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 set<string> MothurOut::getCurrentTypes()  {
  22         try {
  23
  24         set<string> types;
  25         types.insert("fasta");
  26         types.insert("accnos");
  27         types.insert("column");
  28         types.insert("design");
  29         types.insert("group");
  30         types.insert("list");
  31         types.insert("name");
  32         types.insert("oligos");
  33         types.insert("order");
  34         types.insert("ordergroup");
  35         types.insert("phylip");
  36         types.insert("qfile");
  37         types.insert("relabund");
  38         types.insert("sabund");
  39         types.insert("rabund");
  40         types.insert("sff");
  41         types.insert("shared");
  42         types.insert("taxonomy");
  43         types.insert("tree");
  44         types.insert("flow");
  45         types.insert("biom");
  46         types.insert("count");
  47         types.insert("processors");
  48
  49                 return types;
  50         }
  51         catch(exception& e) {
  52                 errorOut(e, "MothurOut", "getCurrentTypes");
  53                 exit(1);
  54         }
  55 }
  56 /*********************************************************************************************/
  57 void MothurOut::printCurrentFiles()  {
  58         try {
  59
  60
  61                 if (accnosfile != "")           {  mothurOut("accnos=" + accnosfile); mothurOutEndLine();                       }
  62                 if (columnfile != "")           {  mothurOut("column=" + columnfile); mothurOutEndLine();                       }
  63                 if (designfile != "")           {  mothurOut("design=" + designfile); mothurOutEndLine();                       }
  64                 if (fastafile != "")            {  mothurOut("fasta=" + fastafile); mothurOutEndLine();                         }
  65                 if (groupfile != "")            {  mothurOut("group=" + groupfile); mothurOutEndLine();                         }
  66                 if (listfile != "")                     {  mothurOut("list=" + listfile); mothurOutEndLine();                           }
  67                 if (namefile != "")                     {  mothurOut("name=" + namefile); mothurOutEndLine();                           }
  68                 if (oligosfile != "")           {  mothurOut("oligos=" + oligosfile); mothurOutEndLine();                       }
  69                 if (orderfile != "")            {  mothurOut("order=" + orderfile); mothurOutEndLine();                         }
  70                 if (ordergroupfile != "")       {  mothurOut("ordergroup=" + ordergroupfile); mothurOutEndLine();       }
  71                 if (phylipfile != "")           {  mothurOut("phylip=" + phylipfile); mothurOutEndLine();                       }
  72                 if (qualfile != "")                     {  mothurOut("qfile=" + qualfile); mothurOutEndLine();                          }
  73                 if (rabundfile != "")           {  mothurOut("rabund=" + rabundfile); mothurOutEndLine();                       }
  74                 if (relabundfile != "")         {  mothurOut("relabund=" + relabundfile); mothurOutEndLine();           }
  75                 if (sabundfile != "")           {  mothurOut("sabund=" + sabundfile); mothurOutEndLine();                       }
  76                 if (sfffile != "")                      {  mothurOut("sff=" + sfffile); mothurOutEndLine();                                     }
  77                 if (sharedfile != "")           {  mothurOut("shared=" + sharedfile); mothurOutEndLine();                       }
  78                 if (taxonomyfile != "")         {  mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine();           }
  79                 if (treefile != "")                     {  mothurOut("tree=" + treefile); mothurOutEndLine();                           }
  80                 if (flowfile != "")                     {  mothurOut("flow=" + flowfile); mothurOutEndLine();                           }
  81         if (biomfile != "")                     {  mothurOut("biom=" + biomfile); mothurOutEndLine();                           }
  82         if (counttablefile != "")       {  mothurOut("count=" + counttablefile); mothurOutEndLine();    }
  83                 if (processors != "1")          {  mothurOut("processors=" + processors); mothurOutEndLine();           }
  84
  85         }
  86         catch(exception& e) {
  87                 errorOut(e, "MothurOut", "printCurrentFiles");
  88                 exit(1);
  89         }
  90 }
  91 /*********************************************************************************************/
  92 bool MothurOut::hasCurrentFiles()  {
  93         try {
  94                 bool hasCurrent = false;
  95
  96                 if (accnosfile != "")           {  return true;                 }
  97                 if (columnfile != "")           {  return true;                 }
  98                 if (designfile != "")           {  return true;                 }
  99                 if (fastafile != "")            {  return true;                 }
 100                 if (groupfile != "")            {  return true;                 }
 101                 if (listfile != "")                     {  return true;                 }
 102                 if (namefile != "")                     {  return true;                 }
 103                 if (oligosfile != "")           {  return true;                 }
 104                 if (orderfile != "")            {  return true;                 }
 105                 if (ordergroupfile != "")       {  return true;                 }
 106                 if (phylipfile != "")           {  return true;                 }
 107                 if (qualfile != "")                     {  return true;                 }
 108                 if (rabundfile != "")           {  return true;                 }
 109                 if (relabundfile != "")         {  return true;                 }
 110                 if (sabundfile != "")           {  return true;                 }
 111                 if (sfffile != "")                      {  return true;                 }
 112                 if (sharedfile != "")           {  return true;                 }
 113                 if (taxonomyfile != "")         {  return true;                 }
 114                 if (treefile != "")                     {  return true;                 }
 115                 if (flowfile != "")                     {  return true;                 }
 116         if (biomfile != "")                     {  return true;                 }
 117         if (counttablefile != "")       {  return true;                 }
 118                 if (processors != "1")          {  return true;                 }
 119
 120                 return hasCurrent;
 121
 122         }
 123         catch(exception& e) {
 124                 errorOut(e, "MothurOut", "hasCurrentFiles");
 125                 exit(1);
 126         }
 127 }
 128
 129 /*********************************************************************************************/
 130 void MothurOut::clearCurrentFiles()  {
 131         try {
 132                 phylipfile = "";
 133                 columnfile = "";
 134                 listfile = "";
 135                 rabundfile = "";
 136                 sabundfile = "";
 137                 namefile = "";
 138                 groupfile = "";
 139                 designfile = "";
 140                 orderfile = "";
 141                 treefile = "";
 142                 sharedfile = "";
 143                 ordergroupfile = "";
 144                 relabundfile = "";
 145                 fastafile = "";
 146                 qualfile = "";
 147                 sfffile = "";
 148                 oligosfile = "";
 149                 accnosfile = "";
 150                 taxonomyfile = "";
 151                 flowfile = "";
 152         biomfile = "";
 153         counttablefile = "";
 154                 processors = "1";
 155         }
 156         catch(exception& e) {
 157                 errorOut(e, "MothurOut", "clearCurrentFiles");
 158                 exit(1);
 159         }
 160 }
 161 /***********************************************************************/
 162 string MothurOut::findProgramPath(string programName){
 163         try {
 164
 165                 string envPath = getenv("PATH");
 166                 string pPath = "";
 167
 168                 //delimiting path char
 169                 char delim;
 170 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 171         delim = ':';
 172 #else
 173         delim = ';';
 174 #endif
 175
 176                 //break apart path variable by ':'
 177                 vector<string> dirs;
 178                 splitAtChar(envPath, dirs, delim);
 179
 180         if (debug) { mothurOut("[DEBUG]: dir's in path: \n"); }
 181
 182                 //get path related to mothur
 183                 for (int i = 0; i < dirs.size(); i++) {
 184
 185             if (debug) { mothurOut("[DEBUG]: " + dirs[i] + "\n"); }
 186
 187                         //to lower so we can find it
 188                         string tempLower = "";
 189                         for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
 190
 191                         //is this mothurs path?
 192                         if (tempLower.find(programName) != -1) {  pPath = dirs[i]; break;  }
 193                 }
 194
 195                 if (debug) { mothurOut("[DEBUG]: programPath = " + pPath + "\n"); }
 196
 197                 if (pPath != "") {
 198                         //add programName so it looks like what argv would look like
 199 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 200             pPath += "/" + programName;
 201 #else
 202             pPath += "\\" + programName;
 203 #endif
 204                 }else {
 205                         //okay programName is not in the path, so the folder programName is in must be in the path
 206                         //lets find out which one
 207
 208                         //get path related to the program
 209                         for (int i = 0; i < dirs.size(); i++) {
 210
 211                 if (debug) { mothurOut("[DEBUG]: looking in " + dirs[i] + " for " + programName + " \n"); }
 212
 213                                 //is this the programs path?
 214                                 ifstream in;
 215                                 string tempIn = dirs[i];
 216 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 217                 tempIn += "/" + programName;
 218 #else
 219                 tempIn += "\\" + programName;
 220 #endif
 221                                 openInputFile(tempIn, in, "");
 222
 223                                 //if this file exists
 224                                 if (in) { in.close(); pPath = tempIn; if (debug) { mothurOut("[DEBUG]: found it, programPath = " + pPath + "\n"); } break;   }
 225                         }
 226                 }
 227
 228                 return pPath;
 229
 230         }
 231         catch(exception& e) {
 232                 errorOut(e, "MothurOut", "findProgramPath");
 233                 exit(1);
 234         }
 235 }
 236 /*********************************************************************************************/
 237 void MothurOut::setFileName(string filename)  {
 238         try {
 239                 logFileName = filename;
 240
 241                 #ifdef USE_MPI
 242                         int pid;
 243                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 244
 245                         if (pid == 0) { //only one process should output to screen
 246                 #endif
 247
 248                 openOutputFile(filename, out);
 249
 250                 #ifdef USE_MPI
 251                         }
 252                 #endif
 253         }
 254         catch(exception& e) {
 255                 errorOut(e, "MothurOut", "setFileName");
 256                 exit(1);
 257         }
 258 }
 259 /*********************************************************************************************/
 260 void MothurOut::setDefaultPath(string pathname)  {
 261         try {
 262
 263                 //add / to name if needed
 264                 string lastChar = pathname.substr(pathname.length()-1);
 265                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 266                         if (lastChar != "/") { pathname += "/"; }
 267                 #else
 268                         if (lastChar != "\\") { pathname += "\\"; }
 269                 #endif
 270
 271                 defaultPath = pathname;
 272
 273         }
 274         catch(exception& e) {
 275                 errorOut(e, "MothurOut", "setDefaultPath");
 276                 exit(1);
 277         }
 278 }
 279 /*********************************************************************************************/
 280 void MothurOut::setOutputDir(string pathname)  {
 281         try {
 282                 outputDir = pathname;
 283         }
 284         catch(exception& e) {
 285                 errorOut(e, "MothurOut", "setOutputDir");
 286                 exit(1);
 287         }
 288 }
 289 /*********************************************************************************************/
 290 void MothurOut::closeLog()  {
 291         try {
 292
 293                 #ifdef USE_MPI
 294                         int pid;
 295                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 296
 297                         if (pid == 0) { //only one process should output to screen
 298                 #endif
 299
 300                 out.close();
 301
 302                 #ifdef USE_MPI
 303                         }
 304                 #endif
 305         }
 306         catch(exception& e) {
 307                 errorOut(e, "MothurOut", "closeLog");
 308                 exit(1);
 309         }
 310 }
 311
 312 /*********************************************************************************************/
 313 MothurOut::~MothurOut() {
 314         try {
 315                 _uniqueInstance = 0;
 316
 317         }
 318         catch(exception& e) {
 319                 errorOut(e, "MothurOut", "MothurOut");
 320                 exit(1);
 321         }
 322 }
 323 /*********************************************************************************************/
 324 void MothurOut::mothurOut(string output) {
 325         try {
 326
 327                 #ifdef USE_MPI
 328                         int pid;
 329                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 330
 331                         if (pid == 0) { //only one process should output to screen
 332                 #endif
 333
 334                 out << output;
 335         logger() << output;
 336
 337                 #ifdef USE_MPI
 338                         }
 339                 #endif
 340         }
 341         catch(exception& e) {
 342                 errorOut(e, "MothurOut", "MothurOut");
 343                 exit(1);
 344         }
 345 }
 346 /*********************************************************************************************/
 347 void MothurOut::mothurOutEndLine() {
 348         try {
 349                 #ifdef USE_MPI
 350                         int pid;
 351                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 352
 353                         if (pid == 0) { //only one process should output to screen
 354                 #endif
 355
 356                 out << endl;
 357         logger() << endl;
 358
 359                 #ifdef USE_MPI
 360                         }
 361                 #endif
 362         }
 363         catch(exception& e) {
 364                 errorOut(e, "MothurOut", "MothurOutEndLine");
 365                 exit(1);
 366         }
 367 }
 368 /*********************************************************************************************/
 369 void MothurOut::mothurOut(string output, ofstream& outputFile) {
 370         try {
 371
 372 #ifdef USE_MPI
 373                 int pid;
 374                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 375
 376                 if (pid == 0) { //only one process should output to screen
 377 #endif
 378
 379
 380                         out << output;
 381                         outputFile << output;
 382             logger() << output;
 383
 384 #ifdef USE_MPI
 385                 }
 386 #endif
 387
 388         }
 389         catch(exception& e) {
 390                 errorOut(e, "MothurOut", "MothurOut");
 391                 exit(1);
 392         }
 393 }
 394 /*********************************************************************************************/
 395 void MothurOut::mothurOutEndLine(ofstream& outputFile) {
 396         try {
 397 #ifdef USE_MPI
 398                 int pid;
 399                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 400
 401                 if (pid == 0) { //only one process should output to screen
 402 #endif
 403
 404                         out << endl;
 405                         outputFile << endl;
 406             logger() << endl;
 407
 408 #ifdef USE_MPI
 409                 }
 410 #endif
 411         }
 412         catch(exception& e) {
 413                 errorOut(e, "MothurOut", "MothurOutEndLine");
 414                 exit(1);
 415         }
 416 }
 417 /*********************************************************************************************/
 418 void MothurOut::mothurOutJustToLog(string output) {
 419         try {
 420                 #ifdef USE_MPI
 421                         int pid;
 422                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 423
 424                         if (pid == 0) { //only one process should output to screen
 425                 #endif
 426
 427                 out << output;
 428
 429                 #ifdef USE_MPI
 430                         }
 431                 #endif
 432         }
 433         catch(exception& e) {
 434                 errorOut(e, "MothurOut", "MothurOutJustToLog");
 435                 exit(1);
 436         }
 437 }
 438 /*********************************************************************************************/
 439 void MothurOut::errorOut(exception& e, string object, string function) {
 440         //double vm, rss;
 441         //mem_usage(vm, rss);
 442
 443         mothurOut("[ERROR]: ");
 444         mothurOut(toString(e.what()));
 445         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.");
 446         mothurOutEndLine();
 447 }
 448 /*********************************************************************************************/
 449 //The following was originally from http://stackoverflow.com/questions/669438/how-to-get-memory-usage-at-run-time-in-c
 450 // process_mem_usage(double &, double &) - takes two doubles by reference,
 451 // attempts to read the system-dependent data for a process' virtual memory
 452 // size and resident set size, and return the results in KB.
