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 #include "ace.h"
  12 #include "sobs.h"
  13 #include "nseqs.h"
  14 #include "chao1.h"
  15 #include "bootstrap.h"
  16 #include "simpson.h"
  17 #include "simpsoneven.h"
  18 #include "invsimpson.h"
  19 #include "npshannon.h"
  20 #include "shannon.h"
  21 #include "smithwilson.h"
  22 #include "heip.h"
  23 #include "shannoneven.h"
  24 #include "jackknife.h"
  25 #include "geom.h"
  26 #include "qstat.h"
  27 #include "logsd.h"
  28 #include "bergerparker.h"
  29 #include "bstick.h"
  30 #include "goodscoverage.h"
  31 #include "efron.h"
  32 #include "boneh.h"
  33 #include "solow.h"
  34 #include "shen.h"
  35 #include "coverage.h"
  36 #include "sharedsobscollectsummary.h"
  37 #include "sharedchao1.h"
  38 #include "sharedace.h"
  39 #include "sharedjabund.h"
  40 #include "sharedsorabund.h"
  41 #include "sharedjclass.h"
  42 #include "sharedsorclass.h"
  43 #include "sharedjest.h"
  44 #include "sharedsorest.h"
  45 #include "sharedthetayc.h"
  46 #include "sharedthetan.h"
  47 #include "sharedkstest.h"
  48 #include "whittaker.h"
  49 #include "sharednseqs.h"
  50 #include "sharedochiai.h"
  51 #include "sharedanderbergs.h"
  52 #include "sharedkulczynski.h"
  53 #include "sharedkulczynskicody.h"
  54 #include "sharedlennon.h"
  55 #include "sharedmorisitahorn.h"
  56 #include "sharedbraycurtis.h"
  57 #include "sharedjackknife.h"
  58 #include "whittaker.h"
  59 #include "odum.h"
  60 #include "canberra.h"
  61 #include "structeuclidean.h"
  62 #include "structchord.h"
  63 #include "hellinger.h"
  64 #include "manhattan.h"
  65 #include "structpearson.h"
  66 #include "soergel.h"
  67 #include "spearman.h"
  68 #include "structkulczynski.h"
  69 #include "structchi2.h"
  70 #include "speciesprofile.h"
  71 #include "hamming.h"
  72 #include "gower.h"
  73 #include "memchi2.h"
  74 #include "memchord.h"
  75 #include "memeuclidean.h"
  76 #include "mempearson.h"
  77 #include "sharedsobs.h"
  78 #include "sharednseqs.h"
  79 #include "sharedjsd.h"
  80 #include "sharedrjsd.h"
  81
  82
  83 /********************************************************************/
  84 ValidCalculators::ValidCalculators() {
  85         try {
  86                 m = MothurOut::getInstance();
  87
  88                 initialSingle();
  89                 initialShared();
  90                 initialRarefaction();
  91                 initialSharedRarefact();
  92                 initialSummary();
  93                 initialSharedSummary();
  94                 initialVennSingle();
  95                 initialVennShared();
  96                 initialTreeGroups();
  97                 initialBoot();
  98                 initialDistance();
  99                 initialMatrix();
 100                 initialHeat();
 101
 102                 for(it = single.begin(); it != single.end(); it++) { allCalcs.insert(it->first); }
 103                 for(it = shared.begin(); it != shared.end(); it++) { allCalcs.insert(it->first); }
 104                 for(it = rarefaction.begin(); it != rarefaction.end(); it++) { allCalcs.insert(it->first); }
 105                 for(it = summary.begin(); it != summary.end(); it++) { allCalcs.insert(it->first); }
 106                 for(it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) { allCalcs.insert(it->first); }
 107                 for(it = sharedsummary.begin(); it != sharedsummary.end(); it++) { allCalcs.insert(it->first); }
 108                 for(it = vennsingle.begin(); it != vennsingle.end(); it++) { allCalcs.insert(it->first); }
 109                 for(it = vennshared.begin(); it != vennshared.end(); it++) { allCalcs.insert(it->first); }
 110                 for(it = treegroup.begin(); it != treegroup.end(); it++) { allCalcs.insert(it->first); }
 111                 for(it = matrix.begin(); it != matrix.end(); it++) { allCalcs.insert(it->first); }
 112                 for(it = heat.begin(); it != heat.end(); it++) { allCalcs.insert(it->first); }
 113                 for(it = boot.begin(); it != boot.end(); it++) { allCalcs.insert(it->first); }
 114                 for(it = distance.begin(); it != distance.end(); it++) { allCalcs.insert(it->first); }
 115
 116         }
 117         catch(exception& e) {
 118                 m->errorOut(e, "ValidCalculator", "ValidCalculator");
 119                 exit(1);
 120         }
 121 }
 122 /********************************************************************/
 123 ValidCalculators::~ValidCalculators() {}
 124 /********************************************************************/
 125 void ValidCalculators::printCitations(vector<string> Estimators) {
 126         try {
 127
 128                 for (int i = 0; i < Estimators.size(); i++) {
 129                         //is this citation, do nothing
 130                         if ((Estimators[i] == "citation") || (Estimators[i] == "default") || (Estimators[i] == "eachgap") || (Estimators[i] == "nogaps") || (Estimators[i] == "onegap")) {}
 131                         //is this a valid calculator
 132                         else if (allCalcs.count(Estimators[i]) != 0) {
 133                                 if (Estimators[i] == "sobs") { Calculator* temp = new Sobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 134                                 }else if (Estimators[i] == "chao") { Calculator* temp = new Chao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 135                                 }else if (Estimators[i] == "nseqs") { Calculator* temp = new NSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 136                                 }else if (Estimators[i] == "coverage") { Calculator* temp = new Coverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 137                                 }else if (Estimators[i] == "ace") { Calculator* temp = new Ace(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 138
 139                                 }else if (Estimators[i] == "jack") { Calculator* temp = new Jackknife(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 140                                 }else if (Estimators[i] == "shannon") { Calculator* temp = new Shannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 141                                 }else if (Estimators[i] == "shannoneven") { Calculator* temp = new ShannonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 142                                 }else if (Estimators[i] == "npshannon") { Calculator* temp = new NPShannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 143                                 }else if (Estimators[i] == "heip") { Calculator* temp = new Heip(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 144
