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