1322                 errorOut(e, "MothurOut", "ceilDist");
1323                 exit(1);
1324         }
1325 }
1326 /**********************************************************************************************************************/
1327 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1328         try {
1329
1330                 //open input file
1331                 ifstream in;
1332                 openInputFile(namefile, in);
1333
1334                 while (!in.eof()) {
1335                         if (control_pressed) { break; }
1336
1337                         string firstCol, secondCol;
1338                         in >> firstCol >> secondCol; gobble(in);
1339
1340                         nameMap[firstCol] = secondCol;
1341                 }
1342                 in.close();
1343
1344                 return 0;
1345
1346         }
1347         catch(exception& e) {
1348                 errorOut(e, "MothurOut", "readNames");
1349                 exit(1);
1350         }
1351 }
1352 /**********************************************************************************************************************/
1353 int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
1354         try {
1355
1356                 //open input file
1357                 ifstream in;
1358                 openInputFile(namefile, in);
1359
1360                 while (!in.eof()) {
1361                         if (control_pressed) { break; }
1362
1363                         string firstCol, secondCol;
1364                         in >> firstCol >> secondCol; gobble(in);
1365
1366                         vector<string> temp;
1367                         splitAtComma(secondCol, temp);
1368
1369                         nameMap[firstCol] = temp;
1370                 }
1371                 in.close();
1372
1373                 return 0;
1374
1375         }
1376         catch(exception& e) {
1377                 errorOut(e, "MothurOut", "readNames");
1378                 exit(1);
1379         }
1380 }
1381 /**********************************************************************************************************************/
1382 map<string, int> MothurOut::readNames(string namefile) {
1383         try {
1384
1385                 map<string, int> nameMap;
1386
1387                 //open input file
1388                 ifstream in;
1389                 openInputFile(namefile, in);
1390
1391                 while (!in.eof()) {
1392                         if (control_pressed) { break; }
1393
1394                         string firstCol, secondCol;
1395                         in >> firstCol >> secondCol; gobble(in);
1396
1397                         int num = getNumNames(secondCol);
1398
1399                         nameMap[firstCol] = num;
1400                 }
1401                 in.close();
1402
1403                 return nameMap;
1404
1405         }
1406         catch(exception& e) {
1407                 errorOut(e, "MothurOut", "readNames");
1408                 exit(1);
1409         }
1410 }
1411 /**********************************************************************************************************************/
1412 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1413         try {
1414                 int error = 0;
1415
1416                 //open input file
1417                 ifstream in;
1418                 openInputFile(namefile, in);
1419
1420                 while (!in.eof()) {
1421                         if (control_pressed) { break; }
1422
1423                         string firstCol, secondCol;
1424                         in >> firstCol >> secondCol; gobble(in);
1425
1426                         int num = getNumNames(secondCol);
1427
1428                         map<string, string>::iterator it = fastamap.find(firstCol);
1429                         if (it == fastamap.end()) {
1430                                 error = 1;
1431                                 mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
1432                         }else {
1433                                 seqPriorityNode temp(num, it->second, firstCol);
1434                                 nameVector.push_back(temp);
1435                         }
1436                 }
1437                 in.close();
1438
1439                 return error;
1440
1441         }
1442         catch(exception& e) {
1443                 errorOut(e, "MothurOut", "readNames");
1444                 exit(1);
1445         }
1446 }
1447
1448 /***********************************************************************/
1449
1450 int MothurOut::getNumNames(string names){
1451         try {
1452                 int count = 0;
1453
1454                 if(names != ""){
1455                         count = 1;
1456                         for(int i=0;i<names.size();i++){
1457                                 if(names[i] == ','){
1458                                         count++;
1459                                 }
1460                         }
1461                 }
1462
1463                 return count;
1464         }
1465         catch(exception& e) {
1466                 errorOut(e, "MothurOut", "getNumNames");
1467                 exit(1);
1468         }
1469 }
1470 /***********************************************************************/
1471
1472 void MothurOut::mothurRemove(string filename){
1473         try {
1474                 filename = getFullPathName(filename);