 453 //
 454 // On failure, returns 0.0, 0.0
 455 int MothurOut::mem_usage(double& vm_usage, double& resident_set) {
 456   #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 457
 458            vm_usage     = 0.0;
 459            resident_set = 0.0;
 460
 461            // 'file' stat seems to give the most reliable results
 462            //
 463            ifstream stat_stream("/proc/self/stat",ios_base::in);
 464
 465            // dummy vars for leading entries in stat that we don't care about
 466            //
 467            string pid, comm, state, ppid, pgrp, session, tty_nr;
 468            string tpgid, flags, minflt, cminflt, majflt, cmajflt;
 469            string utime, stime, cutime, cstime, priority, nice;
 470            string O, itrealvalue, starttime;
 471
 472            // the two fields we want
 473            //
 474            unsigned long vsize;
 475            long rss;
 476
 477            stat_stream >> pid >> comm >> state >> ppid >> pgrp >> session >> tty_nr
 478                                    >> tpgid >> flags >> minflt >> cminflt >> majflt >> cmajflt
 479                                    >> utime >> stime >> cutime >> cstime >> priority >> nice
 480                                    >> O >> itrealvalue >> starttime >> vsize >> rss; // don't care about the rest
 481
 482            long page_size_kb = sysconf(_SC_PAGE_SIZE) / 1024; // in case x86-64 is configured to use 2MB pages
 483            vm_usage     = vsize / 1024.0;
 484            resident_set = rss * page_size_kb;
 485
 486            mothurOut("Memory Usage: vm = " + toString(vm_usage) + " rss = " + toString(resident_set) + "\n");
 487                 return 0;
 488
 489         #else
 490 /*              //windows memory usage
 491                 // Get the list of process identifiers.
 492                 DWORD aProcesses[1024], cbNeeded, cProcesses;
 493
 494                 if ( !EnumProcesses( aProcesses, sizeof(aProcesses), &cbNeeded ) ){ return 1; }
 495
 496                 // Calculate how many process identifiers were returned.
 497                 cProcesses = cbNeeded / sizeof(DWORD);
 498
 499                 // Print the memory usage for each process
 500                 for (int i = 0; i < cProcesses; i++ ) {
 501                         DWORD processID = aProcesses[i];
 502
 503                         PROCESS_MEMORY_COUNTERS pmc;
 504
 505                         HANDLE hProcess = OpenProcess((PROCESS_QUERY_INFORMATION | PROCESS_VM_READ), FALSE, processID);
 506
 507                         // Print the process identifier.
 508                         printf( "\nProcess ID: %u\n", processID);
 509
 510                         if (NULL != hProcess) {
 511
 512                                 if ( GetProcessMemoryInfo( hProcess, &pmc, sizeof(pmc)) ) {
 513                                         printf( "\tPageFaultCount: 0x%08X\n", pmc.PageFaultCount );
 514                                         printf( "\tPeakWorkingSetSize: 0x%08X\n", pmc.PeakWorkingSetSize );
 515                                         printf( "\tWorkingSetSize: 0x%08X\n", pmc.WorkingSetSize );
 516                                         printf( "\tQuotaPeakPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakPagedPoolUsage );
 517                                         printf( "\tQuotaPagedPoolUsage: 0x%08X\n", pmc.QuotaPagedPoolUsage );
 518                                         printf( "\tQuotaPeakNonPagedPoolUsage: 0x%08X\n", pmc.QuotaPeakNonPagedPoolUsage );
 519                                         printf( "\tQuotaNonPagedPoolUsage: 0x%08X\n", pmc.QuotaNonPagedPoolUsage );
 520                                         printf( "\tPagefileUsage: 0x%08X\n", pmc.PagefileUsage );
 521                                         printf( "\tPeakPagefileUsage: 0x%08X\n", pmc.PeakPagefileUsage );
 522                                 }
 523                                 CloseHandle(hProcess);
 524                         }
 525                 }
 526 */
 527                         return 0;
 528
 529         #endif
 530 }
 531
 532
 533 /***********************************************************************/
 534 int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 535         try {
 536                 fileName = getFullPathName(fileName);
 537
 538                 fileHandle.open(fileName.c_str(), ios::app);
 539                 if(!fileHandle) {
 540                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 541                         return 1;
 542                 }
 543                 else {
 544                         return 0;
 545                 }
 546         }
 547         catch(exception& e) {
 548                 errorOut(e, "MothurOut", "openOutputFileAppend");
 549                 exit(1);
 550         }
 551 }
 552 /***********************************************************************/
 553 void MothurOut::gobble(istream& f){
 554         try {
 555
 556                 char d;
 557                 while(isspace(d=f.get()))               { ;}
 558                 if(!f.eof()) { f.putback(d); }
 559         }
 560         catch(exception& e) {
 561                 errorOut(e, "MothurOut", "gobble");
 562                 exit(1);
 563         }
 564 }
 565 /***********************************************************************/
 566 void MothurOut::gobble(istringstream& f){
 567         try {
 568                 char d;
 569                 while(isspace(d=f.get()))               {;}
 570                 if(!f.eof()) { f.putback(d); }
 571         }
 572         catch(exception& e) {
 573                 errorOut(e, "MothurOut", "gobble");
 574                 exit(1);
 575         }
 576 }
 577
 578 /***********************************************************************/
 579
 580 string MothurOut::getline(istringstream& fileHandle) {
 581         try {
 582
 583                 string line = "";
 584
 585                 while (!fileHandle.eof())       {
 586                         //get next character
 587                         char c = fileHandle.get();
 588
 589                         //are you at the end of the line
 590                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 591                         else {          line += c;              }
 592                 }
 593
 594                 return line;
 595
 596         }
 597         catch(exception& e) {
 598                 errorOut(e, "MothurOut", "getline");
 599                 exit(1);
 600         }
 601 }
 602 /***********************************************************************/
 603
 604 string MothurOut::getline(ifstream& fileHandle) {
 605         try {
 606
 607                 string line = "";
 608
 609                 while (fileHandle)      {
 610                         //get next character
 611                         char c = fileHandle.get();
 612
 613                         //are you at the end of the line
 614                         if ((c == '\n') || (c == '\r') || (c == '\f') || (c == EOF)){  break;   }
 615                         else {          line += c;              }
 616                 }
 617
 618                 return line;
 619
 620         }
 621         catch(exception& e) {
 622                 errorOut(e, "MothurOut", "getline");
 623                 exit(1);
 624         }
 625 }
 626 /***********************************************************************/
 627
 628 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 629 #ifdef USE_COMPRESSION
 630 inline bool endsWith(string s, const char * suffix){
 631   size_t suffixLength = strlen(suffix);
 632   return s.size() >= suffixLength && s.substr(s.size() - suffixLength, suffixLength).compare(suffix) == 0;
 633 }
 634 #endif
 635 #endif
 636
 637 string MothurOut::getRootName(string longName){
 638         try {
 639
 640                 string rootName = longName;
 641
 642 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 643 #ifdef USE_COMPRESSION
 644     if (endsWith(rootName, ".gz") || endsWith(rootName, ".bz2")) {
 645       int pos = rootName.find_last_of('.');
 646       rootName = rootName.substr(0, pos);
 647       cerr << "shortening " << longName << " to " << rootName << "\n";
 648     }
 649 #endif
 650 #endif
 651                 if(rootName.find_last_of(".") != rootName.npos){
 652                         int pos = rootName.find_last_of('.')+1;
 653                         rootName = rootName.substr(0, pos);
 654                 }
 655
 656                 return rootName;
 657         }
 658         catch(exception& e) {
 659                 errorOut(e, "MothurOut", "getRootName");
 660                 exit(1);
 661         }
 662 }
 663 /***********************************************************************/
 664
 665 string MothurOut::getSimpleName(string longName){
 666         try {
 667                 string simpleName = longName;
 668
 669                 size_t found;
 670                 found=longName.find_last_of("/\\");
 671
 672                 if(found != longName.npos){
 673                         simpleName = longName.substr(found+1);
 674                 }
 675
 676                 return simpleName;
 677         }
 678         catch(exception& e) {
 679                 errorOut(e, "MothurOut", "getSimpleName");
 680                 exit(1);
 681         }
 682 }
 683
 684 /***********************************************************************/
 685
 686 int MothurOut::getRandomIndex(int highest){
 687         try {
 688
 689                 int random = (int) ((float)(highest+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
 690
 691                 return random;
 692         }
 693         catch(exception& e) {
 694                 errorOut(e, "MothurOut", "getRandomIndex");
 695                 exit(1);
 696         }
 697
 698 }
 699 /**********************************************************************/
 700
 701 string MothurOut::getPathName(string longName){
 702         try {
 703                 string rootPathName = longName;
 704
 705                 if(longName.find_last_of("/\\") != longName.npos){
 706                         int pos = longName.find_last_of("/\\")+1;
 707                         rootPathName = longName.substr(0, pos);
 708                 }
 709
 710                 return rootPathName;
 711         }
 712         catch(exception& e) {
 713                 errorOut(e, "MothurOut", "getPathName");
 714                 exit(1);
 715         }
 716
 717 }
 718 /***********************************************************************/
 719
 720 bool MothurOut::dirCheck(string& dirName){
 721         try {
 722
 723         string tag = "";
 724         #ifdef USE_MPI
 725             int pid;
 726             MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 727
 728             tag = toString(pid);
 729         #endif
 730
 731         //add / to name if needed
 732         string lastChar = dirName.substr(dirName.length()-1);
 733         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 734         if (lastChar != "/") { dirName += "/"; }
 735         #else
 736         if (lastChar != "\\") { dirName += "\\"; }
 737         #endif
 738
 739         //test to make sure directory exists
 740         dirName = getFullPathName(dirName);
 741         string outTemp = dirName + tag + "temp";
 742         ofstream out;
 743         out.open(outTemp.c_str(), ios::trunc);
 744         if(!out) {
 745             mothurOut(dirName + " directory does not exist or is not writable."); mothurOutEndLine();
 746         }else{
 747             out.close();
 748             mothurRemove(outTemp);
 749             return true;
 750         }
 751
 752         return false;
 753     }
 754         catch(exception& e) {
 755                 errorOut(e, "MothurOut", "dirCheck");
 756                 exit(1);
 757         }
 758
 759 }
 760 /***********************************************************************/
 761
 762 string MothurOut::hasPath(string longName){
 763         try {
 764                 string path = "";
 765
 766                 size_t found;
 767                 found=longName.find_last_of("~/\\");
 768
 769                 if(found != longName.npos){
 770                         path = longName.substr(0, found+1);
 771                 }
 772
 773                 return path;
 774         }
 775         catch(exception& e) {
 776                 errorOut(e, "MothurOut", "hasPath");
 777                 exit(1);
 778         }
 779 }
 780
 781 /***********************************************************************/
 782
 783 string MothurOut::getExtension(string longName){
 784         try {
 785                 string extension = "";
 786
 787                 if(longName.find_last_of('.') != longName.npos){
 788                         int pos = longName.find_last_of('.');
 789                         extension = longName.substr(pos, longName.length());
 790                 }
 791
 792                 return extension;
 793         }
 794         catch(exception& e) {
 795                 errorOut(e, "MothurOut", "getExtension");
 796                 exit(1);
 797         }
 798 }
 799 /***********************************************************************/
 800 bool MothurOut::isBlank(string fileName){
 801         try {
 802
 803                 fileName = getFullPathName(fileName);
 804
 805                 ifstream fileHandle;
 806                 fileHandle.open(fileName.c_str());
 807                 if(!fileHandle) {
 808                         mothurOut("[ERROR]: Could not open " + fileName); mothurOutEndLine();
 809                         return false;
 810                 }else {
 811                         //check for blank file
 812                         gobble(fileHandle);
 813                         if (fileHandle.eof()) { fileHandle.close(); return true;  }
 814                         fileHandle.close();
 815                 }
 816                 return false;
 817         }
 818         catch(exception& e) {
 819                 errorOut(e, "MothurOut", "isBlank");
 820                 exit(1);
 821         }
 822 }
 823 /***********************************************************************/
 824
 825 string MothurOut::getFullPathName(string fileName){
 826         try{
 827
 828         string path = hasPath(fileName);
 829         string newFileName;
 830         int pos;
 831
 832         if (path == "") { return fileName; } //its a simple name
 833         else { //we need to complete the pathname
 834                 // ex. ../../../filename
 835                 // cwd = /user/work/desktop
 836
 837                 string cwd;
 838                 //get current working directory
 839                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 840
 841                         if (path.find("~") != -1) { //go to home directory
 842                                 string homeDir;
 843
 844                                 char *homepath = NULL;
 845                                 homepath = getenv ("HOME");
 846                                 if ( homepath != NULL) { homeDir = homepath; }
 847                                 else { homeDir = "";  }
 848
