mothur.h

   1 #ifndef MOTHUR_H
   2 #define MOTHUR_H
   3
   4
   5
   6 /*
   7  *  mothur.h
   8  *  Mothur
   9  *
  10  *  Created by Sarah Westcott on 2/19/09.
  11  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  12  *
  13  */
  14
  15 /* This file contains all the standard incudes we use in the project as well as some common utilities. */
  16
  17 //#include <cstddef>
  18
  19 //io libraries
  20 #include <iostream>
  21 #include <iomanip>
  22 #include <fstream>
  23 #include <sstream>
  24 #include <signal.h>
  25
  26
  27 //exception
  28 #include <stdexcept>
  29 #include <exception>
  30 #include <cstdlib>
  31
  32
  33 //containers
  34 #include <vector>
  35 #include <set>
  36 #include <map>
  37 #include <string>
  38 #include <list>
  39
  40 //math
  41 #include <cmath>
  42 #include <math.h>
  43 #include <algorithm>
  44
  45 //misc
  46 #include <cerrno>
  47 #include <ctime>
  48 #include <limits>
  49
  50 /***********************************************************************/
  51
  52 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  53         #include <sys/wait.h>
  54         #include <unistd.h>
  55
  56         #ifdef USE_READLINE
  57                 #include <readline/readline.h>
  58                 #include <readline/history.h>
  59         #endif
  60
  61         //#include <readline/readline.h>
  62         //#include <readline/history.h>
  63 #else
  64         #include <conio.h> //allows unbuffered screen capture from stdin
  65         #include <direct.h> //get cwd
  66 #endif
  67
  68 using namespace std;
  69
  70 #define exp(x) (exp((double) x))
  71 #define sqrt(x) (sqrt((double) x))
  72 #define log10(x) (log10((double) x))
  73 #define log2(x) (log10(x)/log10(2))
  74 #define isnan(x) ((x) != (x))
  75 #define isinf(x) (fabs(x) == std::numeric_limits<double>::infinity())
  76
  77 typedef unsigned long ull;
  78
  79 struct IntNode {
  80         int lvalue;
  81         int rvalue;
  82         int lcoef;
  83         int rcoef;
  84         IntNode* left;
  85         IntNode* right;
  86
  87         IntNode(int lv, int rv, IntNode* l, IntNode* r) : lvalue(lv), rvalue(rv), left(l), right(r) {};
  88         IntNode() {};
  89 };
  90
  91 struct ThreadNode {
  92         int* pid;
  93         IntNode* left;
  94         IntNode* right;
  95 };
  96
  97 /************************************************************/
  98 struct clusterNode {
  99         int numSeq;
 100         int parent;
 101         int smallChild; //used to make linkTable work with list and rabund. represents bin number of this cluster node
 102         clusterNode(int num, int par, int kid) : numSeq(num), parent(par), smallChild(kid) {};
 103 };
 104 /************************************************************/
 105 struct seqDist {
 106         int seq1;
 107         int seq2;
 108         float dist;
 109         seqDist() {}
 110         seqDist(int s1, int s2, float d) : seq1(s1), seq2(s2), dist(d) {}
 111         ~seqDist() {}
 112 };
 113 //********************************************************************************************************************
 114 //sorts lowest to highest
 115 inline bool compareSequenceDistance(seqDist left, seqDist right){
 116         return (left.dist < right.dist);
 117 }
 118 /***********************************************************************/
 119
 120 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
 121 // works for now, but there should be a way to do it without killing the whole program
 122
 123 class BadConversion : public runtime_error {
 124 public:
 125         BadConversion(const string& s) : runtime_error(s){ }
 126 };
 127
 128 //**********************************************************************************************************************
 129
 130 template<typename T>
 131 inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 132         istringstream i(s);
 133         char c;
 134         if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
 135                 throw BadConversion(s);
 136 }
 137
 138 //**********************************************************************************************************************
 139
 140 template<typename T>
 141 inline bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){
 142         istringstream i(s);
 143         char c;
 144         if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
 145         {
 146                 return false;
 147         }
 148         return true;
 149 }
 150
 151 //**********************************************************************************************************************
 152
 153 template<typename T>
 154 inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
 155         istringstream i(s);
 156         char c;
 157         if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
 158         {
 159                 cout << "unable to be converted into an integer.\n" << endl;
 160                 return false;
 161         }
 162         return true;
 163 }
 164
 165 //**********************************************************************************************************************
 166
 167 template<typename T>
 168 string toString(const T&x){
 169     stringstream output;
 170     output << x;
 171     return output.str();
 172 }
 173
 174 //**********************************************************************************************************************