 145                                 }else if (Estimators[i] == "smithwilson") { Calculator* temp = new SmithWilson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 146                                 }else if (Estimators[i] == "simpson") { Calculator* temp = new Simpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 147                                 }else if (Estimators[i] == "simpsoneven") { Calculator* temp = new SimpsonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 148                                 }else if (Estimators[i] == "invsimpson") { Calculator* temp = new InvSimpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 149                                 }else if (Estimators[i] == "bootstrap") { Calculator* temp = new Bootstrap(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 150
 151                                 }else if (Estimators[i] == "geometric") { Calculator* temp = new Geom(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 152                                 }else if (Estimators[i] == "qstat") { Calculator* temp = new QStat(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 153                                 }else if (Estimators[i] == "logseries") { Calculator* temp = new LogSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 154                                 }else if (Estimators[i] == "bergerparker") { Calculator* temp = new BergerParker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 155                                 }else if (Estimators[i] == "bstick") { Calculator* temp = new BStick(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 156
 157                                 }else if (Estimators[i] == "goodscoverage") { Calculator* temp = new GoodsCoverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 158                                 }else if (Estimators[i] == "efron") { Calculator* temp = new Efron(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 159                                 }else if (Estimators[i] == "boneh") { Calculator* temp = new Boneh(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 160                                 }else if (Estimators[i] == "solow") { Calculator* temp = new Solow(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 161                                 }else if (Estimators[i] == "shen") { Calculator* temp = new Shen(10, 10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 162
 163                                 }else if (Estimators[i] == "sharedchao") { Calculator* temp = new SharedChao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 164                                 }else if (Estimators[i] == "sharedsobs") { Calculator* temp = new SharedSobsCS(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 165                                 }else if (Estimators[i] == "sharedace") { Calculator* temp = new SharedAce(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 166                                 }else if (Estimators[i] == "jabund") {  Calculator* temp = new JAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 167                                 }else if (Estimators[i] == "sorabund") { Calculator* temp = new SorAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 168
 169                                 }else if (Estimators[i] == "jclass") { Calculator* temp = new Jclass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 170                                 }else if (Estimators[i] == "sorclass") { Calculator* temp = new SorClass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 171                                 }else if (Estimators[i] == "jest") { Calculator* temp = new Jest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 172                                 }else if (Estimators[i] == "sorest") { Calculator* temp = new SorEst(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 173                                 }else if (Estimators[i] == "thetayc") { Calculator* temp = new ThetaYC(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 174
 175                                 }else if (Estimators[i] == "thetan") { Calculator* temp = new ThetaN(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 176                                 }else if (Estimators[i] == "kstest") { Calculator* temp = new KSTest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 177                                 }else if (Estimators[i] == "whittaker") { Calculator* temp = new Whittaker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 178                                 }else if (Estimators[i] == "sharednseqs") { Calculator* temp = new SharedNSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 179                                 }else if (Estimators[i] == "ochiai") { Calculator* temp = new Ochiai(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 180
 181                                 }else if (Estimators[i] == "anderberg") { Calculator* temp = new Anderberg(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 182                                 }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 183                                 }else if (Estimators[i] == "kulczynskicody") { Calculator* temp = new KulczynskiCody(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 184                                 }else if (Estimators[i] == "lennon") { Calculator* temp = new Lennon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 185                                 }else if (Estimators[i] == "morisitahorn") { Calculator* temp = new MorHorn(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 186