1475                 remove(filename.c_str());
1476         }
1477         catch(exception& e) {
1478                 errorOut(e, "MothurOut", "mothurRemove");
1479                 exit(1);
1480         }
1481 }
1482 /**************************************************************************************************/
1483
1484 vector<vector<double> > MothurOut::binomial(int maxOrder){
1485         try {
1486         vector<vector<double> > binomial(maxOrder+1);
1487
1488     for(int i=0;i<=maxOrder;i++){
1489                 binomial[i].resize(maxOrder+1);
1490                 binomial[i][0]=1;
1491                 binomial[0][i]=0;
1492     }
1493     binomial[0][0]=1;
1494
1495     binomial[1][0]=1;
1496     binomial[1][1]=1;
1497
1498     for(int i=2;i<=maxOrder;i++){
1499                 binomial[1][i]=0;
1500     }
1501
1502     for(int i=2;i<=maxOrder;i++){
1503                 for(int j=1;j<=maxOrder;j++){
1504                         if(i==j){       binomial[i][j]=1;                                                                       }
1505                         if(j>i) {       binomial[i][j]=0;                                                                       }
1506                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
1507                 }
1508     }
1509
1510         return binomial;
1511
1512         }
1513         catch(exception& e) {
1514                 errorOut(e, "MothurOut", "binomial");
1515                 exit(1);
1516         }
1517 }
1518 /**************************************************************************************************/
1519 unsigned int MothurOut::fromBase36(string base36){
1520         try {
1521                 unsigned int num = 0;
1522
1523                 map<char, int> converts;
1524                 converts['A'] = 0;
1525                 converts['a'] = 0;
1526                 converts['B'] = 1;
1527                 converts['b'] = 1;
1528                 converts['C'] = 2;
1529                 converts['c'] = 2;
1530                 converts['D'] = 3;
1531                 converts['d'] = 3;
1532                 converts['E'] = 4;
1533                 converts['e'] = 4;
1534                 converts['F'] = 5;
1535                 converts['f'] = 5;
1536                 converts['G'] = 6;
1537                 converts['g'] = 6;
1538                 converts['H'] = 7;
1539                 converts['h'] = 7;
1540                 converts['I'] = 8;
1541                 converts['i'] = 8;
1542                 converts['J'] = 9;
1543                 converts['j'] = 9;
1544                 converts['K'] = 10;
1545                 converts['k'] = 10;
1546                 converts['L'] = 11;
1547                 converts['l'] = 11;
1548                 converts['M'] = 12;
1549                 converts['m'] = 12;
1550                 converts['N'] = 13;
1551                 converts['n'] = 13;
1552                 converts['O'] = 14;
1553                 converts['o'] = 14;
1554                 converts['P'] = 15;
1555                 converts['p'] = 15;
1556                 converts['Q'] = 16;
1557                 converts['q'] = 16;
1558                 converts['R'] = 17;
1559                 converts['r'] = 17;
1560                 converts['S'] = 18;
1561                 converts['s'] = 18;
1562                 converts['T'] = 19;
1563                 converts['t'] = 19;
1564                 converts['U'] = 20;
1565                 converts['u'] = 20;
1566                 converts['V'] = 21;
1567                 converts['v'] = 21;
1568                 converts['W'] = 22;
1569                 converts['w'] = 22;
1570                 converts['X'] = 23;
1571                 converts['x'] = 23;
1572                 converts['Y'] = 24;
1573                 converts['y'] = 24;
1574                 converts['Z'] = 25;
1575                 converts['z'] = 25;
1576                 converts['0'] = 26;
1577                 converts['1'] = 27;
1578                 converts['2'] = 28;
1579                 converts['3'] = 29;
1580                 converts['4'] = 30;
1581                 converts['5'] = 31;
1582                 converts['6'] = 32;
1583                 converts['7'] = 33;
1584                 converts['8'] = 34;
1585                 converts['9'] = 35;
1586
1587                 int i = 0;
1588                 while (i < base36.length()) {
1589                         char c = base36[i];
1590                         num = 36 * num + converts[c];
1591                         i++;
1592                 }
1593
1594                 return num;
1595
1596         }
1597         catch(exception& e) {
1598                 errorOut(e, "MothurOut", "fromBase36");
1599                 exit(1);
1600         }
1601 }
1602 /***********************************************************************/
1603
1604 int MothurOut::factorial(int num){
1605         try {
1606                 int total = 1;
1607
1608                 for (int i = 1; i <= num; i++) {
1609                         total *= i;
1610                 }
1611
1612                 return total;
1613         }
1614         catch(exception& e) {
1615                 errorOut(e, "MothurOut", "factorial");
1616                 exit(1);
1617         }
1618 }
1619 /***********************************************************************/
1620
1621 int MothurOut::getNumSeqs(ifstream& file){
1622         try {
1623                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
