validcalculator.cpp

   1 /*
   2  *  validcalculator.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/5/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "validcalculator.h"
  11
  12 /********************************************************************/
  13 ValidCalculators::ValidCalculators() {
  14         try {
  15                  initialSingle();
  16                  initialShared();
  17                  initialRarefaction();
  18                  initialSharedRarefact();
  19                  initialSummary();
  20                  initialSharedSummary();
  21                  initialVennSingle();
  22                  initialVennShared();
  23                  initialTreeGroups();
  24         }
  25         catch(exception& e) {
  26                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29         catch(...) {
  30                 cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  31                 exit(1);
  32         }
  33 }
  34
  35 /********************************************************************/
  36
  37 ValidCalculators::~ValidCalculators() {}
  38
  39 /********************************************************************/
  40
  41 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
  42         try {
  43                 //are you looking for a calculator for a single parameter
  44                 if (parameter == "single") {
  45                         //is it valid
  46                         if ((single.find(calculator)) != (single.end())) {
  47                                 return true;
  48                         }else {
  49                                 cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
  50                                 for (it = single.begin(); it != single.end(); it++) {
  51                                         cout << it->first << ", ";
  52                                 }
  53                                 cout << endl;
  54                                 return false; }
  55                 //are you looking for a calculator for a shared parameter
  56                 }else if (parameter == "shared") {
  57                         //is it valid
  58                         if ((shared.find(calculator)) != (shared.end())) {
  59                                 return true;
  60                         }else {
  61                                 cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
  62                                 for (it = shared.begin(); it != shared.end(); it++) {
  63                                         cout << it->first << ", ";
  64                                 }
  65                                 cout << endl;
  66                                 return false; }
  67                 //are you looking for a calculator for a rarefaction parameter
  68                 }else if (parameter == "rarefaction") {
  69                         //is it valid
  70                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
  71                                 return true;
  72                         }else {
  73                                 cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
  74                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
  75                                         cout << it->first << ", ";
  76                                 }
  77                                 cout << endl;
  78                                 return false; }
  79                 //are you looking for a calculator for a summary parameter
  80                 }else if (parameter == "summary") {
  81                         //is it valid
  82                         if ((summary.find(calculator)) != (summary.end())) {
  83                                 return true;
  84                         }else {
  85                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  86                                 for (it = summary.begin(); it != summary.end(); it++) {
  87                                         cout << it->first << ", ";
  88                                 }
  89                                 cout << endl;
  90                                 return false; }
  91                 //are you looking for a calculator for a sharedsummary parameter
  92                 }else if (parameter == "sharedsummary") {
  93                         //is it valid
  94                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
  95                                 return true;
  96                         }else {
  97                                 cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
  98                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
  99                                         cout << it->first << ", ";
 100                                 }
 101                                 cout << endl;
 102                                 return false; }
 103                 }else if (parameter == "sharedrarefaction") {
 104                         //is it valid
 105                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 106                                 return true;
 107                         }else {
 108                                 cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
 109                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 110                                         cout << it->first << ", ";
 111                                 }
 112                                 cout << endl;
 113                                 return false; }
 114                 }else if (parameter == "vennsingle") {
 115                         //is it valid
 116                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 117                                 return true;
 118                         }else {
 119                                 cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
 120                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 121                                         cout << it->first << ", ";
 122                                 }
 123                                 cout << endl;
 124                                 return false; }
 125                 }else if (parameter == "vennshared") {
 126                         //is it valid
 127                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 128                                 return true;
 129                         }else {
 130                                 cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
 131                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 132                                         cout << it->first << ", ";