 849                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 850                                 return newFileName;
 851                         }else { //find path
 852                                 if (path.rfind("./") == string::npos) { return fileName; } //already complete name
 853                                 else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 854
 855                                 //char* cwdpath = new char[1024];
 856                                 //size_t size;
 857                                 //cwdpath=getcwd(cwdpath,size);
 858                                 //cwd = cwdpath;
 859
 860                                 char *cwdpath = NULL;
 861                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 862                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 863                                 else { cwd = "";  }
 864
 865
 866                                 //rip off first '/'
 867                                 string simpleCWD;
 868                                 if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 869
 870                                 //break apart the current working directory
 871                                 vector<string> dirs;
 872                                 while (simpleCWD.find_first_of('/') != string::npos) {
 873                                         string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 874                                         simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 875                                         dirs.push_back(dir);
 876                                 }
 877                                 //get last one              // ex. ../../../filename = /user/work/desktop/filename
 878                                 dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 879
 880
 881                                 int index = dirs.size()-1;
 882
 883                                 while((pos = path.rfind("./")) != string::npos) { //while you don't have a complete path
 884                                         if (pos == 0) { break;  //you are at the end
 885                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 886                                                 path = path.substr(0, pos-1);
 887                                                 index--;
 888                                                 if (index == 0) {  break; }
 889                                         }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 890                                                 path = path.substr(0, pos);
 891                                         }else if (pos == 1) { break;  //you are at the end
 892                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 893                                 }
 894
 895                                 for (int i = index; i >= 0; i--) {
 896                                         newFileName = dirs[i] +  "/" + newFileName;
 897                                 }
 898
 899                                 newFileName =  "/" +  newFileName;
 900                                 return newFileName;
 901                         }
 902                 #else
 903                         if (path.find("~") != string::npos) { //go to home directory
 904                                 string homeDir = getenv ("HOMEPATH");
 905                                 newFileName = homeDir + fileName.substr(fileName.find("~")+1);
 906                                 return newFileName;
 907                         }else { //find path
 908                                 if (path.rfind(".\\") == string::npos) { return fileName; } //already complete name
 909                                 else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 910
 911                                 char *cwdpath = NULL;
 912                                 cwdpath = getcwd(NULL, 0); // or _getcwd
 913                                 if ( cwdpath != NULL) { cwd = cwdpath; }
 914                                 else { cwd = "";  }
 915
 916                                 //break apart the current working directory
 917                                 vector<string> dirs;
 918                                 while (cwd.find_first_of('\\') != -1) {
 919                                         string dir = cwd.substr(0,cwd.find_first_of('\\'));
 920                                         cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 921                                         dirs.push_back(dir);
 922
 923                                 }
 924                                 //get last one
 925                                 dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 926
 927                                 int index = dirs.size()-1;
 928
 929                                 while((pos = path.rfind(".\\")) != string::npos) { //while you don't have a complete path
 930                                         if (pos == 0) { break;  //you are at the end
 931                                         }else if (path[(pos-1)] == '.') { //you want your parent directory ../
 932                                                 path = path.substr(0, pos-1);
 933                                                 index--;
 934                                                 if (index == 0) {  break; }
 935                                         }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 936                                                 path = path.substr(0, pos);
 937                                         }else if (pos == 1) { break;  //you are at the end
 938                                         }else { mothurOut("cannot resolve path for " +  fileName + "\n"); return fileName; }
 939                                 }
 940
 941                                 for (int i = index; i >= 0; i--) {
 942                                         newFileName = dirs[i] +  "\\\\" + newFileName;
 943                                 }
 944
 945                                 return newFileName;
 946                         }
 947
 948                 #endif
 949         }
 950         }
 951         catch(exception& e) {
 952                 errorOut(e, "MothurOut", "getFullPathName");
 953                 exit(1);
 954         }
 955 }
 956 /***********************************************************************/
 957
 958 int MothurOut::openInputFile(string fileName, ifstream& fileHandle, string m){
 959         try {
 960                         //get full path name
 961                         string completeFileName = getFullPathName(fileName);
 962 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 963 #ifdef USE_COMPRESSION
 964       // check for gzipped or bzipped file
 965       if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
 966         string tempName = string(tmpnam(0));
 967         mkfifo(tempName.c_str(), 0666);
 968         int fork_result = fork();
 969         if (fork_result < 0) {
 970           cerr << "Error forking.\n";
 971           exit(1);
 972         } else if (fork_result == 0) {
 973           string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
 974           cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
 975           system(command.c_str());
 976           cerr << "Done decompressing " << completeFileName << "\n";
 977           mothurRemove(tempName);
 978           exit(EXIT_SUCCESS);
 979         } else {
 980           cerr << "waiting on child process " << fork_result << "\n";
 981           completeFileName = tempName;
 982         }
 983       }
 984 #endif
 985 #endif
 986                         fileHandle.open(completeFileName.c_str());
 987                         if(!fileHandle) {
 988                                 //mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
 989                                 return 1;
 990                         }else {
 991                                 //check for blank file
 992                                 gobble(fileHandle);
 993                                 return 0;
 994                         }
 995         }
 996         catch(exception& e) {
 997                 errorOut(e, "MothurOut", "openInputFile - no Error");
 998                 exit(1);
 999         }
1000 }
1001 /***********************************************************************/
1002
1003 int MothurOut::openInputFile(string fileName, ifstream& fileHandle){
1004         try {
1005
1006                 //get full path name
1007                 string completeFileName = getFullPathName(fileName);
1008 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1009 #ifdef USE_COMPRESSION
1010   // check for gzipped or bzipped file
1011   if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
1012     string tempName = string(tmpnam(0));
1013     mkfifo(tempName.c_str(), 0666);
1014     int fork_result = fork();
1015     if (fork_result < 0) {
1016       cerr << "Error forking.\n";
1017       exit(1);
1018     } else if (fork_result == 0) {
1019       string command = (endsWith(completeFileName, ".gz") ? "zcat " : "bzcat ") + completeFileName + string(" > ") + tempName;
1020       cerr << "Decompressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
1021       system(command.c_str());
1022       cerr << "Done decompressing " << completeFileName << "\n";
1023       mothurRemove(tempName);
1024       exit(EXIT_SUCCESS);
1025     } else {
1026       cerr << "waiting on child process " << fork_result << "\n";
1027       completeFileName = tempName;
1028     }
1029   }
1030 #endif
1031 #endif
1032
1033                 fileHandle.open(completeFileName.c_str());
1034                 if(!fileHandle) {
1035                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
1036                         return 1;
1037                 }
1038                 else {
1039                         //check for blank file
1040                         gobble(fileHandle);
1041                         if (fileHandle.eof()) { mothurOut("[ERROR]: " + completeFileName + " is blank. Please correct."); mothurOutEndLine();  }
1042
1043                         return 0;
1044                 }
1045         }
1046         catch(exception& e) {
1047                 errorOut(e, "MothurOut", "openInputFile");
1048                 exit(1);
1049         }
1050 }
1051 /***********************************************************************/
1052
1053 int MothurOut::renameFile(string oldName, string newName){
1054         try {
1055
1056         if (oldName == newName) { return 0; }
1057
1058                 ifstream inTest;
1059                 int exist = openInputFile(newName, inTest, "");
1060                 inTest.close();
1061
1062         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1063                 if (exist == 0) { //you could open it so you want to delete it
1064                         string command = "rm " + newName;
1065                         system(command.c_str());
1066                 }
1067
1068                 string command = "mv " + oldName + " " + newName;
1069                 system(command.c_str());
1070         #else
1071                 mothurRemove(newName);
1072                 int renameOk = rename(oldName.c_str(), newName.c_str());
1073         #endif
1074                 return 0;
1075
1076         }
1077         catch(exception& e) {
1078                 errorOut(e, "MothurOut", "renameFile");
1079                 exit(1);
1080         }
1081 }
1082
1083 /***********************************************************************/
1084
1085 int MothurOut::openOutputFile(string fileName, ofstream& fileHandle){
1086         try {
1087
1088                 string completeFileName = getFullPathName(fileName);
1089 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1090 #ifdef USE_COMPRESSION
1091     // check for gzipped file
1092     if (endsWith(completeFileName, ".gz") || endsWith(completeFileName, ".bz2")) {
1093       string tempName = string(tmpnam(0));
1094       mkfifo(tempName.c_str(), 0666);
1095       cerr << "Compressing " << completeFileName << " via temporary named pipe " << tempName << "\n";
1096       int fork_result = fork();
1097       if (fork_result < 0) {
1098         cerr << "Error forking.\n";
1099         exit(1);
1100       } else if (fork_result == 0) {
1101         string command = string(endsWith(completeFileName, ".gz") ?  "gzip" : "bzip2") + " -v > " + completeFileName + string(" < ") + tempName;
1102         system(command.c_str());
1103         exit(0);
1104       } else {
1105         completeFileName = tempName;
1106       }
1107     }
1108 #endif
1109 #endif
1110                 fileHandle.open(completeFileName.c_str(), ios::trunc);
1111                 if(!fileHandle) {
1112                         mothurOut("[ERROR]: Could not open " + completeFileName); mothurOutEndLine();
1113                         return 1;
1114                 }
1115                 else {
1116                         return 0;
1117                 }
1118         }
1119         catch(exception& e) {
1120                 errorOut(e, "MothurOut", "openOutputFile");
1121                 exit(1);
1122         }
1123
1124 }
1125
1126 /**************************************************************************************************/
1127 int MothurOut::appendFiles(string temp, string filename) {
1128         try{
1129                 ofstream output;
1130                 ifstream input;
1131
1132                 //open output file in append mode
1133                 openOutputFileAppend(filename, output);
1134                 int ableToOpen = openInputFile(temp, input, "no error");
1135                 //int ableToOpen = openInputFile(temp, input);
1136
1137                 int numLines = 0;
1138                 if (ableToOpen == 0) { //you opened it
1139
1140             char buffer[4096];
1141             while (!input.eof()) {
1142                 input.read(buffer, 4096);
1143                 output.write(buffer, input.gcount());
1144                 //count number of lines
1145                 for (int i = 0; i < input.gcount(); i++) {  if (buffer[i] == '\n') {numLines++;} }
1146             }
1147                         input.close();
1148                 }
1149
1150                 output.close();
1151
1152                 return numLines;
1153         }
1154         catch(exception& e) {
1155                 errorOut(e, "MothurOut", "appendFiles");
1156                 exit(1);
1157         }
1158 }
1159
1160 /**************************************************************************************************/
1161 string MothurOut::sortFile(string distFile, string outputDir){
1162         try {
1163
1164                 //if (outputDir == "") {  outputDir += hasPath(distFile);  }
1165                 string outfile = getRootName(distFile) + "sorted.dist";
1166
1167
1168                 //if you can, use the unix sort since its been optimized for years
1169                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1170                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
1171                         system(command.c_str());
1172                 #else //you are stuck with my best attempt...