 175
 176 template<typename T>
 177 string toHex(const T&x){
 178         stringstream output;
 179
 180         output << hex << x;
 181
 182     return output.str();
 183 }
 184 //**********************************************************************************************************************
 185
 186 template<typename T>
 187 string toString(const T&x, int i){
 188         stringstream output;
 189
 190         output.precision(i);
 191     output << fixed << x;
 192
 193     return output.str();
 194 }
 195 /***********************************************************************/
 196 inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
 197
 198         fileHandle.open(fileName.c_str(), ios::app);
 199         if(!fileHandle) {
 200                 cout << "Error: Could not open " << fileName << endl;
 201                 return 1;
 202         }
 203         else {
 204                 return 0;
 205         }
 206
 207 }
 208 /***********************************************************************/
 209
 210 inline void gobble(istream& f){
 211
 212         char d;
 213     while(isspace(d=f.get()))           {;}
 214         f.putback(d);
 215
 216 }
 217 /***********************************************************************/
 218
 219 inline string getline(ifstream& fileHandle) {
 220         try {
 221
 222                 string line = "";
 223
 224                 while (!fileHandle.eof())       {
 225                         //get next character
 226                         char c = fileHandle.get();
 227
 228                         //are you at the end of the line
 229                         if ((c == '\n') || (c == '\r') || (c == '\f')){  break; }
 230                         else {          line += c;              }
 231                 }
 232
 233                 return line;
 234
 235         }
 236         catch(exception& e) {
 237                 cout << "Error in mothur function getline" << endl;
 238                 exit(1);
 239         }
 240 }
 241
 242 /***********************************************************************/
 243
 244 inline bool isTrue(string f){
 245
 246         if ((f == "TRUE") || (f == "T") || (f == "true") || (f == "t")) {       return true;    }
 247         else {  return false;  }
 248 }
 249
 250 /***********************************************************************/
 251
 252 inline float roundDist(float dist, int precision){
 253
 254         return int(dist * precision + 0.5)/float(precision);
 255
 256 }
 257
 258 /***********************************************************************/
 259
 260 inline int getNumNames(string names){
 261
 262         int count = 0;
 263
 264         if(names != ""){
 265                 count = 1;
 266                 for(int i=0;i<names.size();i++){
 267                         if(names[i] == ','){
 268                                 count++;
 269                         }
 270                 }
 271         }
 272
 273         return count;
 274
 275 }
 276
 277 /**************************************************************************************************/
 278
 279 inline vector<vector<double> > binomial(int maxOrder){
 280
 281         vector<vector<double> > binomial(maxOrder+1);
 282
 283     for(int i=0;i<=maxOrder;i++){
 284                 binomial[i].resize(maxOrder+1);
 285                 binomial[i][0]=1;
 286                 binomial[0][i]=0;
 287     }
 288     binomial[0][0]=1;
 289
 290     binomial[1][0]=1;
 291     binomial[1][1]=1;
 292
 293     for(int i=2;i<=maxOrder;i++){
 294                 binomial[1][i]=0;
 295     }
 296
 297     for(int i=2;i<=maxOrder;i++){
 298                 for(int j=1;j<=maxOrder;j++){
 299                         if(i==j){       binomial[i][j]=1;                                                                       }
 300                         if(j>i) {       binomial[i][j]=0;                                                                       }
 301                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
 302                 }
 303     }
 304
 305         return binomial;
 306 }
 307
 308 /***********************************************************************/
 309
 310 inline string getRootName(string longName){
 311
 312         string rootName = longName;
 313
 314         if(longName.find_last_of(".") != longName.npos){
 315                 int pos = longName.find_last_of('.')+1;
 316                 rootName = longName.substr(0, pos);
 317         }
 318
 319         return rootName;
 320 }
 321 /***********************************************************************/
 322
 323 inline string getSimpleName(string longName){
 324
 325         string simpleName = longName;
 326
 327         size_t found;
 328         found=longName.find_last_of("/\\");
 329
 330         if(found != longName.npos){
 331                 simpleName = longName.substr(found+1);
 332         }
 333
 334                 //if(longName.find_last_of("/") != longName.npos){
 335                 //      int pos = longName.find_last_of('/')+1;
 336                 //      simpleName = longName.substr(pos, longName.length());
 337                 //}
 338
 339         return simpleName;
 340 }
 341
 342 /***********************************************************************/
 343
 344 inline int factorial(int num){
 345         int total = 1;
 346
 347         for (int i = 1; i <= num; i++) {
 348                 total *= i;