1624                 file.seekg(0);
1625                 return numSeqs;
1626         }
1627         catch(exception& e) {
1628                 errorOut(e, "MothurOut", "getNumSeqs");
1629                 exit(1);
1630         }
1631 }
1632 /***********************************************************************/
1633 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
1634         try {
1635                 string input;
1636                 numSeqs = 0;
1637                 while(!file.eof()){
1638                         input = getline(file);
1639                         if (input.length() != 0) {
1640                                 if(input[0] == '>'){ numSeqs++; }
1641                         }
1642                 }
1643         }
1644         catch(exception& e) {
1645                 errorOut(e, "MothurOut", "getNumSeqs");
1646                 exit(1);
1647         }
1648 }
1649 /***********************************************************************/
1650
1651 //This function parses the estimator options and puts them in a vector
1652 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
1653         try {
1654                 string individual = "";
1655                 int estimLength = estim.size();
1656                 for(int i=0;i<estimLength;i++){
1657                         if(estim[i] == symbol){
1658                                 container.push_back(individual);
1659                                 individual = "";
1660                         }
1661                         else{
1662                                 individual += estim[i];
1663                         }
1664                 }
1665                 container.push_back(individual);
1666
1667         }
1668         catch(exception& e) {
1669                 errorOut(e, "MothurOut", "splitAtChar");
1670                 exit(1);
1671         }
1672 }
1673
1674 /***********************************************************************/
1675
1676 //This function parses the estimator options and puts them in a vector
1677 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
1678         try {
1679                 string individual = "";
1680                 int estimLength = estim.size();
1681                 for(int i=0;i<estimLength;i++){
1682                         if(estim[i] == '-'){
1683                                 container.push_back(individual);
1684                                 individual = "";
1685                         }
1686                         else{
1687                                 individual += estim[i];
1688                         }
1689                 }
1690                 container.push_back(individual);
1691
1692
1693         /*      string individual;
1694
1695                 while (estim.find_first_of('-') != -1) {
1696                         individual = estim.substr(0,estim.find_first_of('-'));
1697                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1698                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1699                                 container.push_back(individual);
1700                         }
1701                 }
1702                 //get last one
1703                 container.push_back(estim); */
1704         }
1705         catch(exception& e) {
1706                 errorOut(e, "MothurOut", "splitAtDash");
1707                 exit(1);
1708         }
1709 }
1710
1711 /***********************************************************************/
1712 //This function parses the label options and puts them in a set
1713 void MothurOut::splitAtDash(string& estim, set<string>& container) {
1714         try {
1715                 string individual = "";
1716                 int estimLength = estim.size();
1717                 for(int i=0;i<estimLength;i++){
1718                         if(estim[i] == '-'){
1719                                 container.insert(individual);
1720                                 individual = "";
1721                         }
1722                         else{
1723                                 individual += estim[i];
1724                         }
1725                 }
1726                 container.insert(individual);
1727
1728         //      string individual;
1729
1730         //      while (estim.find_first_of('-') != -1) {
1731         //              individual = estim.substr(0,estim.find_first_of('-'));
1732         //              if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1733         //                      estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1734         //                      container.insert(individual);
1735         //              }
1736         //      }
1737                 //get last one
1738         //      container.insert(estim);
1739
1740         }
1741         catch(exception& e) {
1742                 errorOut(e, "MothurOut", "splitAtDash");
1743                 exit(1);
1744         }
1745 }
1746 /***********************************************************************/
1747 //This function parses the line options and puts them in a set
1748 void MothurOut::splitAtDash(string& estim, set<int>& container) {
1749         try {
1750                 string individual;
1751                 int lineNum;
1752
1753                 while (estim.find_first_of('-') != -1) {
1754                         individual = estim.substr(0,estim.find_first_of('-'));