1173                         //windows sort does not have a way to specify a column, only a character in the line
1174                         //since we cannot assume that the distance will always be at the the same character location on each line
1175                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
1176
1177                         //read in file line by file and put distance first
1178                         string tempDistFile = distFile + ".temp";
1179                         ifstream input;
1180                         ofstream output;
1181                         openInputFile(distFile, input);
1182                         openOutputFile(tempDistFile, output);
1183
1184                         string firstName, secondName;
1185                         float dist;
1186                         while (input) {
1187                                 input >> firstName >> secondName >> dist;
1188                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
1189                                 gobble(input);
1190                         }
1191                         input.close();
1192                         output.close();
1193
1194
1195                         //sort using windows sort
1196                         string tempOutfile = outfile + ".temp";
1197                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
1198                         system(command.c_str());
1199
1200                         //read in sorted file and put distance at end again
1201                         ifstream input2;
1202                         openInputFile(tempOutfile, input2);
1203                         openOutputFile(outfile, output);
1204
1205                         while (input2) {
1206                                 input2 >> dist >> firstName >> secondName;
1207                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
1208                                 gobble(input2);
1209                         }
1210                         input2.close();
1211                         output.close();
1212
1213                         //remove temp files
1214                         mothurRemove(tempDistFile);
1215                         mothurRemove(tempOutfile);
1216                 #endif
1217
1218                 return outfile;
1219         }
1220         catch(exception& e) {
1221                 errorOut(e, "MothurOut", "sortFile");
1222                 exit(1);
1223         }
1224 }
1225 /**************************************************************************************************/
1226 vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
1227         try {
1228                         vector<unsigned long long> positions;
1229                         ifstream inFASTA;
1230                         //openInputFile(filename, inFASTA);
1231                         inFASTA.open(filename.c_str(), ios::binary);
1232
1233                         string input;
1234                         unsigned long long count = 0;
1235                         while(!inFASTA.eof()){
1236                                 //input = getline(inFASTA);
1237                                 //cout << input << '\t' << inFASTA.tellg() << endl;
1238                                 //if (input.length() != 0) {
1239                                 //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
1240                                 //}
1241                                 //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
1242                                 char c = inFASTA.get(); count++;
1243                                 if (c == '>') {
1244                                         positions.push_back(count-1);
1245                                         //cout << count << endl;
1246                                 }
1247                         }
1248                         inFASTA.close();
1249
1250                         num = positions.size();
1251
1252                         /*FILE * pFile;
1253                         long size;
1254
1255                         //get num bytes in file
1256                         pFile = fopen (filename.c_str(),"rb");
1257                         if (pFile==NULL) perror ("Error opening file");
1258                         else{
1259                                 fseek (pFile, 0, SEEK_END);
1260                                 size=ftell (pFile);
1261                                 fclose (pFile);
1262                         }*/
1263
1264                         unsigned long long size = positions[(positions.size()-1)];
1265                         ifstream in;
1266                         openInputFile(filename, in);
1267
1268                         in.seekg(size);
1269
1270                         while(in.get()){
1271                                 if(in.eof())            {       break;  }
1272                                 else                            {       size++; }
1273                         }
1274                         in.close();
1275
1276                         positions.push_back(size);
1277                         positions[0] = 0;
1278
1279                         return positions;
1280         }
1281         catch(exception& e) {
1282                 errorOut(e, "MothurOut", "setFilePosFasta");
1283                 exit(1);
1284         }
1285 }
1286 /**************************************************************************************************/
1287 vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
1288         try {
1289                         filename = getFullPathName(filename);
1290
1291                         vector<unsigned long long> positions;
1292                         ifstream in;
1293                         //openInputFile(filename, in);
1294                         in.open(filename.c_str(), ios::binary);
1295
1296                         string input;
1297                         unsigned long long count = 0;
1298                         positions.push_back(0);
1299
1300                         while(!in.eof()){
1301                                 //getline counting reads
1302                                 char d = in.get(); count++;
1303                                 while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
1304                                         //get next character
1305                                         d = in.get();
1306                                         count++;
1307                                 }
1308
1309                                 if (!in.eof()) {
1310                                         d=in.get(); count++;
1311                                         while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
1312                                 }
1313                                 positions.push_back(count-1);
1314                                 //cout << count-1 << endl;
1315                         }
1316                         in.close();
1317
1318                         num = positions.size()-1;
1319
1320                         FILE * pFile;
1321                         unsigned long long size;
1322
1323                         //get num bytes in file
1324                         pFile = fopen (filename.c_str(),"rb");
1325                         if (pFile==NULL) perror ("Error opening file");
1326                         else{
1327                                 fseek (pFile, 0, SEEK_END);
1328                                 size=ftell (pFile);
1329                                 fclose (pFile);
1330                         }
1331
1332                         positions[(positions.size()-1)] = size;
1333
1334                         return positions;
1335         }
1336         catch(exception& e) {
1337                 errorOut(e, "MothurOut", "setFilePosEachLine");
1338                 exit(1);
1339         }
1340 }
1341 /**************************************************************************************************/
1342
1343 vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
1344         try{
1345                 vector<unsigned long long> filePos;
1346                 filePos.push_back(0);
1347
1348                 FILE * pFile;
1349                 unsigned long long size;
1350
1351                 filename = getFullPathName(filename);
1352
1353                 //get num bytes in file
1354                 pFile = fopen (filename.c_str(),"rb");
1355                 if (pFile==NULL) perror ("Error opening file");
1356                 else{
1357                         fseek (pFile, 0, SEEK_END);
1358                         size=ftell (pFile);
1359                         fclose (pFile);
1360                 }
1361
1362         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1363
1364                 //estimate file breaks
1365                 unsigned long long chunkSize = 0;
1366                 chunkSize = size / proc;
1367
1368                 //file to small to divide by processors
1369                 if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
1370
1371                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
1372                 for (int i = 0; i < proc; i++) {
1373                         unsigned long long spot = (i+1) * chunkSize;
1374
1375                         ifstream in;
1376                         openInputFile(filename, in);
1377                         in.seekg(spot);
1378
1379                         //look for next '>'
1380                         unsigned long long newSpot = spot;
1381                         while (!in.eof()) {
1382                            char c = in.get();
1383
1384                            if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
1385                            else if (int(c) == -1) { break; }
1386
1387                         }
1388
1389                         //there was not another sequence before the end of the file
1390                         unsigned long long sanityPos = in.tellg();
1391
1392                         if (sanityPos == -1) {  break;  }
1393                         else {  filePos.push_back(newSpot);  }
1394
1395                         in.close();
1396                 }
1397
1398                 //save end pos
1399                 filePos.push_back(size);
1400
1401                 //sanity check filePos
1402                 for (int i = 0; i < (filePos.size()-1); i++) {
1403                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
1404                 }
1405
1406                 proc = (filePos.size() - 1);
1407 #else
1408                 mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
1409                 proc=1;
1410                 filePos.push_back(size);
1411 #endif
1412                 return filePos;
1413         }
1414         catch(exception& e) {
1415                 errorOut(e, "MothurOut", "divideFile");
1416                 exit(1);
1417         }
1418 }
1419 /**************************************************************************************************/
1420 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
1421         try{
1422
1423                 vector<unsigned long long> filePos = divideFile(filename, proc);
1424
1425                 for (int i = 0; i < (filePos.size()-1); i++) {
1426
1427                         //read file chunk
1428                         ifstream in;
1429                         openInputFile(filename, in);
1430                         in.seekg(filePos[i]);
1431                         unsigned long long size = filePos[(i+1)] - filePos[i];
1432                         char* chunk = new char[size];
1433                         in.read(chunk, size);
1434                         in.close();
1435
1436                         //open new file
1437                         string fileChunkName = filename + "." + toString(i) + ".tmp";
1438                         ofstream out;
1439                         openOutputFile(fileChunkName, out);
1440
1441                         out << chunk << endl;
1442                         out.close();
1443                         delete[] chunk;
1444
1445                         //save name
1446                         files.push_back(fileChunkName);
1447                 }
1448
1449                 return 0;
1450         }
1451         catch(exception& e) {
1452                 errorOut(e, "MothurOut", "divideFile");
1453                 exit(1);
1454         }
1455 }
1456 /***********************************************************************/
1457
1458 bool MothurOut::isTrue(string f){
1459         try {
1460
1461                 for (int i = 0; i < f.length(); i++) { f[i] = toupper(f[i]); }
1462
1463                 if ((f == "TRUE") || (f == "T")) {      return true;    }
1464                 else {  return false;  }
1465         }
1466         catch(exception& e) {
1467                 errorOut(e, "MothurOut", "isTrue");
1468                 exit(1);
1469         }
1470 }
1471
1472 /***********************************************************************/
1473
1474 float MothurOut::roundDist(float dist, int precision){
1475         try {
1476                 return int(dist * precision + 0.5)/float(precision);
1477         }
1478         catch(exception& e) {
1479                 errorOut(e, "MothurOut", "roundDist");
1480                 exit(1);
1481         }
1482 }
1483 /***********************************************************************/
1484
1485 float MothurOut::ceilDist(float dist, int precision){
1486         try {
1487                 return int(ceil(dist * precision))/float(precision);
1488         }
1489         catch(exception& e) {
1490                 errorOut(e, "MothurOut", "ceilDist");
1491                 exit(1);
1492         }
1493 }
1494 /***********************************************************************/
1495
1496 vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){
1497         try {
1498         vector<string> pieces;
1499
1500         for (int i = 0; i < size; i++) {
1501             if (!isspace(buffer[i]))  { rest += buffer[i];  }
1502             else {
1503                 if (rest != "") { pieces.push_back(rest);  rest = ""; }
1504                 while (i < size) {  //gobble white space
1505                     if (isspace(buffer[i])) { i++; }
1506                     else { rest = buffer[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
1507                 }
1508             }
1509         }
1510
1511         return pieces;
1512         }
1513         catch(exception& e) {
1514                 errorOut(e, "MothurOut", "splitWhiteSpace");
1515                 exit(1);
1516         }
1517 }
1518 /***********************************************************************/
1519 vector<string> MothurOut::splitWhiteSpace(string input){
1520         try {
1521         vector<string> pieces;
1522         string rest = "";
1523
1524         for (int i = 0; i < input.length(); i++) {
1525             if (!isspace(input[i]))  { rest += input[i];  }
1526             else {
1527                 if (rest != "") { pieces.push_back(rest);  rest = ""; }
1528                 while (i < input.length()) {  //gobble white space
1529                     if (isspace(input[i])) { i++; }
1530                     else { rest = input[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