 349         }
 350
 351         return total;
 352 }
 353 /**************************************************************************************************
 354
 355 double min(double x, double y)
 356 {
 357     if(x<y){    return x;    }
 358     else   {    return y;    }
 359 }
 360
 361 /***********************************************************************/
 362
 363 inline string getPathName(string longName){
 364
 365         string rootPathName = longName;
 366
 367         if(longName.find_last_of("/\\") != longName.npos){
 368                 int pos = longName.find_last_of("/\\")+1;
 369                 rootPathName = longName.substr(0, pos);
 370         }
 371
 372         return rootPathName;
 373 }
 374 /***********************************************************************/
 375
 376 inline string hasPath(string longName){
 377
 378         string path = "";
 379
 380         size_t found;
 381         found=longName.find_last_of("/\\");
 382
 383         if(found != longName.npos){
 384                 path = longName.substr(0, found+1);
 385         }
 386
 387         return path;
 388 }
 389
 390 /***********************************************************************/
 391
 392 inline string getExtension(string longName){
 393
 394         string extension = longName;
 395
 396         if(longName.find_last_of('.') != longName.npos){
 397                 int pos = longName.find_last_of('.');
 398                 extension = longName.substr(pos, longName.length());
 399         }
 400
 401         return extension;
 402 }
 403 /***********************************************************************/
 404 inline bool isBlank(string fileName){
 405
 406         ifstream fileHandle;
 407         fileHandle.open(fileName.c_str());
 408         if(!fileHandle) {
 409                 cout << "Error: Could not open " << fileName << endl;
 410                 return false;
 411         }else {
 412                 //check for blank file
 413                 gobble(fileHandle);
 414                 if (fileHandle.eof()) { fileHandle.close(); return true;  }
 415         }
 416         return false;
 417 }
 418 /***********************************************************************/
 419
 420 inline string getFullPathName(string fileName){
 421         try{
 422
 423         string path = hasPath(fileName);
 424         string newFileName;
 425         int pos;
 426
 427         if (path == "") { return fileName; } //its a simple name
 428         else { //we need to complete the pathname
 429                 // ex. ../../../filename
 430                 // cwd = /user/work/desktop
 431
 432                 string cwd;
 433                 //get current working directory
 434                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 435                         if (path.rfind("./") == -1) { return fileName; } //already complete name
 436                         else { newFileName = fileName.substr(fileName.rfind("./")+2); } //save the complete part of the name
 437
 438                         char* cwdpath = new char[1024];
 439
 440                         size_t size;
 441                         cwdpath=getcwd(cwdpath,size);
 442
 443                         cwd = cwdpath;
 444
 445                         //rip off first '/'
 446                         string simpleCWD;
 447                         if (cwd.length() > 0) { simpleCWD = cwd.substr(1); }
 448
 449                         //break apart the current working directory
 450                         vector<string> dirs;
 451                         while (simpleCWD.find_first_of('/') != -1) {
 452                                 string dir = simpleCWD.substr(0,simpleCWD.find_first_of('/'));
 453                                 simpleCWD = simpleCWD.substr(simpleCWD.find_first_of('/')+1, simpleCWD.length());
 454                                 dirs.push_back(dir);
 455                         }
 456                         //get last one              // ex. ../../../filename = /user/work/desktop/filename
 457                         dirs.push_back(simpleCWD);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 458
 459
 460                         int index = dirs.size()-1;
 461
 462                         while((pos = path.rfind("./")) != -1) { //while you don't have a complete path
 463                                 if (path[(pos-1)] == '.') { //you want your parent directory ../
 464                                         path = path.substr(0, pos-1);
 465                                         index--;
 466                                         if (index == 0) {  break; }
 467                                 }else if (path[(pos-1)] == '/') { //you want the current working dir ./
 468                                         path = path.substr(0, pos);
 469                                 }else if (pos == 1) { break;
 470                                 }else { cout << "cannot resolve path for " <<  fileName << endl; return fileName; }
 471                         }
 472
 473                         for (int i = index; i >= 0; i--) {
 474                                 newFileName = dirs[i] +  "/" + newFileName;
 475                         }
 476
 477                         newFileName =  "/" +  newFileName;
 478                         return newFileName;
 479
 480                 #else
 481                         if (path.rfind(".\\") == -1) { return fileName; } //already complete name
