utilities.hpp

   1 #ifndef UTILITIES_H
   2 #define UTILITIES_H
   3
   4 using namespace std;
   5
   6 #include "mothur.h"
   7
   8 typedef unsigned long long ull;
   9
  10 /***********************************************************************/
  11
  12 // snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
  13 // works for now, but there should be a way to do it without killing the whole program
  14
  15 class BadConversion : public runtime_error {
  16 public:
  17         BadConversion(const string& s) : runtime_error(s){ }
  18 };
  19
  20 //**********************************************************************************************************************
  21
  22 template<typename T>
  23 inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
  24         istringstream i(s);
  25         char c;
  26         if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
  27                 throw BadConversion(s);
  28 }
  29 //**********************************************************************************************************************
  30
  31 template<typename T>
  32 inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
  33         istringstream i(s);
  34         char c;
  35         if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
  36         {
  37                 cout << "'" << s << "' is unable to be converted into an integer.\n";
  38                 return false;
  39         }
  40         return true;
  41 }
  42
  43 //**********************************************************************************************************************
  44
  45 template<typename T>
  46 string toString(const T&x){
  47     stringstream output;
  48     output << x;
  49     return output.str();
  50 }
  51
  52 //**********************************************************************************************************************
  53
  54 template<typename T>
  55 string toString(const T&x, int i){
  56         stringstream output;
  57
  58         output.precision(i);
  59     output << fixed << x;
  60
  61     return output.str();
  62 }
  63
  64
  65 /***********************************************************************/
  66
  67 inline void gobble(istream& f){
  68
  69         char d;
  70     while(isspace(d=f.get()))           {;}
  71         f.putback(d);
  72
  73 }
  74
  75 /***********************************************************************/
  76
  77 inline float roundDist(float dist, int precision){
  78
  79         return int(dist * precision + 0.5)/float(precision);
  80
  81 }
  82
  83 /***********************************************************************/
  84
  85 inline int getNumNames(string names){
  86
  87         int count = 0;
  88
  89         if(names != ""){
  90                 count = 1;
  91                 for(int i=0;i<names.size();i++){
  92                         if(names[i] == ','){
  93                                 count++;
  94                         }
  95                 }
  96         }
  97
  98         return count;
  99
 100 }
 101
 102 /**************************************************************************************************/
 103
 104 inline vector<vector<double> > binomial(int maxOrder){
 105
 106         vector<vector<double> > binomial(maxOrder+1);
 107
 108     for(int i=0;i<=maxOrder;i++){
 109                 binomial[i].resize(maxOrder+1);
 110                 binomial[i][0]=1;
 111                 binomial[0][i]=0;
 112     }
 113     binomial[0][0]=1;
 114
 115     binomial[1][0]=1;
 116     binomial[1][1]=1;
 117
 118     for(int i=2;i<=maxOrder;i++){
 119                 binomial[1][i]=0;
 120     }
 121
 122     for(int i=2;i<=maxOrder;i++){
 123                 for(int j=1;j<=maxOrder;j++){
 124                         if(i==j){       binomial[i][j]=1;                                                                       }
 125                         if(j>i) {       binomial[i][j]=0;                                                                       }
 126                         else    {       binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j];     }
 127                 }
 128     }
 129
 130         return binomial;
 131 }
 132
 133 /***********************************************************************/
 134
 135 inline string getRootName(string longName){
 136
 137         string rootName = longName;
 138
 139         if(longName.find_last_of(".") != longName.npos){
 140                 int pos = longName.find_last_of('.')+1;
 141                 rootName = longName.substr(0, pos);
 142         }
 143
 144         return rootName;
 145 }
 146 /***********************************************************************/
 147
 148 inline string getSimpleName(string longName){
 149
 150         string simpleName = longName;
 151
 152         if(longName.find_last_of("/") != longName.npos){
 153                 int pos = longName.find_last_of('/')+1;
 154                 simpleName = longName.substr(pos, longName.length());
 155         }
 156
 157         return simpleName;
 158 }
 159
 160 /***********************************************************************/
 161
 162 inline string getPathName(string longName){
 163
 164         string rootPathName = longName;
 165
 166         if(longName.find_last_of("/") != longName.npos){
 167                 int pos = longName.find_last_of('/')+1;
 168                 rootPathName = longName.substr(0, pos);
 169         }
 170
 171         return rootPathName;
 172 }
 173
 174 /***********************************************************************/
 175
 176 inline int openInputFile(string fileName, ifstream& fileHandle){
 177
 178         fileHandle.open(fileName.c_str());
 179         if(!fileHandle) {
 180                 cerr << "Error: Could not open " << fileName << endl;
 181                 return 1;
 182         }
 183         else {
 184                 return 0;
 185         }
 186
 187 }
 188
 189 /***********************************************************************/
 190
 191 inline int openOutputFile(string fileName, ofstream& fileHandle){
 192
 193         fileHandle.open(fileName.c_str(), ios::trunc);
 194         if(!fileHandle) {