1531                 }
1532             }
1533         }
1534
1535         if (rest != "") { pieces.push_back(rest); }
1536
1537         return pieces;
1538         }
1539         catch(exception& e) {
1540                 errorOut(e, "MothurOut", "splitWhiteSpace");
1541                 exit(1);
1542         }
1543 }
1544 /***********************************************************************/
1545 vector<string> MothurOut::splitWhiteSpaceWithQuotes(string input){
1546         try {
1547         vector<string> pieces;
1548         string rest = "";
1549
1550         int pos = input.find('\'');
1551         int pos2 = input.find('\"');
1552
1553         if ((pos == string::npos) && (pos2 == string::npos)) { return splitWhiteSpace(input); } //no quotes to worry about
1554         else {
1555             for (int i = 0; i < input.length(); i++) {
1556                 if ((input[i] == '\'') || (input[i] == '\"') || (rest == "\'") || (rest == "\"")) { //grab everything til end or next ' or "
1557                     rest += input[i];
1558                     for (int j = i+1; j < input.length(); j++) {
1559                         if ((input[j] == '\'') || (input[j] == '\"')) {  //then quit
1560                             rest += input[j];
1561                             i = j+1;
1562                             j+=input.length();
1563                         }else { rest += input[j]; }
1564                     }
1565                 }else if (!isspace(input[i]))  { rest += input[i];  }
1566                 else {
1567                     if (rest != "") { pieces.push_back(rest);  rest = ""; }
1568                     while (i < input.length()) {  //gobble white space
1569                         if (isspace(input[i])) { i++; }
1570                         else { rest = input[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
1571                     }
1572                 }
1573             }
1574
1575             if (rest != "") { pieces.push_back(rest); }
1576         }
1577         return pieces;
1578         }
1579         catch(exception& e) {
1580                 errorOut(e, "MothurOut", "splitWhiteSpace");
1581                 exit(1);
1582         }
1583 }
1584 //**********************************************************************************************************************
1585 int MothurOut::readTax(string namefile, map<string, string>& taxMap) {
1586         try {
1587         //open input file
1588                 ifstream in;
1589                 openInputFile(namefile, in);
1590
1591         string rest = "";
1592         char buffer[4096];
1593         bool pairDone = false;
1594         bool columnOne = true;
1595         string firstCol, secondCol;
1596
1597                 while (!in.eof()) {
1598                         if (control_pressed) { break; }
1599
1600             in.read(buffer, 4096);
1601             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1602
1603             for (int i = 0; i < pieces.size(); i++) {
1604                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1605                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1606
1607                 if (pairDone) {
1608                     //are there confidence scores, if so remove them
1609                     if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);    }
1610                     taxMap[firstCol] = secondCol;
1611                     if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
1612                     pairDone = false;
1613                 }
1614             }
1615                 }
1616                 in.close();
1617
1618         if (rest != "") {
1619             vector<string> pieces = splitWhiteSpace(rest);
1620
1621             for (int i = 0; i < pieces.size(); i++) {
1622                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1623                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1624
1625                 if (pairDone) {
1626                     //are there confidence scores, if so remove them
1627                     if (secondCol.find_first_of('(') != -1) {  removeConfidences(secondCol);    }
1628                     taxMap[firstCol] = secondCol;
1629                     if (debug) {  mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n");  }
1630                     pairDone = false;
1631                 }
1632             }
1633         }
1634
1635                 return taxMap.size();
1636
1637         }
1638         catch(exception& e) {
1639                 errorOut(e, "MothurOut", "readTax");
1640                 exit(1);
1641         }
1642 }
1643 /**********************************************************************************************************************/
1644 int MothurOut::readNames(string namefile, map<string, string>& nameMap, bool redund) {
1645         try {
1646                 //open input file
1647                 ifstream in;
1648                 openInputFile(namefile, in);
1649
1650         string rest = "";
1651         char buffer[4096];
1652         bool pairDone = false;
1653         bool columnOne = true;
1654         string firstCol, secondCol;
1655
1656                 while (!in.eof()) {
1657                         if (control_pressed) { break; }
1658
1659             in.read(buffer, 4096);
1660             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1661
1662             for (int i = 0; i < pieces.size(); i++) {
1663                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1664                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1665
1666                 if (pairDone) {
1667                     //parse names into vector
1668                     vector<string> theseNames;
1669                     splitAtComma(secondCol, theseNames);
1670                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1671                     pairDone = false;
1672                 }
1673             }
1674                 }
1675                 in.close();
1676
1677         if (rest != "") {
1678             vector<string> pieces = splitWhiteSpace(rest);
1679
1680             for (int i = 0; i < pieces.size(); i++) {
1681                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1682                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1683
1684                 if (pairDone) {
1685                     //parse names into vector
1686                     vector<string> theseNames;
1687                     splitAtComma(secondCol, theseNames);
1688                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1689                     pairDone = false;
1690                 }
1691             }
1692         }
1693
1694                 return nameMap.size();
1695
1696         }
1697         catch(exception& e) {
1698                 errorOut(e, "MothurOut", "readNames");
1699                 exit(1);
1700         }
1701 }
1702 /**********************************************************************************************************************/
1703 int MothurOut::readNames(string namefile, map<string, string>& nameMap, int flip) {
1704         try {
1705                 //open input file
1706                 ifstream in;
1707                 openInputFile(namefile, in);
1708
1709         string rest = "";
1710         char buffer[4096];
1711         bool pairDone = false;
1712         bool columnOne = true;
1713         string firstCol, secondCol;
1714
1715                 while (!in.eof()) {
1716                         if (control_pressed) { break; }
1717
1718             in.read(buffer, 4096);
1719             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1720
1721             for (int i = 0; i < pieces.size(); i++) {
1722                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1723                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1724
1725                 if (pairDone) {
1726                     nameMap[secondCol] = firstCol;
1727                     pairDone = false;
1728                 }
1729             }
1730                 }
1731                 in.close();
1732
1733         if (rest != "") {
1734             vector<string> pieces = splitWhiteSpace(rest);
1735
1736             for (int i = 0; i < pieces.size(); i++) {
1737                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1738                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1739
1740                 if (pairDone) {
1741                     nameMap[secondCol] = firstCol;
1742                     pairDone = false;
1743                 }
1744             }
1745         }
1746
1747                 return nameMap.size();
1748
1749         }
1750         catch(exception& e) {
1751                 errorOut(e, "MothurOut", "readNames");
1752                 exit(1);
1753         }
1754 }
1755 /**********************************************************************************************************************/
1756 int MothurOut::readNames(string namefile, map<string, string>& nameMap, map<string, int>& nameCount) {
1757         try {
1758                 nameMap.clear(); nameCount.clear();
1759                 //open input file
1760                 ifstream in;
1761                 openInputFile(namefile, in);
1762
1763         string rest = "";
1764         char buffer[4096];
1765         bool pairDone = false;
1766         bool columnOne = true;
1767         string firstCol, secondCol;
1768
1769                 while (!in.eof()) {
1770                         if (control_pressed) { break; }
1771
1772             in.read(buffer, 4096);
1773             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1774
1775             for (int i = 0; i < pieces.size(); i++) {
1776                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1777                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1778
1779                 if (pairDone) {
1780                     //parse names into vector
1781                     vector<string> theseNames;
1782                     splitAtComma(secondCol, theseNames);
1783                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1784                     nameCount[firstCol] = theseNames.size();
1785                     pairDone = false;
1786                 }
1787             }
1788                 }
1789                 in.close();
1790
1791         if (rest != "") {
1792             vector<string> pieces = splitWhiteSpace(rest);
1793
1794             for (int i = 0; i < pieces.size(); i++) {
1795                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1796                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1797
1798                 if (pairDone) {
1799                     //parse names into vector
1800                     vector<string> theseNames;
1801                     splitAtComma(secondCol, theseNames);
1802                     for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = firstCol;  }
1803                     nameCount[firstCol] = theseNames.size();
1804                     pairDone = false;
1805                 }
1806             }
1807
1808         }
1809                 return nameMap.size();
1810
1811         }
1812         catch(exception& e) {
1813                 errorOut(e, "MothurOut", "readNames");
1814                 exit(1);
1815         }
1816 }
1817 /**********************************************************************************************************************/
1818 int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
1819         try {
1820                 //open input file
1821                 ifstream in;
1822                 openInputFile(namefile, in);
1823
1824         string rest = "";
1825         char buffer[4096];
1826         bool pairDone = false;
1827         bool columnOne = true;
1828         string firstCol, secondCol;
1829
1830                 while (!in.eof()) {
1831                         if (control_pressed) { break; }
1832
1833             in.read(buffer, 4096);
1834             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1835
1836             for (int i = 0; i < pieces.size(); i++) {
1837                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1838                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1839
1840                 if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
1841             }
1842                 }
1843                 in.close();
1844
1845         if (rest != "") {
1846             vector<string> pieces = splitWhiteSpace(rest);
1847
1848             for (int i = 0; i < pieces.size(); i++) {
1849                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1850                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1851
1852                 if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
1853             }
1854         }
1855
1856                 return nameMap.size();
1857
1858         }
1859         catch(exception& e) {
1860                 errorOut(e, "MothurOut", "readNames");
1861                 exit(1);
1862         }
1863 }
1864 /**********************************************************************************************************************/
1865 int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap) {
1866         try {
1867                 //open input file
1868                 ifstream in;
1869                 openInputFile(namefile, in);
1870
1871         string rest = "";
1872         char buffer[4096];
1873         bool pairDone = false;
1874         bool columnOne = true;
1875         string firstCol, secondCol;
1876
1877                 while (!in.eof()) {
1878                         if (control_pressed) { break; }
1879
1880             in.read(buffer, 4096);
1881             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1882
1883             for (int i = 0; i < pieces.size(); i++) {
1884                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1885                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1886
1887                 if (pairDone) {
1888                     vector<string> temp;
1889                     splitAtComma(secondCol, temp);
1890                     nameMap[firstCol] = temp;
1891                     pairDone = false;
1892                 }
1893             }
1894                 }
1895                 in.close();
1896
1897         if (rest != "") {
1898             vector<string> pieces = splitWhiteSpace(rest);
1899
1900             for (int i = 0; i < pieces.size(); i++) {
1901                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1902                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1903
1904                 if (pairDone) {
1905                     vector<string> temp;
1906                     splitAtComma(secondCol, temp);
1907                     nameMap[firstCol] = temp;
1908                     pairDone = false;
1909                 }
1910             }
1911         }
1912
1913                 return nameMap.size();
1914         }
1915         catch(exception& e) {
1916                 errorOut(e, "MothurOut", "readNames");
1917                 exit(1);
1918         }
1919 }
1920 /**********************************************************************************************************************/