1755                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
1756                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
1757                                 convert(individual, lineNum); //convert the string to int
1758                                 container.insert(lineNum);
1759                         }
1760                 }
1761                 //get last one
1762                 convert(estim, lineNum); //convert the string to int
1763                 container.insert(lineNum);
1764         }
1765         catch(exception& e) {
1766                 errorOut(e, "MothurOut", "splitAtDash");
1767                 exit(1);
1768         }
1769 }
1770 /***********************************************************************/
1771 //This function parses the a string and puts peices in a vector
1772 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
1773         try {
1774                 string individual = "";
1775                 int estimLength = estim.size();
1776                 for(int i=0;i<estimLength;i++){
1777                         if(estim[i] == ','){
1778                                 container.push_back(individual);
1779                                 individual = "";
1780                         }
1781                         else{
1782                                 individual += estim[i];
1783                         }
1784                 }
1785                 container.push_back(individual);
1786
1787
1788
1789
1790 //              string individual;
1791 //
1792 //              while (estim.find_first_of(',') != -1) {
1793 //                      individual = estim.substr(0,estim.find_first_of(','));
1794 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
1795 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
1796 //                              container.push_back(individual);
1797 //                      }
1798 //              }
1799 //              //get last one
1800 //              container.push_back(estim);
1801         }
1802         catch(exception& e) {
1803                 errorOut(e, "MothurOut", "splitAtComma");
1804                 exit(1);
1805         }
1806 }
1807 /***********************************************************************/
1808
1809 //This function splits up the various option parameters
1810 void MothurOut::splitAtComma(string& prefix, string& suffix){
1811         try {
1812                 prefix = suffix.substr(0,suffix.find_first_of(','));
1813                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
1814                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
1815                         string space = " ";
1816                         while(suffix.at(0) == ' ')
1817                                 suffix = suffix.substr(1, suffix.length());
1818                 }
1819
1820         }
1821         catch(exception& e) {
1822                 errorOut(e, "MothurOut", "splitAtComma");
1823                 exit(1);
1824         }
1825 }
1826 /***********************************************************************/
1827
1828 //This function separates the key value from the option value i.e. dist=96_...
1829 void MothurOut::splitAtEquals(string& key, string& value){
1830         try {
1831                 if(value.find_first_of('=') != -1){
1832                         key = value.substr(0,value.find_first_of('='));
1833                         if ((value.find_first_of('=')+1) <= value.length()) {
1834                                 value = value.substr(value.find_first_of('=')+1, value.length());
1835                         }
1836                 }else{
1837                         key = value;
1838                         value = 1;
1839                 }
1840         }
1841         catch(exception& e) {
1842                 errorOut(e, "MothurOut", "splitAtEquals");
1843                 exit(1);
1844         }
1845 }
1846
1847 /**************************************************************************************************/
1848
1849 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
1850         try {
1851                 for (int i = 0; i < Groups.size(); i++) {
1852                         if (groupname == Groups[i]) { return true; }
1853                 }
1854                 return false;
1855         }
1856         catch(exception& e) {
1857                 errorOut(e, "MothurOut", "inUsersGroups");
1858                 exit(1);
1859         }
1860 }
1861 /**************************************************************************************************/
1862 //returns true if any of the strings in first vector are in second vector
1863 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
1864         try {
1865
1866                 for (int i = 0; i < groupnames.size(); i++) {
1867                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
1868                 }
1869                 return false;
1870         }
1871         catch(exception& e) {
1872                 errorOut(e, "MothurOut", "inUsersGroups");
1873                 exit(1);
1874         }
1875 }
1876 /***********************************************************************/
1877 //this function determines if the user has given us labels that are smaller than the given label.
1878 //if so then it returns true so that the calling function can run the previous valid distance.
1879 //it's a "smart" distance function.  It also checks for invalid labels.