 195                 cerr << "Error: Could not open " << fileName << endl;
 196                 return 1;
 197         }
 198         else {
 199                 return 0;
 200         }
 201
 202 }
 203
 204 /***********************************************************************/
 205
 206 //This function parses the estimator options and puts them in a vector
 207 inline void splitAtDash(string& estim, vector<string>& container) {
 208         try {
 209                 string individual;
 210
 211                 while (estim.find_first_of('-') != -1) {
 212                         individual = estim.substr(0,estim.find_first_of('-'));
 213                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 214                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 215                                 container.push_back(individual);
 216                         }
 217                 }
 218                 //get last one
 219                 container.push_back(estim);
 220         }
 221         catch(exception& e) {
 222                 cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 223                 exit(1);
 224         }
 225         catch(...) {
 226                 cout << "An unknown error has occurred in the utilities class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 227                 exit(1);
 228         }
 229
 230 }
 231
 232 /***********************************************************************/
 233 //This function parses the label options and puts them in a set
 234 inline void splitAtDash(string& estim, set<string>& container) {
 235         try {
 236                 string individual;
 237
 238                 while (estim.find_first_of('-') != -1) {
 239                         individual = estim.substr(0,estim.find_first_of('-'));
 240                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 241                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 242                                 container.insert(individual);
 243                         }
 244                 }
 245                 //get last one
 246                 container.insert(estim);
 247         }
 248         catch(exception& e) {
 249                 cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 250                 exit(1);
 251         }
 252         catch(...) {
 253                 cout << "An unknown error has occurred in the utilities class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 254                 exit(1);
 255         }
 256
 257 }
 258 /***********************************************************************/
 259 //This function parses the line options and puts them in a set
 260 inline void splitAtDash(string& estim, set<int>& container) {
 261         try {
 262                 string individual;
 263                 int lineNum;
 264
 265                 while (estim.find_first_of('-') != -1) {
 266                         individual = estim.substr(0,estim.find_first_of('-'));
 267                         if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
 268                                 estim = estim.substr(estim.find_first_of('-')+1, estim.length());
 269                                 convert(individual, lineNum); //convert the string to int
 270                                 container.insert(lineNum);
 271                         }
 272                 }
 273                 //get last one
 274                 convert(estim, lineNum); //convert the string to int
 275                 container.insert(lineNum);
 276         }
 277         catch(exception& e) {
 278                 cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 279                 exit(1);
 280         }
 281         catch(...) {
 282                 cout << "An unknown error has occurred in the utilities class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 283                 exit(1);
 284         }
 285
 286 }
 287 /***********************************************************************/
 288
 289 //This function splits up the various option parameters
 290 inline void splitAtComma(string& prefix, string& suffix){
 291         try {
 292                 prefix = suffix.substr(0,suffix.find_first_of(','));
 293                 if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
 294                         suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
 295                         string space = " ";
 296                         while(suffix.at(0) == ' ')
 297                                 suffix = suffix.substr(1, suffix.length());
 298                 }
 299
 300         }
 301         catch(exception& e) {
 302                 cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 303                 exit(1);
 304         }
 305         catch(...) {
 306                 cout << "An unknown error has occurred in the utilities class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 307                 exit(1);
 308         }
 309
 310 }
 311 /***********************************************************************/
 312
 313 //This function separates the key value from the option value i.e. dist=96_...
 314 inline void splitAtEquals(string& key, string& value){
 315         try {
 316                 if(value.find_first_of('=') != -1){
 317                         key = value.substr(0,value.find_first_of('='));
 318                         if ((value.find_first_of('=')+1) <= value.length()) {
 319                                 value = value.substr(value.find_first_of('=')+1, value.length());
 320                         }
 321                 }else{
 322                         key = value;
 323                         value = 1;
 324                 }
 325         }
 326         catch(exception& e) {
 327                 cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 328                 exit(1);
 329         }
 330         catch(...) {
 331                 cout << "An unknown error has occurred in the utilities class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 332                 exit(1);
 333         }
 334
 335 }
 336 /*******************************************************/
 337
 338
 339
 340 #endif