 482                         else { newFileName = fileName.substr(fileName.rfind(".\\")+2); } //save the complete part of the name
 483
 484                         char *cwdpath = NULL;
 485                         cwdpath = getcwd(NULL, 0); // or _getcwd
 486                         if ( cwdpath != NULL) { cwd = cwdpath; }
 487                         else { cwd = "";  }
 488
 489                         //break apart the current working directory
 490                         vector<string> dirs;
 491                         while (cwd.find_first_of('\\') != -1) {
 492                                 string dir = cwd.substr(0,cwd.find_first_of('\\'));
 493                                 cwd = cwd.substr(cwd.find_first_of('\\')+1, cwd.length());
 494                                 dirs.push_back(dir);
 495
 496                         }
 497                         //get last one
 498                         dirs.push_back(cwd);  //ex. dirs[0] = user, dirs[1] = work, dirs[2] = desktop
 499
 500                         int index = dirs.size()-1;
 501
 502                         while((pos = path.rfind(".\\")) != -1) { //while you don't have a complete path
 503                                 if (path[(pos-1)] == '.') { //you want your parent directory ../
 504                                         path = path.substr(0, pos-1);
 505                                         index--;
 506                                         if (index == 0) {  break; }
 507                                 }else if (path[(pos-1)] == '\\') { //you want the current working dir ./
 508                                         path = path.substr(0, pos);
 509                                 }else if (pos == 1) { break;
 510                                 }else {  cout << "cannot resolve path for " <<  fileName << endl;  return fileName; }
 511                         }
 512
 513                         for (int i = index; i >= 0; i--) {
 514                                 newFileName = dirs[i] +  "\\" + newFileName;
 515                         }
 516
 517                         return newFileName;
 518
 519                 #endif
 520         }
 521         }
 522         catch(exception& e) {
 523                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function getFullPathName. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 524                 exit(1);
 525         }
 526 }
 527 /***********************************************************************/
 528
 529 inline int openInputFile(string fileName, ifstream& fileHandle, string m){
 530
 531         //get full path name
 532         string completeFileName = getFullPathName(fileName);
 533
 534         fileHandle.open(completeFileName.c_str());
 535         if(!fileHandle) {
 536                 return 1;
 537         }else {
 538                 //check for blank file
 539                 gobble(fileHandle);
 540                 return 0;
 541         }
 542 }
 543 /***********************************************************************/
 544
 545 inline int openInputFile(string fileName, ifstream& fileHandle){
 546
 547         //get full path name
 548         string completeFileName = getFullPathName(fileName);
 549
 550         fileHandle.open(completeFileName.c_str());
 551         if(!fileHandle) {
 552                 cout << "Error: Could not open " << completeFileName << endl;
 553                 return 1;
 554         }
 555         else {
 556                 //check for blank file
 557                 gobble(fileHandle);
 558                 if (fileHandle.eof()) { cout << completeFileName << " is blank. Please correct." << endl;  return 1;  }
 559
 560                 return 0;
 561         }
 562
 563 }
 564 /***********************************************************************/
 565
 566 inline int renameFile(string oldName, string newName){
 567
 568         ifstream inTest;
 569         int exist = openInputFile(newName, inTest, "");
 570
 571 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 572         if (exist == 0) { //you could open it so you want to delete it
 573                 inTest.close();
 574                 string command = "rm " + newName;
 575                 system(command.c_str());
 576         }
 577
 578         string command = "mv " + oldName + " " + newName;
 579         system(command.c_str());
 580 #else
 581         remove(newName.c_str());
 582         int renameOk = rename(oldName.c_str(), newName.c_str());
 583 #endif
 584         return 0;
 585 }
 586
 587 /***********************************************************************/
 588
 589 inline int openOutputFile(string fileName, ofstream& fileHandle){
 590
 591         string completeFileName = getFullPathName(fileName);
 592
 593         fileHandle.open(completeFileName.c_str(), ios::trunc);
 594         if(!fileHandle) {
 595                 cout << "Error: Could not open " << completeFileName << endl;
 596                 return 1;
 597         }
 598         else {
 599                 return 0;
 600         }
 601
 602 }
 603
 604 /***********************************************************************/
 605
 606 inline int getNumSeqs(ifstream& file){
 607
 608         int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
 609         file.seekg(0);
 610         return numSeqs;
 611
 612 }
 613 /***********************************************************************/
 614