1921 map<string, int> MothurOut::readNames(string namefile) {
1922         try {
1923                 map<string, int> nameMap;
1924
1925                 //open input file
1926                 ifstream in;
1927                 openInputFile(namefile, in);
1928
1929         string rest = "";
1930         char buffer[4096];
1931         bool pairDone = false;
1932         bool columnOne = true;
1933         string firstCol, secondCol;
1934
1935                 while (!in.eof()) {
1936                         if (control_pressed) { break; }
1937
1938             in.read(buffer, 4096);
1939             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1940
1941             for (int i = 0; i < pieces.size(); i++) {
1942                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1943                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1944
1945                 if (pairDone) {
1946                     int num = getNumNames(secondCol);
1947                     nameMap[firstCol] = num;
1948                     pairDone = false;
1949                 }
1950             }
1951                 }
1952         in.close();
1953
1954         if (rest != "") {
1955             vector<string> pieces = splitWhiteSpace(rest);
1956             for (int i = 0; i < pieces.size(); i++) {
1957                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1958                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
1959
1960                 if (pairDone) {
1961                     int num = getNumNames(secondCol);
1962                     nameMap[firstCol] = num;
1963                     pairDone = false;
1964                 }
1965             }
1966         }
1967
1968                 return nameMap;
1969
1970         }
1971         catch(exception& e) {
1972                 errorOut(e, "MothurOut", "readNames");
1973                 exit(1);
1974         }
1975 }
1976 /**********************************************************************************************************************/
1977 int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, map<string, string>& fastamap) {
1978         try {
1979                 int error = 0;
1980
1981                 //open input file
1982                 ifstream in;
1983                 openInputFile(namefile, in);
1984
1985         string rest = "";
1986         char buffer[4096];
1987         bool pairDone = false;
1988         bool columnOne = true;
1989         string firstCol, secondCol;
1990
1991                 while (!in.eof()) {
1992                         if (control_pressed) { break; }
1993
1994             in.read(buffer, 4096);
1995             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
1996
1997             for (int i = 0; i < pieces.size(); i++) {
1998                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
1999                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
2000
2001                 if (pairDone) {
2002                     int num = getNumNames(secondCol);
2003
2004                     map<string, string>::iterator it = fastamap.find(firstCol);
2005                     if (it == fastamap.end()) {
2006                         error = 1;
2007                         mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
2008                     }else {
2009                         seqPriorityNode temp(num, it->second, firstCol);
2010                         nameVector.push_back(temp);
2011                     }
2012
2013                     pairDone = false;
2014                 }
2015             }
2016                 }
2017         in.close();
2018
2019         if (rest != "") {
2020             vector<string> pieces = splitWhiteSpace(rest);
2021
2022             for (int i = 0; i < pieces.size(); i++) {
2023                 if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
2024                 else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
2025
2026                 if (pairDone) {
2027                     int num = getNumNames(secondCol);
2028
2029                     map<string, string>::iterator it = fastamap.find(firstCol);
2030                     if (it == fastamap.end()) {
2031                         error = 1;
2032                         mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
2033                     }else {
2034                         seqPriorityNode temp(num, it->second, firstCol);
2035                         nameVector.push_back(temp);
2036                     }
2037
2038                     pairDone = false;
2039                 }
2040             }
2041         }
2042                 return error;
2043         }
2044         catch(exception& e) {
2045                 errorOut(e, "MothurOut", "readNames");
2046                 exit(1);
2047         }
2048 }
2049 //**********************************************************************************************************************
2050 set<string> MothurOut::readAccnos(string accnosfile){
2051         try {
2052                 set<string> names;
2053                 ifstream in;
2054                 openInputFile(accnosfile, in);
2055                 string name;
2056
2057         string rest = "";
2058         char buffer[4096];
2059
2060                 while (!in.eof()) {
2061                         if (control_pressed) { break; }
2062
2063             in.read(buffer, 4096);
2064             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
2065
2066             for (int i = 0; i < pieces.size(); i++) {  names.insert(pieces[i]);  }
2067         }
2068                 in.close();
2069
2070         if (rest != "") {
2071             vector<string> pieces = splitWhiteSpace(rest);
2072             for (int i = 0; i < pieces.size(); i++) {  names.insert(pieces[i]);  }
2073         }
2074                 return names;
2075         }
2076         catch(exception& e) {
2077                 errorOut(e, "MothurOut", "readAccnos");
2078                 exit(1);
2079         }
2080 }
2081 //**********************************************************************************************************************
2082 int MothurOut::readAccnos(string accnosfile, vector<string>& names){
2083         try {
2084         names.clear();
2085                 ifstream in;
2086                 openInputFile(accnosfile, in);
2087                 string name;
2088
2089         string rest = "";
2090         char buffer[4096];
2091
2092                 while (!in.eof()) {
2093                         if (control_pressed) { break; }
2094
2095             in.read(buffer, 4096);
2096             vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
2097
2098             for (int i = 0; i < pieces.size(); i++) {  names.push_back(pieces[i]);  }
2099         }
2100                 in.close();
2101
2102         if (rest != "") {
2103             vector<string> pieces = splitWhiteSpace(rest);
2104             for (int i = 0; i < pieces.size(); i++) {  names.push_back(pieces[i]);  }
2105         }
2106
2107                 return 0;
2108         }
2109         catch(exception& e) {
2110                 errorOut(e, "MothurOut", "readAccnos");
2111                 exit(1);
2112         }
2113 }
2114 /***********************************************************************/
2115
2116 int MothurOut::getNumNames(string names){
2117         try {
2118                 int count = 0;
2119
2120                 if(names != ""){
2121                         count = 1;
2122                         for(int i=0;i<names.size();i++){
2123                                 if(names[i] == ','){
2124                                         count++;
2125                                 }
2126                         }
2127                 }
2128
2129                 return count;
2130         }
2131         catch(exception& e) {
2132                 errorOut(e, "MothurOut", "getNumNames");
2133                 exit(1);
2134         }
2135 }
2136 /***********************************************************************/
2137
2138 int MothurOut::getNumChar(string line, char c){
2139         try {
2140                 int count = 0;
2141
2142                 if(line != ""){
2143                         for(int i=0;i<line.size();i++){
2144                                 if(line[i] == c){
2145                                         count++;
2146                                 }
2147                         }
2148                 }
2149
2150                 return count;
2151         }
2152         catch(exception& e) {
2153                 errorOut(e, "MothurOut", "getNumChar");
2154                 exit(1);
2155         }
2156 }
2157 //**********************************************************************************************************************
2158 bool MothurOut::isSubset(vector<string> bigset, vector<string> subset) {
2159         try {
2160
2161
2162                 if (subset.size() > bigset.size()) { return false;  }
2163
2164                 //check if each guy in suset is also in bigset
2165                 for (int i = 0; i < subset.size(); i++) {
2166                         bool match = false;
2167                         for (int j = 0; j < bigset.size(); j++) {
2168                                 if (subset[i] == bigset[j]) { match = true; break; }
2169                         }
2170
2171                         //you have a guy in subset that had no match in bigset
2172                         if (match == false) { return false; }
2173                 }
2174
2175                 return true;
2176
2177         }
2178         catch(exception& e) {
2179                 errorOut(e, "MothurOut", "isSubset");
2180                 exit(1);
2181         }
2182 }
2183 /***********************************************************************/
2184 int MothurOut::mothurRemove(string filename){
2185         try {
2186                 filename = getFullPathName(filename);
2187                 int error = remove(filename.c_str());
2188                 //if (error != 0) {
2189                 //      if (errno != ENOENT) { //ENOENT == file does not exist
2190                 //              string message = "Error deleting file " + filename;
2191                 //              perror(message.c_str());
2192                 //      }
2193                 //}
2194                 return error;
2195         }
2196         catch(exception& e) {
2197                 errorOut(e, "MothurOut", "mothurRemove");
2198                 exit(1);
2199         }
2200 }
2201 /***********************************************************************/
2202 bool MothurOut::mothurConvert(string item, int& num){
2203         try {
2204                 bool error = false;
2205
2206                 if (isNumeric1(item)) {
2207                         convert(item, num);
2208                 }else {
2209                         num = 0;
2210                         error = true;
2211                         mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
2212                         commandInputsConvertError = true;
2213                 }
2214
2215                 return error;
2216         }
2217         catch(exception& e) {
2218                 errorOut(e, "MothurOut", "mothurConvert");
2219                 exit(1);
2220         }
2221 }
2222 /***********************************************************************/
2223 bool MothurOut::mothurConvert(string item, intDist& num){
2224         try {
2225                 bool error = false;
2226
2227                 if (isNumeric1(item)) {
2228                         convert(item, num);
2229                 }else {
2230                         num = 0;
2231                         error = true;
2232                         mothurOut("[ERROR]: cannot convert " + item + " to an integer."); mothurOutEndLine();
2233                         commandInputsConvertError = true;
2234                 }
2235
2236                 return error;
2237         }
2238         catch(exception& e) {
2239                 errorOut(e, "MothurOut", "mothurConvert");
2240                 exit(1);
2241         }
2242 }
2243
2244 /***********************************************************************/
2245 bool MothurOut::isNumeric1(string stringToCheck){
2246         try {
2247                 bool numeric = false;
2248
2249                 if(stringToCheck.find_first_not_of("0123456789.-") == string::npos) { numeric = true; }
2250
2251                 return numeric;
2252         }
2253         catch(exception& e) {
2254                 errorOut(e, "MothurOut", "isNumeric1");
2255                 exit(1);
2256         }
2257
2258 }
2259 /***********************************************************************/
2260 bool MothurOut::mothurConvert(string item, float& num){
2261         try {
2262                 bool error = false;
2263
2264                 if (isNumeric1(item)) {
2265                         convert(item, num);
2266                 }else {
2267                         num = 0;
2268                         error = true;
2269                         mothurOut("[ERROR]: cannot convert " + item + " to a float."); mothurOutEndLine();
2270                         commandInputsConvertError = true;
2271                 }
2272
2273                 return error;
2274         }
2275         catch(exception& e) {
2276                 errorOut(e, "MothurOut", "mothurConvert");
2277                 exit(1);
2278         }
2279 }
2280 /***********************************************************************/
2281 bool MothurOut::mothurConvert(string item, double& num){
2282         try {
2283                 bool error = false;
2284
2285                 if (isNumeric1(item)) {
2286                         convert(item, num);
2287                 }else {
2288                         num = 0;
2289                         error = true;
2290                         mothurOut("[ERROR]: cannot convert " + item + " to a double."); mothurOutEndLine();
2291                         commandInputsConvertError = true;
2292                 }
2293
2294                 return error;
2295         }
2296         catch(exception& e) {
2297                 errorOut(e, "MothurOut", "mothurConvert");
2298                 exit(1);
2299         }
2300 }
2301 /**************************************************************************************************/
2302
2303 vector<vector<double> > MothurOut::binomial(int maxOrder){
2304         try {
2305         vector<vector<double> > binomial(maxOrder+1);
2306
2307     for(int i=0;i<=maxOrder;i++){
2308                 binomial[i].resize(maxOrder+1);
2309                 binomial[i][0]=1;
2310                 binomial[0][i]=0;
2311     }
2312     binomial[0][0]=1;
2313
2314     binomial[1][0]=1;
2315     binomial[1][1]=1;
2316
2317     for(int i=2;i<=maxOrder;i++){
2318                 binomial[1][i]=0;
2319     }
2320
2321     for(int i=2;i<=maxOrder;i++){
2322                 for(int j=1;j<=maxOrder;j++){
2323                         if(i==j){       binomial[i][j]=1;                                                                       }
2324                         if(j>i) {       binomial[i][j]=0;                                                                       }