 187                                 }else if (Estimators[i] == "braycurtis") { Calculator* temp = new BrayCurtis(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 188                                 }else if (Estimators[i] == "odum") { Calculator* temp = new Odum(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 189                                 }else if (Estimators[i] == "canberra") { Calculator* temp = new Canberra(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 190                                 }else if (Estimators[i] == "structeuclidean") { Calculator* temp = new StructEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 191                                 }else if (Estimators[i] == "structchord") { Calculator* temp = new StructChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 192
 193                                 }else if (Estimators[i] == "hellinger") { Calculator* temp = new Hellinger(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 194                                 }else if (Estimators[i] == "manhattan") { Calculator* temp = new Manhattan(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 195                                 }else if (Estimators[i] == "structpearson") { Calculator* temp = new StructPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 196                                 }else if (Estimators[i] == "soergel") { Calculator* temp = new Soergel(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 197                                 }else if (Estimators[i] == "spearman") { Calculator* temp = new Spearman(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 198
 199                                 }else if (Estimators[i] == "structkulczynski") { Calculator* temp = new StructKulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 200                                 }else if (Estimators[i] == "speciesprofile") { Calculator* temp = new SpeciesProfile(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 201                                 }else if (Estimators[i] == "hamming") { Calculator* temp = new Hamming(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 202                                 }else if (Estimators[i] == "structchi2") { Calculator* temp = new StructChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 203                                 }else if (Estimators[i] == "gower") { Calculator* temp = new Gower(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 204
 205                                 }else if (Estimators[i] == "memchi2") { Calculator* temp = new MemChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 206                                 }else if (Estimators[i] == "memchord") { Calculator* temp = new MemChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 207                                 }else if (Estimators[i] == "memeuclidean") { Calculator* temp = new MemEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 208                                 }else if (Estimators[i] == "mempearson") { Calculator* temp = new MemPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 209                                 }else if (Estimators[i] == "sharedobserved") { Calculator* temp = new SharedSobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 210                                 }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 211                 }else if (Estimators[i] == "jsd") { Calculator* temp = new JSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 212                 }else if (Estimators[i] == "rjsd") { Calculator* temp = new RJSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 213                                 }else { m->mothurOut("[ERROR]: Missing else if for " + Estimators[i] + " in printCitations."); m->mothurOutEndLine(); }
 214                         }else { m->mothurOut(Estimators[i] + " is not a valid calculator, no citation will be given."); m->mothurOutEndLine(); }
 215                 }
 216
 217         }
 218         catch(exception& e) {
 219                 m->errorOut(e, "ValidCalculator", "printCitations");
 220                 exit(1);
 221         }
 222 }
 223 /********************************************************************/
 224
 225 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 226         try {
 227                 //are you looking for a calculator for a single parameter
 228                 if (parameter == "single") {
 229                         //is it valid
 230                         if ((single.find(calculator)) != (single.end())) {
 231                                 return true;
 232                         }else {
 233                                 m->mothurOut(calculator + " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ");
 234                                 for (it = single.begin(); it != single.end(); it++) {
 235                                         m->mothurOut(it->first + ", ");
 236                                 }
 237                                 m->mothurOutEndLine();
 238                                 return false; }
 239                 //are you looking for a calculator for a shared parameter
 240                 }else if (parameter == "shared") {
 241                         //is it valid
 242                         if ((shared.find(calculator)) != (shared.end())) {
 243                                 return true;
 244                         }else {
 245                                 m->mothurOut(calculator +  " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ");
 246                                 for (it = shared.begin(); it != shared.end(); it++) {
 247                                         m->mothurOut(it->first + ", ");
 248                                 }
 249                                 m->mothurOutEndLine();
 250                                 return false; }
 251                 //are you looking for a calculator for a rarefaction parameter
 252                 }else if (parameter == "rarefaction") {
 253                         //is it valid
 254                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
 255                                 return true;
 256                         }else {
 257                                 m->mothurOut(calculator + " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ");
 258                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 259                                         m->mothurOut(it->first + ", ");
 260                                 }
 261                                 m->mothurOutEndLine();