 615 inline bool inVector(string member, vector<string> group){
 616
 617         for (int i = 0; i < group.size(); i++) {
 618                 if (group[i] == member) {  return true;         }
 619         }
 620
 621         return false;
 622 }
 623 /***********************************************************************/
 624
 625 //This function parses the estimator options and puts them in a vector
 626 inline void splitAtDash(string& estim, vector<string>& container) {
 627         try {
 628                 string individual;
 629
 630                 while (estim.find_first_of('-') != -1) {
 631                         individual = estim.substr(0,estim.find_first_of('-'));
 632                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 633                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 634                                 container.push_back(individual);
 635                         }
 636                 }
 637                 //get last one
 638                 container.push_back(estim);
 639         }
 640         catch(exception& e) {
 641                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 642                 exit(1);
 643         }
 644 }
 645
 646 /***********************************************************************/
 647 //This function parses the label options and puts them in a set
 648 inline void splitAtDash(string& estim, set<string>& container) {
 649         try {
 650                 string individual;
 651
 652                 while (estim.find_first_of('-') != -1) {
 653                         individual = estim.substr(0,estim.find_first_of('-'));
 654                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 655                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 656                                 container.insert(individual);
 657                         }
 658                 }
 659                 //get last one
 660                 container.insert(estim);
 661         }
 662         catch(exception& e) {
 663                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 664                 exit(1);
 665         }
 666 }
 667 /***********************************************************************/
 668 //This function parses the line options and puts them in a set
 669 inline void splitAtDash(string& estim, set<int>& container) {
 670         try {
 671                 string individual;
 672                 int lineNum;
 673
 674                 while (estim.find_first_of('-') != -1) {
 675                         individual = estim.substr(0,estim.find_first_of('-'));
 676                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 677                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 678                                 convert(individual, lineNum); //convert the string to int
 679                                 container.insert(lineNum);
 680                         }
 681                 }
 682                 //get last one
 683                 convert(estim, lineNum); //convert the string to int
 684                 container.insert(lineNum);
 685         }
 686         catch(exception& e) {
 687                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtDash. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 688                 exit(1);
 689         }
 690 }
 691 /***********************************************************************/
 692 //This function parses the a string and puts peices in a vector
 693 inline void splitAtComma(string& estim, vector<string>& container) {
 694         try {
 695                 string individual;
 696
 697                 while (estim.find_first_of(',') != -1) {
 698                         individual = estim.substr(0,estim.find_first_of(','));
 699                         if ((estim.find_first_of(',')+1) <= estim.length()) { //checks to make sure you don't have comma at end of string
 700                                 estim = estim.substr(estim.find_first_of(',')+1, estim.length());
 701                                 container.push_back(individual);
 702                         }
 703                 }
 704                 //get last one
 705                 container.push_back(estim);
 706         }
 707         catch(exception& e) {
 708                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 709                 exit(1);
 710         }
 711 }
 712 /***********************************************************************/
 713
 714 //This function splits up the various option parameters
 715 inline void splitAtComma(string& prefix, string& suffix){
 716         try {
 717                 prefix = suffix.substr(0,suffix.find_first_of(','));
 718                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 719                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
 720                         string space = " ";
 721                         while(suffix.at(0) == ' ')
 722                                 suffix = suffix.substr(1, suffix.length());
 723                 }
 724
 725         }
 726         catch(exception& e) {
 727                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtComma. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 728                 exit(1);
 729         }
 730 }
 731 /***********************************************************************/
 732
 733 //This function separates the key value from the option value i.e. dist=96_...