 133                                 }
 134                                 cout << endl;
 135                                 return false; }
 136                 }else if (parameter == "treegroup") {
 137                         //is it valid
 138                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 139                                 return true;
 140                         }else {
 141                                 cout << calculator << " is not a valid estimator for the tree.groups command in shared mode and will be disregarded. Valid estimators are ";
 142                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 143                                         cout << it->first << ", ";
 144                                 }
 145                                 cout << endl;
 146                                 return false; }
 147
 148                 //not a valid parameter
 149                 }else { return false; }
 150
 151         }
 152         catch(exception& e) {
 153                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 154                 exit(1);
 155         }
 156         catch(...) {
 157                 cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 158                 exit(1);
 159         }
 160 }
 161
 162 /********************************************************************/
 163 void ValidCalculators::initialSingle() {
 164         try {
 165                 single["sobs"]          = "sobs";
 166                 single["chao"]              = "chao";
 167                 single["ace"]               = "ace";
 168                 single["jack"]              = "jack";
 169                 single["shannon"]           = "shannon";
 170                 single["npshannon"]     = "npshannon";
 171                 single["simpson"]           = "simpson";
 172                 single["bergerparker"]  = "bergerparker";
 173                 single["bootstrap"]     = "bootstrap";
 174                 single["geom"]          = "geom";
 175                 single["logsd"]         = "logsd";
 176                 single["qstat"]         = "qstat";
 177                 single["bstick"]        = "bstick";
 178                 single["nseqs"]                 = "nseqs";
 179                 single["default"]           = "default";
 180         }
 181         catch(exception& e) {
 182                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 183                 exit(1);
 184         }
 185         catch(...) {
 186                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 187                 exit(1);
 188         }
 189 }
 190
 191 /********************************************************************/
 192 void ValidCalculators::initialShared() {
 193         try {
 194                 shared["sharedsobs"]                    = "sharedsobs";
 195                 shared["sharedchao"]                    = "sharedchao";
 196                 shared["sharedace"]                             = "sharedace";
 197                 shared["jabund"]                                = "jabund";
 198                 shared["sorensonabund"]                 = "sorensonabund";
 199                 shared["jclass"]                                = "jclass";
 200                 shared["sorclass"]                              = "sorclass";
 201                 shared["jest"]                                  = "jest";
 202                 shared["sorest"]                                = "sorest";
 203                 shared["thetayc"]                               = "thetayc";
 204                 shared["thetan"]                                = "thetan";
 205                 shared["kstest"]                                = "kstest";
 206                 shared["bdiversity"]                    = "bdiversity";
 207                 shared["sharednseqs"]                   = "sharednseqs";
 208                 shared["ochiai"]                                = "ochiai";
 209                 shared["anderberg"]                             = "anderberg";
 210                 shared["kulczynski"]                    = "kulczynski";
 211                 shared["kulczynskicody"]                = "kulczynskicody";
 212                 shared["lennon"]                                = "lennon";
 213                 shared["morisitahorn"]                  = "morisitahorn";
 214                 shared["braycurtis"]                    = "braycurtis";
 215                 shared["default"]                   = "default";
 216         }
 217         catch(exception& e) {
 218                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 219                 exit(1);
 220         }
 221         catch(...) {
 222                 cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 223                 exit(1);
 224         }
 225 }
 226
 227 /********************************************************************/
 228 void ValidCalculators::initialRarefaction() {
 229         try {
 230                 rarefaction["sobs"]                     = "sobs";
 231                 rarefaction["chao"]                     = "chao";
 232                 rarefaction["ace"]                      = "ace";
 233                 rarefaction["jack"]                     = "jack";
 234                 rarefaction["shannon"]          = "shannon";
 235                 rarefaction["npshannon"]        = "npshannon";
 236                 rarefaction["simpson"]          = "simpson";
 237                 rarefaction["bootstrap"]        = "bootstrap";
 238                 rarefaction["nseqs"]            = "nseqs";
 239                 rarefaction["default"]      = "default";
 240         }
 241         catch(exception& e) {
 242                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 243                 exit(1);
 244         }
 245         catch(...) {
 246                 cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 247                 exit(1);
 248         }
 249 }
 250
 251 /********************************************************************/
 252
 253 void ValidCalculators::initialSummary() {
 254         try {
 255                 summary["sobs"]                 = "sobs";
 256                 summary["chao"]                 = "chao";
 257                 summary["ace"]                  = "ace";
 258                 summary["jack"]                 = "jack";
 259                 summary["shannon"]              = "shannon";
 260                 summary["npshannon"]    = "npshannon";
 261                 summary["simpson"]              = "simpson";
 262                 summary["bergerparker"] = "bergerparker";
