validparameter.cpp

   1 /*
   2  *  validparameter.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 "validparameter.h"
  11
  12 /***********************************************************************/
  13
  14 ValidParameters::ValidParameters() {
  15         try {
  16                 initialReaddist();
  17                 initialReadotu();
  18                 initialReadtree();
  19                 initialCluster();
  20                 initialDeconvolute();
  21                 initialParsimony();
  22                 initialCollectsingle();
  23                 initialCollectshared();
  24                 initialRarefactsingle();
  25                 initialRarefactshared();
  26                 initialSummarysingle();
  27                 initialSummaryshared();
  28                 initialUnifracweighted();
  29                 initialUnifracunweighted();
  30                 initialLibshuff();
  31         }
  32         catch(exception& e) {
  33                 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  34                 exit(1);
  35         }
  36         catch(...) {
  37                 cout << "An unknown error has occurred in the ValidParameters class function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  38                 exit(1);
  39         }
  40 }
  41
  42 /***********************************************************************/
  43
  44 ValidParameters::~ValidParameters() {}
  45
  46 /***********************************************************************/
  47 bool ValidParameters::isValidParameter(string parameter, string command) {
  48         try {
  49
  50                 if (command == "read.dist") {
  51                         //is it valid
  52                         if ((readdist.find(parameter)) != (readdist.end())) {
  53                                 return true;
  54                         }else {
  55                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
  56                                 for (it = readdist.begin(); it != readdist.end(); it++) {
  57                                         cout << it->first << ", ";
  58                                 }
  59                                 cout << endl;
  60                                 return false; }
  61                 }else if (command == "read.otu") {
  62                         //is it valid
  63                         if ((readotu.find(parameter)) != (readotu.end())) {
  64                                 return true;
  65                         }else {
  66                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
  67                                 for (it = readotu.begin(); it != readotu.end(); it++) {
  68                                         cout << it->first << ", ";
  69                                 }
  70                                 cout << endl;
  71                                 return false; }
  72                 //are you looking for a calculator for a rarefaction parameter
  73                 }else if (command == "read.tree") {
  74                         //is it valid
  75                         if ((readtree.find(parameter)) != (readtree.end())) {
  76                                 return true;
  77                         }else {
  78                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
  79                                 for (it = readtree.begin(); it != readtree.end(); it++) {
  80                                         cout << it->first << ", ";
  81                                 }
  82                                 cout << endl;
  83                                 return false; }
  84                 //are you looking for a calculator for a summary parameter
  85                 }else if (command == "cluster") {
  86                         //is it valid
  87                         if ((cluster.find(parameter)) != (cluster.end())) {
  88                                 return true;
  89                         }else {
  90                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
  91                                 for (it = cluster.begin(); it != cluster.end(); it++) {
  92                                         cout << it->first << ", ";
  93                                 }
  94                                 cout << endl;
  95                                 return false; }         //are you looking for a calculator for a sharedsummary parameter
  96                 }else if (command == "deconvolute") {
  97                         //is it valid
  98                         if ((deconvolute.find(parameter)) != (deconvolute.end())) {
  99                                 return true;
 100                         }else {
 101                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 102                                 for (it = deconvolute.begin(); it != deconvolute.end(); it++) {
 103                                         cout << it->first;
 104                                 }
 105                                 cout << endl;
 106                                 return false; }
 107                 }else if (command == "parsimony") {
 108                         //is it valid
 109                         if ((parsimony.find(parameter)) != (parsimony.end())) {
 110                                 return true;
 111                         }else {
 112                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 113                                 for (it = parsimony.begin(); it != parsimony.end(); it++) {
 114                                         cout << it->first << ", ";
 115                                 }
 116                                 cout << endl;
 117                                 return false; }
 118                 }else if (command == "collect.single") {
 119                         //is it valid
 120                         if ((collectsingle.find(parameter)) != (collectsingle.end())) {
 121                                 return true;
 122                         }else {
 123                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 124                                 for (it = collectsingle.begin(); it != collectsingle.end(); it++) {
 125                                         cout << it->first << ", ";
 126                                 }
 127                                 cout << endl;