 734 inline void splitAtEquals(string& key, string& value){
 735         try {
 736                 if(value.find_first_of('=') != -1){
 737                         key = value.substr(0,value.find_first_of('='));
 738                         if ((value.find_first_of('=')+1) <= value.length()) {
 739                                 value = value.substr(value.find_first_of('=')+1, value.length());
 740                         }
 741                 }else{
 742                         key = value;
 743                         value = 1;
 744                 }
 745         }
 746         catch(exception& e) {
 747                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function splitAtEquals. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 748                 exit(1);
 749         }
 750 }
 751 /**************************************************************************************************/
 752
 753 inline bool inUsersGroups(string groupname, vector<string> Groups) {
 754         try {
 755                 for (int i = 0; i < Groups.size(); i++) {
 756                         if (groupname == Groups[i]) { return true; }
 757                 }
 758                 return false;
 759         }
 760         catch(exception& e) {
 761                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 762                 exit(1);
 763         }
 764 }
 765 /**************************************************************************************************/
 766 //returns true if any of the strings in first vector are in second vector
 767 inline bool inUsersGroups(vector<string> groupnames, vector<string> Groups) {
 768         try {
 769
 770                 for (int i = 0; i < groupnames.size(); i++) {
 771                         if (inUsersGroups(groupnames[i], Groups)) { return true; }
 772                 }
 773                 return false;
 774         }
 775         catch(exception& e) {
 776                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function inUsersGroups. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 777                 exit(1);
 778         }
 779 }
 780 /***********************************************************************/
 781 //this function determines if the user has given us labels that are smaller than the given label.
 782 //if so then it returns true so that the calling function can run the previous valid distance.
 783 //it's a "smart" distance function.  It also checks for invalid labels.
 784 inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
 785         try {
 786
 787                 set<string>::iterator it;
 788                 vector<float> orderFloat;
 789                 map<string, float> userMap;  //the conversion process removes trailing 0's which we need to put back
 790                 map<string, float>::iterator it2;
 791                 float labelFloat;
 792                 bool smaller = false;
 793
 794                 //unique is the smallest line
 795                 if (label == "unique") {  return false;  }
 796                 else { convert(label, labelFloat); }
 797
 798                 //go through users set and make them floats
 799                 for(it = userLabels.begin(); it != userLabels.end(); ++it) {
 800
 801                         float temp;
 802                         if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
 803                                 convert(*it, temp);
 804                                 orderFloat.push_back(temp);
 805                                 userMap[*it] = temp;
 806                         }else if (*it == "unique") {
 807                                 orderFloat.push_back(-1.0);
 808                                 userMap["unique"] = -1.0;
 809                         }else {
 810                                 if (errorOff == "") {  cout << *it << " is not a valid label." << endl;  }
 811                                 userLabels.erase(*it);
 812                                 it--;
 813                         }
 814                 }
 815
 816                 //sort order
 817                 sort(orderFloat.begin(), orderFloat.end());
 818
 819                 /*************************************************/
 820                 //is this label bigger than any of the users labels
 821                 /*************************************************/
 822
 823                 //loop through order until you find a label greater than label
 824                 for (int i = 0; i < orderFloat.size(); i++) {
 825                         if (orderFloat[i] < labelFloat) {
 826                                 smaller = true;
 827                                 if (orderFloat[i] == -1) {
 828                                         if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
 829                                         userLabels.erase("unique");
 830                                 }
 831                                 else {
 832                                         if (errorOff == "") { cout << "Your file does not include the label " << endl; }
 833                                         string s = "";
 834                                         for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
 835                                                 if (it2->second == orderFloat[i]) {
 836                                                         s = it2->first;