 262                                 return false; }
 263                 //are you looking for a calculator for a summary parameter
 264                 }else if (parameter == "summary") {
 265                         //is it valid
 266                         if ((summary.find(calculator)) != (summary.end())) {
 267                                 return true;
 268                         }else {
 269                                 m->mothurOut(calculator + " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
 270                                 for (it = summary.begin(); it != summary.end(); it++) {
 271                                         m->mothurOut(it->first + ", ");
 272                                 }
 273                                 m->mothurOutEndLine();
 274                                 return false; }
 275                 //are you looking for a calculator for a sharedsummary parameter
 276                 }else if (parameter == "sharedsummary") {
 277                         //is it valid
 278                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
 279                                 return true;
 280                         }else {
 281                                 m->mothurOut(calculator +  " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
 282                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 283                                         m->mothurOut(it->first + ", ");
 284                                 }
 285                                 m->mothurOutEndLine();
 286                                 return false; }
 287                 }else if (parameter == "sharedrarefaction") {
 288                         //is it valid
 289                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 290                                 return true;
 291                         }else {
 292                                 m->mothurOut(calculator + " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ");
 293                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 294                                         m->mothurOut(it->first + ", ");
 295                                 }
 296                                 m->mothurOutEndLine();
 297                                 return false; }
 298                 }else if (parameter == "vennsingle") {
 299                         //is it valid
 300                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 301                                 return true;
 302                         }else {
 303                                 m->mothurOut(calculator + " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ");
 304                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 305                                         m->mothurOut(it->first + ", ");
 306                                 }
 307                                 m->mothurOutEndLine();
 308                                 return false; }
 309                 }else if (parameter == "vennshared") {
 310                         //is it valid
 311                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 312                                 return true;
 313                         }else {
 314                                 m->mothurOut(calculator + " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ");
 315                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 316                                         m->mothurOut(it->first + ", ");
 317                                 }
 318                                 m->mothurOutEndLine();
 319                                 return false; }
 320                 }else if (parameter == "treegroup") {
 321                         //is it valid
 322                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 323                                 return true;
 324                         }else {
 325                                 m->mothurOut(calculator + " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ");
 326                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 327                                         m->mothurOut(it->first + ", ");
 328                                 }
 329                                 m->mothurOutEndLine();
 330                                 return false; }
 331                 }else if (parameter == "matrix") {
 332                         //is it valid
 333                         if ((matrix.find(calculator)) != (matrix.end())) {
 334                                 return true;
 335                         }else {
 336                                 m->mothurOut(calculator +  " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ");
 337                                 for (it = matrix.begin(); it != matrix.end(); it++) {
 338                                         m->mothurOut(it->first + ", ");
 339                                 }
 340                                 m->mothurOutEndLine();
 341                                 return false; }
 342                 }else if (parameter == "heat") {
 343                         //is it valid
 344                         if ((heat.find(calculator)) != (heat.end())) {
 345                                 return true;
 346                         }else {
 347                                 m->mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
 348                                 for (it = heat.begin(); it != heat.end(); it++) {
 349                                         m->mothurOut(it->first + ", ");
 350                                 }
 351                                 m->mothurOutEndLine();
 352                                 return false; }
 353                 }else if (parameter == "boot") {
 354                         //is it valid
 355                         if ((boot.find(calculator)) != (boot.end())) {
 356                                 return true;
 357                         }else {
 358                                 m->mothurOut(calculator + " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ");
 359                                 for (it = boot.begin(); it != boot.end(); it++) {
 360                                         m->mothurOut(it->first + ", ");
 361                                 }