 128                                 return false; }
 129                 }else if (command == "collect.shared") {
 130                         //is it valid
 131                         if ((collectshared.find(parameter)) != (collectshared.end())) {
 132                                 return true;
 133                         }else {
 134                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 135                                 for (it = collectshared.begin(); it != collectshared.end(); it++) {
 136                                         cout << it->first << ", ";
 137                                 }
 138                                 cout << endl;
 139                                 return false; }
 140                 }else if (command == "rarefaction.single") {
 141                         //is it valid
 142                         if ((rarefactsingle.find(parameter)) != (rarefactsingle.end())) {
 143                                 return true;
 144                         }else {
 145                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 146                                 for (it = rarefactsingle.begin(); it != rarefactsingle.end(); it++) {
 147                                         cout << it->first << ", ";
 148                                 }
 149                                 cout << endl;
 150                                 return false; }
 151                 }else if (command == "rarefaction.shared") {
 152                         //is it valid
 153                         if ((rarefactshared.find(parameter)) != (rarefactshared.end())) {
 154                                 return true;
 155                         }else {
 156                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 157                                 for (it = rarefactshared.begin(); it != rarefactshared.end(); it++) {
 158                                         cout << it->first << ", ";
 159                                 }
 160                                 cout << endl;
 161                                 return false; }
 162                 }else if (command == "summary.single") {
 163                         //is it valid
 164                         if ((summarysingle.find(parameter)) != (summarysingle.end())) {
 165                                 return true;
 166                         }else {
 167                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 168                                 for (it = summarysingle.begin(); it != summarysingle.end(); it++) {
 169                                         cout << it->first << ", ";
 170                                 }
 171                                 cout << endl;
 172                                 return false; }
 173                 }else if (command == "summary.shared") {
 174                         //is it valid
 175                         if ((summaryshared.find(parameter)) != (summaryshared.end())) {
 176                                 return true;
 177                         }else {
 178                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 179                                 for (it = summaryshared.begin(); it != summaryshared.end(); it++) {
 180                                         cout << it->first << ", ";
 181                                 }
 182                                 cout << endl;
 183                                 return false; }
 184                 }else if (command == "unifrac.weighted") {
 185                         //is it valid
 186                         if ((unifracweighted.find(parameter)) != (unifracweighted.end())) {
 187                                 return true;
 188                         }else {
 189                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 190                                 for (it = unifracweighted.begin(); it != unifracweighted.end(); it++) {
 191                                         cout << it->first << ", ";
 192                                 }
 193                                 cout << endl;
 194                                 return false; }
 195                 }else if (command == "unifrac.unweighted") {
 196                         //is it valid
 197                         if ((unifracunweighted.find(parameter)) != (unifracunweighted.end())) {
 198                                 return true;
 199                         }else {
 200                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 201                                 for (it = unifracunweighted.begin(); it != unifracunweighted.end(); it++) {
 202                                         cout << it->first << ", ";
 203                                 }
 204                                 cout << endl;
 205                                 return false; }
 206                 }else if (command == "libshuff") {
 207                         //is it valid
 208                         if ((libshuff.find(parameter)) != (libshuff.end())) {
 209                                 return true;
 210                         }else {
 211                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 212                                 for (it = libshuff.begin(); it != libshuff.end(); it++) {
 213                                         cout << it->first << ", ";
 214                                 }
 215                                 cout << endl;
 216                                 return false; }
 217                 }else if (command == "heatmap") {
 218                         //is it valid
 219                         if ((heatmap.find(parameter)) != (heatmap.end())) {
 220                                 return true;
 221                         }else {
 222                                 cout << parameter << " is not a valid parameter for the " + command + " command. Valid parameters are ";
 223                                 for (it = heatmap.begin(); it != heatmap.end(); it++) {
 224                                         cout << it->first << ", ";
 225                                 }
 226                                 cout << endl;
 227                                 return false; }
 228
 229                 //not a valid paramter
 230                 }else if (command == "help") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