2325                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
2326                 }
2327     }
2328
2329         return binomial;
2330
2331         }
2332         catch(exception& e) {
2333                 errorOut(e, "MothurOut", "binomial");
2334                 exit(1);
2335         }
2336 }
2337 /**************************************************************************************************/
2338 unsigned int MothurOut::fromBase36(string base36){
2339         try {
2340                 unsigned int num = 0;
2341
2342                 map<char, int> converts;
2343                 converts['A'] = 0;
2344                 converts['a'] = 0;
2345                 converts['B'] = 1;
2346                 converts['b'] = 1;
2347                 converts['C'] = 2;
2348                 converts['c'] = 2;
2349                 converts['D'] = 3;
2350                 converts['d'] = 3;
2351                 converts['E'] = 4;
2352                 converts['e'] = 4;
2353                 converts['F'] = 5;
2354                 converts['f'] = 5;
2355                 converts['G'] = 6;
2356                 converts['g'] = 6;
2357                 converts['H'] = 7;
2358                 converts['h'] = 7;
2359                 converts['I'] = 8;
2360                 converts['i'] = 8;
2361                 converts['J'] = 9;
2362                 converts['j'] = 9;
2363                 converts['K'] = 10;
2364                 converts['k'] = 10;
2365                 converts['L'] = 11;
2366                 converts['l'] = 11;
2367                 converts['M'] = 12;
2368                 converts['m'] = 12;
2369                 converts['N'] = 13;
2370                 converts['n'] = 13;
2371                 converts['O'] = 14;
2372                 converts['o'] = 14;
2373                 converts['P'] = 15;
2374                 converts['p'] = 15;
2375                 converts['Q'] = 16;
2376                 converts['q'] = 16;
2377                 converts['R'] = 17;
2378                 converts['r'] = 17;
2379                 converts['S'] = 18;
2380                 converts['s'] = 18;
2381                 converts['T'] = 19;
2382                 converts['t'] = 19;
2383                 converts['U'] = 20;
2384                 converts['u'] = 20;
2385                 converts['V'] = 21;
2386                 converts['v'] = 21;
2387                 converts['W'] = 22;
2388                 converts['w'] = 22;
2389                 converts['X'] = 23;
2390                 converts['x'] = 23;
2391                 converts['Y'] = 24;
2392                 converts['y'] = 24;
2393                 converts['Z'] = 25;
2394                 converts['z'] = 25;
2395                 converts['0'] = 26;
2396                 converts['1'] = 27;
2397                 converts['2'] = 28;
2398                 converts['3'] = 29;
2399                 converts['4'] = 30;
2400                 converts['5'] = 31;
2401                 converts['6'] = 32;
2402                 converts['7'] = 33;
2403                 converts['8'] = 34;
2404                 converts['9'] = 35;
2405
2406                 int i = 0;
2407                 while (i < base36.length()) {
2408                         char c = base36[i];
2409                         num = 36 * num + converts[c];
2410                         i++;
2411                 }
2412
2413                 return num;
2414
2415         }
2416         catch(exception& e) {
2417                 errorOut(e, "MothurOut", "fromBase36");
2418                 exit(1);
2419         }
2420 }
2421 /***********************************************************************/
2422
2423 int MothurOut::factorial(int num){
2424         try {
2425                 int total = 1;
2426
2427                 for (int i = 1; i <= num; i++) {
2428                         total *= i;
2429                 }
2430
2431                 return total;
2432         }
2433         catch(exception& e) {
2434                 errorOut(e, "MothurOut", "factorial");
2435                 exit(1);
2436         }
2437 }
2438 /***********************************************************************/
2439
2440 int MothurOut::getNumSeqs(ifstream& file){
2441         try {
2442                 int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
2443                 file.seekg(0);
2444                 return numSeqs;
2445         }
2446         catch(exception& e) {
2447                 errorOut(e, "MothurOut", "getNumSeqs");
2448                 exit(1);
2449         }
2450 }
2451 /***********************************************************************/
2452 void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
2453         try {
2454                 string input;
2455                 numSeqs = 0;
2456                 while(!file.eof()){
2457                         input = getline(file);
2458                         if (input.length() != 0) {
2459                                 if(input[0] == '>'){ numSeqs++; }
2460                         }
2461                 }
2462         }
2463         catch(exception& e) {
2464                 errorOut(e, "MothurOut", "getNumSeqs");
2465                 exit(1);
2466         }
2467 }
2468 /***********************************************************************/
2469
2470 //This function parses the estimator options and puts them in a vector
2471 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
2472         try {
2473                 string individual = "";
2474                 int estimLength = estim.size();
2475                 for(int i=0;i<estimLength;i++){
2476                         if(estim[i] == symbol){
2477                                 container.push_back(individual);
2478                                 individual = "";
2479                         }
2480                         else{
2481                                 individual += estim[i];
2482                         }
2483                 }
2484                 container.push_back(individual);
2485
2486         }
2487         catch(exception& e) {
2488                 errorOut(e, "MothurOut", "splitAtChar");
2489                 exit(1);
2490         }
2491 }
2492
2493 /***********************************************************************/
2494
2495 //This function parses the estimator options and puts them in a vector
2496 void MothurOut::splitAtDash(string& estim, vector<string>& container) {
2497         try {
2498                 string individual = "";
2499                 int estimLength = estim.size();
2500                 bool prevEscape = false;
2501                 for(int i=0;i<estimLength;i++){
2502                         if(prevEscape){
2503                                 individual += estim[i];
2504                                 prevEscape = false;
2505                         }
2506                         else{
2507                                 if(estim[i] == '\\'){
2508                                         prevEscape = true;
2509                                 }
2510                                 else if(estim[i] == '-'){
2511                                         container.push_back(individual);
2512                                         individual = "";
2513                                         prevEscape = false;
2514                                 }
2515                                 else{
2516                                         individual += estim[i];
2517                                         prevEscape = false;
2518                                 }
2519                         }
2520                 }
2521                 container.push_back(individual);
2522         }
2523         catch(exception& e) {
2524                 errorOut(e, "MothurOut", "splitAtDash");
2525                 exit(1);
2526         }
2527 }
2528
2529 /***********************************************************************/
2530 //This function parses the label options and puts them in a set
2531 void MothurOut::splitAtDash(string& estim, set<string>& container) {
2532         try {
2533                 string individual = "";
2534                 int estimLength = estim.size();
2535                 bool prevEscape = false;
2536                 for(int i=0;i<estimLength;i++){
2537                         if(prevEscape){
2538                                 individual += estim[i];
2539                                 prevEscape = false;
2540                         }
2541                         else{
2542                                 if(estim[i] == '\\'){
2543                                         prevEscape = true;
2544                                 }
2545                                 else if(estim[i] == '-'){
2546                                         container.insert(individual);
2547                                         individual = "";
2548                                         prevEscape = false;
2549                                 }
2550                                 else{
2551                                         individual += estim[i];
2552                                         prevEscape = false;
2553                                 }
2554                         }
2555                 }
2556                 container.insert(individual);
2557
2558         }
2559         catch(exception& e) {
2560                 errorOut(e, "MothurOut", "splitAtDash");
2561                 exit(1);
2562         }
2563 }
2564 /***********************************************************************/
2565 //This function parses the line options and puts them in a set
2566 void MothurOut::splitAtDash(string& estim, set<int>& container) {
2567         try {
2568                 string individual = "";
2569                 int lineNum;
2570                 int estimLength = estim.size();
2571                 bool prevEscape = false;
2572                 for(int i=0;i<estimLength;i++){
2573                         if(prevEscape){
2574                                 individual += estim[i];
2575                                 prevEscape = false;
2576                         }
2577                         else{
2578                                 if(estim[i] == '\\'){
2579                                         prevEscape = true;
2580                                 }
2581                                 else if(estim[i] == '-'){
2582                                         convert(individual, lineNum); //convert the string to int
2583                                         container.insert(lineNum);
2584                                         individual = "";
2585                                         prevEscape = false;
2586                                 }
2587                                 else{
2588                                         individual += estim[i];
2589                                         prevEscape = false;
2590                                 }
2591                         }
2592                 }
2593                 convert(individual, lineNum); //convert the string to int
2594                 container.insert(lineNum);
2595         }
2596         catch(exception& e) {
2597                 errorOut(e, "MothurOut", "splitAtDash");
2598                 exit(1);
2599         }
2600 }
2601 /***********************************************************************/
2602 string MothurOut::makeList(vector<string>& names) {
2603         try {
2604                 string list = "";
2605
2606         if (names.size() == 0) { return list; }
2607
2608         for (int i = 0; i < names.size()-1; i++) { list += names[i] + ",";  }
2609
2610         //get last name
2611         list += names[names.size()-1];
2612
2613         return list;
2614     }
2615         catch(exception& e) {
2616                 errorOut(e, "MothurOut", "makeList");
2617                 exit(1);
2618         }
2619 }
2620
2621 /***********************************************************************/
2622 //This function parses the a string and puts peices in a vector
2623 void MothurOut::splitAtComma(string& estim, vector<string>& container) {
2624         try {
2625                 string individual = "";
2626                 int estimLength = estim.size();
2627                 for(int i=0;i<estimLength;i++){
2628                         if(estim[i] == ','){
2629                                 container.push_back(individual);
2630                                 individual = "";
2631                         }
2632                         else{
2633                                 individual += estim[i];
2634                         }
2635                 }
2636                 container.push_back(individual);
2637
2638
2639
2640
2641 //              string individual;
2642 //
2643 //              while (estim.find_first_of(',') != -1) {
2644 //                      individual = estim.substr(0,estim.find_first_of(','));
2645 //                      if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
2646 //                              estim = estim.substr(estim.find_first_of(',')+1, estim.length());
2647 //                              container.push_back(individual);
2648 //                      }
2649 //              }
2650 //              //get last one
2651 //              container.push_back(estim);
2652         }
2653         catch(exception& e) {
2654                 errorOut(e, "MothurOut", "splitAtComma");
2655                 exit(1);
2656         }
2657 }
2658 /***********************************************************************/
2659 //This function splits up the various option parameters
2660 void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
2661         try {
2662                 prefix = suffix.substr(0,suffix.find_first_of(c));
2663                 if ((suffix.find_first_of(c)+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
2664                         suffix = suffix.substr(suffix.find_first_of(c)+1, suffix.length());
2665                         string space = " ";
2666                         while(suffix.at(0) == ' ')
2667                                 suffix = suffix.substr(1, suffix.length());
2668                 }
2669
2670         }
2671         catch(exception& e) {
2672                 errorOut(e, "MothurOut", "splitAtComma");
2673                 exit(1);
2674         }
2675 }
2676
2677 /***********************************************************************/
2678
2679 //This function splits up the various option parameters
2680 void MothurOut::splitAtComma(string& prefix, string& suffix){
2681         try {
2682                 prefix = suffix.substr(0,suffix.find_first_of(','));
2683                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
2684                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
2685                         string space = " ";
2686                         while(suffix.at(0) == ' ')
2687                                 suffix = suffix.substr(1, suffix.length());
2688                 }
2689
2690         }
2691         catch(exception& e) {
2692                 errorOut(e, "MothurOut", "splitAtComma");
2693                 exit(1);
2694         }
2695 }
2696 /***********************************************************************/
2697
2698 //This function separates the key value from the option value i.e. dist=96_...