 263                 summary["geom"]         = "geom";
 264                 summary["bootstrap"]    = "bootstrap";
 265                 summary["logsd"]        = "logsd";
 266                 summary["qstat"]        = "qstat";
 267                 summary["bstick"]       = "bstick";
 268                 summary["nseqs"]                = "nseqs";
 269                 summary["default"]          = "default";
 270         }
 271         catch(exception& e) {
 272                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 273                 exit(1);
 274         }
 275         catch(...) {
 276                 cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 277                 exit(1);
 278         }
 279 }
 280
 281 /********************************************************************/
 282 void ValidCalculators::initialSharedSummary() {
 283         try {
 284                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 285                 sharedsummary["sharedchao"]                             = "sharedchao";
 286                 sharedsummary["sharedace"]                              = "sharedace";
 287                 sharedsummary["jabund"]                                 = "jabund";
 288                 sharedsummary["sorensonabund"]                  = "sorensonabund";
 289                 sharedsummary["jclass"]                                 = "jclass";
 290                 sharedsummary["sorclass"]                               = "sorclass";
 291                 sharedsummary["jest"]                                   = "jest";
 292                 sharedsummary["sorest"]                                 = "sorest";
 293                 sharedsummary["thetayc"]                                = "thetayc";
 294                 sharedsummary["thetan"]                                 = "thetan";
 295                 sharedsummary["kstest"]                                 = "kstest";
 296                 sharedsummary["bdiversity"]                             = "bdiversity";
 297                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 298                 sharedsummary["ochiai"]                                 = "ochiai";
 299                 sharedsummary["anderberg"]                              = "anderberg";
 300                 sharedsummary["kulczynski"]                             = "kulczynski";
 301                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 302                 sharedsummary["lennon"]                                 = "lennon";
 303                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 304                 sharedsummary["braycurtis"]                             = "braycurtis";
 305                 sharedsummary["default"]                                = "default";
 306         }
 307         catch(exception& e) {
 308                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 309                 exit(1);
 310         }
 311         catch(...) {
 312                 cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 313                 exit(1);
 314         }
 315 }
 316
 317
 318 /********************************************************************/
 319
 320 void ValidCalculators::initialSharedRarefact() {
 321         try {
 322                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 323                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 324                 sharedrarefaction["default"]        = "default";
 325         }
 326         catch(exception& e) {
 327                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. 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 ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 332                 exit(1);
 333         }
 334 }
 335
 336
 337 /********************************************************************/
 338 void ValidCalculators::initialVennSingle() {
 339         try {
 340                 vennsingle["sobs"]              = "sobs";
 341                 vennsingle["chao"]                  = "chao";
 342                 vennsingle["ace"]                       = "ace";
 343                 vennsingle["jack"]                  = "jack";
 344                 vennsingle["default"]           = "default";
 345         }
 346         catch(exception& e) {
 347                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 348                 exit(1);
 349         }
 350         catch(...) {
 351                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 352                 exit(1);
 353         }
 354 }
 355
 356 /********************************************************************/
 357 void ValidCalculators::initialVennShared() {
 358         try {
 359                 vennshared["sharedsobs"]        = "sharedsobs";
 360                 vennshared["sharedchao"]        = "sharedchao";
 361                 vennshared["sharedace"]         = "sharedace";
 362                 vennshared["default"]           = "default";
 363         }
 364         catch(exception& e) {
 365                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 366                 exit(1);
 367         }
 368         catch(...) {
 369                 cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 370                 exit(1);
 371         }
 372 }
 373
 374 /********************************************************************/
 375 void ValidCalculators::initialTreeGroups() {
 376         try {
 377                 treegroup["jabund"]                                     = "jabund";
 378                 treegroup["sorensonabund"]                      = "sorensonabund";
 379                 treegroup["jclass"]                                     = "jclass";
 380                 treegroup["sorclass"]                           = "sorclass";
 381                 treegroup["jest"]                                       = "jest";
 382                 treegroup["sorest"]                                     = "sorest";
 383                 treegroup["thetayc"]                            = "thetayc";
 384                 treegroup["thetan"]                                     = "thetan";
 385                 treegroup["morisitahorn"]                       = "morisitahorn";
 386         }
 387         catch(exception& e) {
 388                 cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 389                 exit(1);
 390         }
 391         catch(...) {
 392                 cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 393                 exit(1);
 394         }
 395 }
 396
 397
 398 /********************************************************************/
 399
 400
 401
 402