 231                 }else if (command == "quit") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
 232                 }else if (command == "get.group") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
 233                 }else if (command == "get.label") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl;
 234                 }else if (command == "get.line") { cout << parameter << " is not a valid parameter for the " + command + " command. There are no vaild parameters." << endl; }
 235
 236                 return false;
 237
 238         }
 239         catch(exception& e) {
 240                 cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243         catch(...) {
 244                 cout << "An unknown error has occurred in the ValidParameters class function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247 }
 248
 249 /***********************************************************************/
 250 void ValidParameters::initialReaddist() {
 251         readdist["phylip"]              = "phylip";
 252         readdist["column"]              = "column";
 253         readdist["name"]                = "name";
 254         readdist["group"]               = "group";
 255         readdist["cutoff"]              = "cutoff";
 256         readdist["precision"]   = "precision";
 257 }
 258 /***********************************************************************/
 259 void ValidParameters::initialReadotu() {
 260         readotu["list"]                 = "list";
 261         readotu["rabund"]               = "rabund";
 262         readotu["sabund"]               = "sabund";
 263         readotu["shared"]               = "shared";
 264         readotu["group"]                = "group";
 265         readotu["order"]                = "order";
 266         readotu["label"]                = "label";
 267         readotu["line"]                 = "line";
 268 }
 269 /***********************************************************************/
 270 void ValidParameters::initialReadtree() {
 271         readtree["group"]       = "group";
 272         readtree["tree"]        = "tree";
 273 }
 274 /***********************************************************************/
 275 void ValidParameters::initialCluster() {
 276         cluster["cutoff"]               = "cutoff";
 277         cluster["method"]               = "method";
 278         cluster["precision"]    = "precision";
 279 }
 280 /***********************************************************************/
 281 void ValidParameters::initialDeconvolute() {
 282         deconvolute["fasta"]    = "fasta";
 283 }
 284 /***********************************************************************/
 285 void ValidParameters::initialParsimony() {
 286         parsimony["iters"]              = "iters";
 287         parsimony["random"]             = "random";
 288         parsimony["groups"]             = "groups";
 289 }
 290 /***********************************************************************/
 291 void ValidParameters::initialCollectsingle() {
 292         collectsingle["label"]          = "label";
 293         collectsingle["line"]           = "line";
 294         collectsingle["freq"]           = "freq";
 295         collectsingle["calc"]           = "calc";
 296 }
 297 /***********************************************************************/
 298 void ValidParameters::initialCollectshared() {
 299         collectshared["label"]          = "label";
 300         collectshared["line"]           = "line";
 301         collectshared["freq"]           = "freq";
 302         collectshared["calc"]           = "calc";
 303         collectshared["jumble"]         = "jumble";
 304 }
 305 /***********************************************************************/
 306 void ValidParameters::initialRarefactsingle() {
 307         rarefactsingle["label"]         = "label";
 308         rarefactsingle["line"]          = "line";
 309         rarefactsingle["freq"]          = "freq";
 310         rarefactsingle["calc"]          = "calc";
 311         rarefactsingle["iters"]         = "iters";
 312 }
 313 /***********************************************************************/
 314 void ValidParameters::initialRarefactshared() {
 315         rarefactshared["label"]         = "label";
 316         rarefactshared["line"]          = "line";
 317         rarefactshared["jumble"]        = "jumble";
 318         rarefactshared["calc"]          = "calc";
 319         rarefactshared["iters"]         = "iters";
 320 }
 321 /***********************************************************************/
 322 void ValidParameters::initialSummarysingle() {
 323         summarysingle["label"]          = "label";
 324         summarysingle["line"]           = "line";
 325         summarysingle["calc"]           = "calc";
 326 }
 327 /***********************************************************************/
 328 void ValidParameters::initialSummaryshared() {
 329         summaryshared["label"]          = "label";
 330         summaryshared["line"]           = "line";
 331         summaryshared["calc"]           = "calc";
 332         summaryshared["jumble"]         = "jumble";
 333
 334 }
 335 /***********************************************************************/
 336 void ValidParameters::initialUnifracweighted() {
 337         unifracweighted["iters"]                = "iters";
 338         unifracweighted["groups"]               = "groups";
 339 }
 340 /***********************************************************************/
 341 void ValidParameters::initialUnifracunweighted() {
 342         unifracunweighted["iters"]              = "iters";
 343         unifracunweighted["groups"]             = "groups";
 344 }
 345 /***********************************************************************/
 346 void ValidParameters::initialLibshuff() {
 347         libshuff["cutoff"]              = "cutoff";
 348         libshuff["iters"]               = "iters";
 349         libshuff["groups"]              = "groups";
 350         libshuff["step"]                = "step";
 351         libshuff["form"]                = "form";
 352 }
 353 /***********************************************************************/
 354 void ValidParameters::initialHeatmap() {
 355         heatmap["label"]        = "label";
 356         heatmap["line"]         = "line";
 357 }
 358
 359 /***********************************************************************/