2699 void MothurOut::splitAtEquals(string& key, string& value){
2700         try {
2701                 if(value.find_first_of('=') != -1){
2702                         key = value.substr(0,value.find_first_of('='));
2703                         if ((value.find_first_of('=')+1) <= value.length()) {
2704                                 value = value.substr(value.find_first_of('=')+1, value.length());
2705                         }
2706                 }else{
2707                         key = value;
2708                         value = 1;
2709                 }
2710         }
2711         catch(exception& e) {
2712                 errorOut(e, "MothurOut", "splitAtEquals");
2713                 exit(1);
2714         }
2715 }
2716
2717 /**************************************************************************************************/
2718
2719 bool MothurOut::inUsersGroups(string groupname, vector<string> Groups) {
2720         try {
2721                 for (int i = 0; i < Groups.size(); i++) {
2722                         if (groupname == Groups[i]) { return true; }
2723                 }
2724                 return false;
2725         }
2726         catch(exception& e) {
2727                 errorOut(e, "MothurOut", "inUsersGroups");
2728                 exit(1);
2729         }
2730 }
2731 /**************************************************************************************************/
2732
2733 bool MothurOut::inUsersGroups(vector<int> set, vector< vector<int> > sets) {
2734         try {
2735                 for (int i = 0; i < sets.size(); i++) {
2736                         if (set == sets[i]) { return true; }
2737                 }
2738                 return false;
2739         }
2740         catch(exception& e) {
2741                 errorOut(e, "MothurOut", "inUsersGroups");
2742                 exit(1);
2743         }
2744 }
2745 /**************************************************************************************************/
2746
2747 bool MothurOut::inUsersGroups(int groupname, vector<int> Groups) {
2748         try {
2749                 for (int i = 0; i < Groups.size(); i++) {
2750                         if (groupname == Groups[i]) { return true; }
2751                 }
2752                 return false;
2753         }
2754         catch(exception& e) {
2755                 errorOut(e, "MothurOut", "inUsersGroups");
2756                 exit(1);
2757         }
2758 }
2759
2760 /**************************************************************************************************/
2761 //returns true if any of the strings in first vector are in second vector
2762 bool MothurOut::inUsersGroups(vector<string> groupnames, vector<string> Groups) {
2763         try {
2764
2765                 for (int i = 0; i < groupnames.size(); i++) {
2766                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
2767                 }
2768                 return false;
2769         }
2770         catch(exception& e) {
2771                 errorOut(e, "MothurOut", "inUsersGroups");
2772                 exit(1);
2773         }
2774 }
2775 /***********************************************************************/
2776 //this function determines if the user has given us labels that are smaller than the given label.
2777 //if so then it returns true so that the calling function can run the previous valid distance.
2778 //it's a "smart" distance function.  It also checks for invalid labels.
2779 bool MothurOut::anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
2780         try {
2781
2782                 set<string>::iterator it;
2783                 vector<float> orderFloat;
2784                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
2785                 map<string, float>::iterator it2;
2786                 float labelFloat;
2787                 bool smaller = false;
2788
2789                 //unique is the smallest line
2790                 if (label == "unique") {  return false;  }
2791                 else {
2792                         if (convertTestFloat(label, labelFloat)) {
2793                                 convert(label, labelFloat);
2794                         }else { //cant convert
2795                                 return false;
2796                         }
2797                 }
2798
2799                 //go through users set and make them floats
2800                 for(it = userLabels.begin(); it != userLabels.end();) {
2801
2802                         float temp;
2803                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
2804                                 convert(*it, temp);
2805                                 orderFloat.push_back(temp);
2806                                 userMap[*it] = temp;
2807                                 it++;
2808                         }else if (*it == "unique") {
2809                                 orderFloat.push_back(-1.0);
2810                                 userMap["unique"] = -1.0;
2811                                 it++;
2812                         }else {
2813                                 if (errorOff == "") {  mothurOut(*it + " is not a valid label."); mothurOutEndLine();  }
2814                                 userLabels.erase(it++);
2815                         }
2816                 }
2817
2818                 //sort order
2819                 sort(orderFloat.begin(), orderFloat.end());
2820
2821                 /*************************************************/
2822                 //is this label bigger than any of the users labels
2823                 /*************************************************/
2824
2825                 //loop through order until you find a label greater than label
2826                 for (int i = 0; i < orderFloat.size(); i++) {
2827                         if (orderFloat[i] < labelFloat) {
2828                                 smaller = true;
2829                                 if (orderFloat[i] == -1) {
2830                                         if (errorOff == "") { mothurOut("Your file does not include the label unique."); mothurOutEndLine(); }
2831                                         userLabels.erase("unique");
2832                                 }
2833                                 else {
2834                                         if (errorOff == "") { mothurOut("Your file does not include the label "); mothurOutEndLine(); }
2835                                         string s = "";
2836                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
2837                                                 if (it2->second == orderFloat[i]) {
2838                                                         s = it2->first;
2839                                                         //remove small labels
2840                                                         userLabels.erase(s);
2841                                                         break;
2842                                                 }
2843                                         }
2844                                         if (errorOff == "") {mothurOut( s +  ". I will use the next smallest distance. "); mothurOutEndLine(); }
2845                                 }
2846                         //since they are sorted once you find a bigger one stop looking
2847                         }else { break; }
2848                 }
2849
2850                 return smaller;
2851
2852         }
2853         catch(exception& e) {
2854                 errorOut(e, "MothurOut", "anyLabelsToProcess");
2855                 exit(1);
2856         }
2857 }
2858
2859 /**************************************************************************************************/
2860 bool MothurOut::checkReleaseVersion(ifstream& file, string version) {
2861         try {
2862
2863                 bool good = true;
2864
2865                 string line = getline(file);
2866
2867                 //before we added this check
2868                 if (line[0] != '#') {  good = false;  }
2869                 else {
2870                         //rip off #
2871                         line = line.substr(1);
2872
2873                         vector<string> versionVector;
2874                         splitAtChar(version, versionVector, '.');
2875
2876                         //check file version
2877                         vector<string> linesVector;
2878                         splitAtChar(line, linesVector, '.');
2879
2880                         if (versionVector.size() != linesVector.size()) { good = false; }
2881                         else {
2882                                 for (int j = 0; j < versionVector.size(); j++) {
2883                                         int num1, num2;
2884                                         convert(versionVector[j], num1);
2885                                         convert(linesVector[j], num2);
2886
2887                                         //if mothurs version is newer than this files version, then we want to remake it
2888                                         if (num1 > num2) {  good = false; break;  }
2889                                 }
2890                         }
2891
2892                 }
2893
2894                 if (!good) {  file.close();  }
2895                 else { file.seekg(0);  }
2896
2897                 return good;
2898         }
2899         catch(exception& e) {
2900                 errorOut(e, "MothurOut", "checkReleaseVersion");
2901                 exit(1);
2902         }
2903 }
2904 /**************************************************************************************************/
2905 bool MothurOut::isContainingOnlyDigits(string input) {
2906         try{
2907
2908                 //are you a digit in ascii code
2909                 for (int i = 0;i < input.length(); i++){
2910                         if( input[i]>47 && input[i]<58){}
2911                         else { return false; }
2912                 }
2913
2914                 return true;
2915         }
2916         catch(exception& e) {
2917                 errorOut(e, "MothurOut", "isContainingOnlyDigits");
2918                 exit(1);
2919         }
2920 }
2921 /**************************************************************************************************/
2922 int MothurOut::removeConfidences(string& tax) {
2923         try {
2924
2925                 string taxon;
2926                 string newTax = "";
2927
2928                 while (tax.find_first_of(';') != -1) {
2929
2930                         if (control_pressed) { return 0; }
2931
2932                         //get taxon
2933                         taxon = tax.substr(0,tax.find_first_of(';'));
2934
2935                         int pos = taxon.find_last_of('(');
2936                         if (pos != -1) {
2937                                 //is it a number?
2938                                 int pos2 = taxon.find_last_of(')');
2939                                 if (pos2 != -1) {
2940                                         string confidenceScore = taxon.substr(pos+1, (pos2-(pos+1)));
2941                                         if (isNumeric1(confidenceScore)) {
2942                                                 taxon = taxon.substr(0, pos); //rip off confidence
2943                                         }
2944                                 }
2945                         }
2946                         taxon += ";";
2947
2948                         tax = tax.substr(tax.find_first_of(';')+1, tax.length());
2949                         newTax += taxon;
2950                 }
2951
2952                 tax = newTax;
2953
2954                 return 0;
2955         }
2956         catch(exception& e) {
2957                 errorOut(e, "MothurOut", "removeConfidences");
2958                 exit(1);
2959         }
2960 }
2961 /**************************************************************************************************/
2962 string MothurOut::removeQuotes(string tax) {
2963         try {
2964
2965                 string taxon;
2966                 string newTax = "";
2967
2968                 for (int i = 0; i < tax.length(); i++) {
2969
2970                         if (control_pressed) { return newTax; }
2971
2972             if ((tax[i] != '\'') && (tax[i] != '\"')) { newTax += tax[i]; }
2973
2974         }
2975
2976                 return newTax;
2977         }
2978         catch(exception& e) {
2979                 errorOut(e, "MothurOut", "removeQuotes");
2980                 exit(1);
2981         }
2982 }
2983 /**************************************************************************************************/
2984 // function for calculating standard deviation
2985 double MothurOut::getStandardDeviation(vector<int>& featureVector){
2986     try {
2987         //finds sum
2988         double average = 0;
2989         for (int i = 0; i < featureVector.size(); i++) { average += featureVector[i]; }
2990         average /= (double) featureVector.size();
2991
2992         //find standard deviation
2993         double stdDev = 0;
2994         for (int i = 0; i < featureVector.size(); i++) { //compute the difference of each dist from the mean, and square the result of each
2995             stdDev += ((featureVector[i] - average) * (featureVector[i] - average));
2996         }
2997
2998         stdDev /= (double) featureVector.size();
2999         stdDev = sqrt(stdDev);
3000
3001         return stdDev;
3002     }
3003         catch(exception& e) {
3004                 errorOut(e, "MothurOut", "getStandardDeviation");
3005                 exit(1);
3006         }
3007 }
3008 /**************************************************************************************************/
3009
3010
3011