1880 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
1881         try {
1882
1883                 set<string>::iterator it;
1884                 vector<float> orderFloat;
1885                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
1886                 map<string, float>::iterator it2;
1887                 float labelFloat;
1888                 bool smaller = false;
1889
1890                 //unique is the smallest line
1891                 if (label == "unique") {  return false;  }
1892                 else {
1893                         if (convertTestFloat(label, labelFloat)) {
1894                                 convert(label, labelFloat);
1895                         }else { //cant convert
1896                                 return false;
1897                         }
1898                 }
1899
1900                 //go through users set and make them floats
1901                 for(it = userLabels.begin(); it != userLabels.end();) {
1902
1903                         float temp;
1904                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
1905                                 convert(*it, temp);
1906                                 orderFloat.push_back(temp);
1907                                 userMap[*it] = temp;
1908                                 it++;
1909                         }else if (*it == "unique") {
1910                                 orderFloat.push_back(-1.0);
1911                                 userMap["unique"] = -1.0;
1912                                 it++;
1913                         }else {
1914                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
1915                                 userLabels.erase(it++);
1916                         }
1917                 }
1918
1919                 //sort order
1920                 sort(orderFloat.begin(), orderFloat.end());
1921
1922                 /*************************************************/
1923                 //is this label bigger than any of the users labels
1924                 /*************************************************/
1925
1926                 //loop through order until you find a label greater than label
1927                 for (int i = 0; i < orderFloat.size(); i++) {
1928                         if (orderFloat[i] < labelFloat) {
1929                                 smaller = true;
1930                                 if (orderFloat[i] == -1) {
1931                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
1932                                         userLabels.erase("unique");
1933                                 }
1934                                 else {
1935                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
1936                                         string s = "";
1937                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
1938                                                 if (it2->second == orderFloat[i]) {
1939                                                         s = it2->first;
1940                                                         //remove small labels
1941                                                         userLabels.erase(s);
1942                                                         break;
1943                                                 }
1944                                         }
1945                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
1946                                 }
1947                         //since they are sorted once you find a bigger one stop looking
1948                         }else { break; }
1949                 }
1950
1951                 return smaller;
1952
1953         }
1954         catch(exception& e) {
1955                 errorOut(e, "MothurOut", "anyLabelsToProcess");
1956                 exit(1);
1957         }
1958 }
1959
1960 /**************************************************************************************************/
1961 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
1962         try {
1963
1964                 bool good = true;
1965
1966                 string line = getline(file);
1967
1968                 //before we added this check
1969                 if (line[0] != '#') {  good = false;  }
1970                 else {
1971                         //rip off #
1972                         line = line.substr(1);
1973
1974                         vector<string> versionVector;
1975                         splitAtChar(version, versionVector, '.');
1976
1977                         //check file version
1978                         vector<string> linesVector;
1979                         splitAtChar(line, linesVector, '.');
1980
1981                         if (versionVector.size() != linesVector.size()) { good = false; }
1982                         else {
1983                                 for (int j = 0; j < versionVector.size(); j++) {
1984                                         int num1, num2;
1985                                         convert(versionVector[j], num1);
1986                                         convert(linesVector[j], num2);
1987
1988                                         //if mothurs version is newer than this files version, then we want to remake it
1989                                         if (num1 > num2) {  good = false; break;  }
1990                                 }
1991                         }
1992
1993                 }
1994
1995                 if (!good) {  file.close();  }
1996                 else { file.seekg(0);  }
1997
1998                 return good;
1999         }
2000         catch(exception& e) {
2001                 errorOut(e, "MothurOut", "checkReleaseVersion");
2002                 exit(1);
2003         }
2004 }
2005 /**************************************************************************************************/
2006 bool MothurOut::isContainingOnlyDigits(string input) {
2007         try{
2008
2009                 //are you a digit in ascii code
2010                 for (int i = 0;i < input.length(); i++){
2011                         if( input[i]>47 && input[i]<58){}
2012                         else { return false; }
2013                 }
2014
2015                 return true;
2016         }
2017         catch(exception& e) {
2018                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
2019                 exit(1);
2020         }
2021 }
2022 /**************************************************************************************************/
2023 int MothurOut::removeConfidences(string& tax) {
2024         try {
2025
2026                 string taxon;
2027                 string newTax = "";
2028
2029                 while (tax.find_first_of(';') != -1) {
2030
2031                         if (control_pressed) { return 0; }
2032
2033                         //get taxon
2034                         taxon = tax.substr(0,tax.find_first_of(';'));
2035
2036                         int pos = taxon.find_last_of('(');
2037                         if (pos != -1) {
2038                                 //is it a number?
2039                                 int pos2 = taxon.find_last_of(')');
2040                                 if (pos2 != -1) {
2041                                         string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
2042                                         if (isContainingOnlyDigits(confidenceScore)) {
2043                                                 taxon = taxon.substr(0, pos); //rip off confidence
2044                                         }
2045                                 }
2046                         }
2047                         taxon += ";";
2048
2049                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
2050                         newTax += taxon;
2051                 }
2052
2053                 tax = newTax;
2054
2055                 return 0;
2056         }
2057         catch(exception& e) {
2058                 errorOut(e, "MothurOut", "removeConfidences");
2059                 exit(1);
2060         }
2061 }
2062 /**************************************************************************************************/
2063
2064
2065
2066
2067