 837                                                         //remove small labels
 838                                                         userLabels.erase(s);
 839                                                         break;
 840                                                 }
 841                                         }
 842                                         if (errorOff == "") {cout << s <<  ". I will use the next smallest distance. " << endl; }
 843                                 }
 844                         //since they are sorted once you find a bigger one stop looking
 845                         }else { break; }
 846                 }
 847
 848                 return smaller;
 849
 850         }
 851         catch(exception& e) {
 852                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function anyLabelsToProcess. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 853                 exit(1);
 854         }
 855 }
 856
 857 /**************************************************************************************************/
 858 inline void appendFiles(string temp, string filename) {
 859         try{
 860                 ofstream output;
 861                 ifstream input;
 862
 863                 //open output file in append mode
 864                 openOutputFileAppend(filename, output);
 865                 openInputFile(temp, input);
 866
 867                 while(char c = input.get()){
 868                         if(input.eof())         {       break;                  }
 869                         else                            {       output << c;    }
 870                 }
 871
 872                 input.close();
 873                 output.close();
 874         }
 875         catch(exception& e) {
 876                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function appendFiles. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 877                 exit(1);
 878         }
 879 }
 880
 881 /**************************************************************************************************/
 882 inline string sortFile(string distFile){
 883         try {
 884                 string outfile = getRootName(distFile) + "sorted.dist";
 885
 886                 //if you can, use the unix sort since its been optimized for years
 887                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 888                         string command = "sort -n -k +3 " + distFile + " -o " + outfile;
 889                         system(command.c_str());
 890                 #else //you are stuck with my best attempt...
 891                         //windows sort does not have a way to specify a column, only a character in the line
 892                         //since we cannot assume that the distance will always be at the the same character location on each line
 893                         //due to variable sequence name lengths, I chose to force the distance into first position, then sort and then put it back.
 894
 895                         //read in file line by file and put distance first
 896                         string tempDistFile = distFile + ".temp";
 897                         ifstream input;
 898                         ofstream output;
 899                         openInputFile(distFile, input);
 900                         openOutputFile(tempDistFile, output);
 901
 902                         string firstName, secondName;
 903                         float dist;
 904                         while (input) {
 905                                 input >> firstName >> secondName >> dist;
 906                                 output << dist << '\t' << firstName << '\t' << secondName << endl;
 907                                 gobble(input);
 908                         }
 909                         input.close();
 910                         output.close();
 911
 912
 913                         //sort using windows sort
 914                         string tempOutfile = outfile + ".temp";
 915                         string command = "sort " + tempDistFile + " /O " + tempOutfile;
 916                         system(command.c_str());
 917
 918                         //read in sorted file and put distance at end again
 919                         ifstream input2;
 920                         openInputFile(tempOutfile, input2);
 921                         openOutputFile(outfile, output);
 922
 923                         while (input2) {
 924                                 input2 >> dist >> firstName >> secondName;
 925                                 output << firstName << '\t' << secondName << '\t' << dist << endl;
 926                                 gobble(input2);
 927                         }
 928                         input2.close();
 929                         output.close();
 930
 931                         //remove temp files
 932                         remove(tempDistFile.c_str());
 933                         remove(tempOutfile.c_str());
 934                 #endif
 935
 936                 return outfile;
 937         }
 938         catch(exception& e) {
 939                 cout << "Standard Error: " << e.what() << " has occurred in the mothur.h function sortfile. Please contact Pat Schloss at mothur.bugs@gmail.com." << "\n";
 940                 exit(1);
 941         }
 942 }
 943 /**************************************************************************************************/
 944 #endif
 945