 362                                 m->mothurOutEndLine();
 363                                 return false; }
 364                 }else if (parameter == "distance") {
 365                         //is it valid
 366                         if ((distance.find(calculator)) != (distance.end())) {
 367                                 return true;
 368                         }else {
 369                                 m->mothurOut(calculator +  " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ");
 370                                 for (it = distance.begin(); it != distance.end(); it++) {
 371                                         m->mothurOut(it->first + ", ");
 372                                 }
 373                                 m->mothurOutEndLine();
 374                                 return false; }
 375                 //not a valid parameter
 376                 }else { return false; }
 377
 378         }
 379         catch(exception& e) {
 380                 m->errorOut(e, "ValidCalculator", "isValidCalculator");
 381                 exit(1);
 382         }
 383 }
 384
 385 /********************************************************************/
 386 void ValidCalculators::initialSingle() {
 387         try {
 388                 single["sobs"]          = "sobs";
 389                 single["chao"]              = "chao";
 390                 single["ace"]               = "ace";
 391                 single["jack"]              = "jack";
 392                 single["shannon"]           = "shannon";
 393                 single["npshannon"]     = "npshannon";
 394                 single["shannoneven"]   = "shannoneven";
 395                 single["smithwilson"]   = "smithwilson";
 396                 single["heip"]                  = "heip";
 397                 single["simpson"]           = "simpson";
 398                 single["simpsoneven"]   = "simpsoneven";
 399                 single["invsimpson"]    = "invsimpson";
 400                 single["bergerparker"]  = "bergerparker";
 401                 single["bootstrap"]     = "bootstrap";
 402                 single["geometric"]     = "geometric";
 403                 single["logseries"]             = "logseries";
 404                 single["qstat"]         = "qstat";
 405                 single["bstick"]        = "bstick";
 406                 single["goodscoverage"] = "goodscoverage";
 407                 single["nseqs"]                 = "nseqs";
 408                 single["coverage"]              = "coverage";
 409                 single["efron"]         = "efron";
 410                 single["boneh"]         = "boneh";
 411                 single["solow"]         = "solow";
 412                 single["shen"]          = "shen";
 413                 single["default"]           = "default";
 414         }
 415         catch(exception& e) {
 416                 m->errorOut(e, "ValidCalculator", "initialSingle");
 417                 exit(1);
 418         }
 419 }
 420
 421 /********************************************************************/
 422 void ValidCalculators::initialShared() {
 423         try {
 424                 shared["sharedsobs"]                    = "sharedsobs";
 425                 shared["sharedchao"]                    = "sharedchao";
 426                 shared["sharedace"]                             = "sharedace";
 427                 shared["jabund"]                                = "jabund";
 428                 shared["sorabund"]                              = "sorabund";
 429                 shared["jclass"]                                = "jclass";
 430                 shared["sorclass"]                              = "sorclass";
 431                 shared["jest"]                                  = "jest";
 432                 shared["sorest"]                                = "sorest";
 433                 shared["thetayc"]                               = "thetayc";
 434                 shared["thetan"]                                = "thetan";
 435                 shared["kstest"]                                = "kstest";
 436                 shared["whittaker"]                         = "whittaker";
 437                 shared["sharednseqs"]                   = "sharednseqs";
 438                 shared["ochiai"]                                = "ochiai";
 439                 shared["anderberg"]                             = "anderberg";
 440                 shared["kulczynski"]                    = "kulczynski";
 441                 shared["kulczynskicody"]                = "kulczynskicody";
 442                 shared["lennon"]                                = "lennon";
 443                 shared["morisitahorn"]                  = "morisitahorn";
 444                 shared["braycurtis"]                    = "braycurtis";
 445                 shared["odum"]                                  = "odum";
 446                 shared["canberra"]                              = "canberra";
 447                 shared["structeuclidean"]               = "structeuclidean";
 448                 shared["structchord"]                   = "structchord";
 449                 shared["hellinger"]                             = "hellinger";
 450                 shared["manhattan"]                             = "manhattan";
 451                 shared["structpearson"]                 = "structpearson";
 452                 shared["soergel"]                               = "soergel";
 453                 shared["spearman"]                              = "spearman";
 454                 shared["structkulczynski"]              = "structkulczynski";
 455                 shared["structchi2"]                    = "structchi2";
 456                 shared["speciesprofile"]                = "speciesprofile";
 457                 shared["hamming"]                               = "hamming";
 458                 shared["gower"]                                 = "gower";
 459                 shared["memchi2"]                               = "memchi2";
 460                 shared["memchord"]                              = "memchord";
 461                 shared["memeuclidean"]                  = "memeuclidean";
 462                 shared["mempearson"]                    = "mempearson";
 463         shared["jsd"]                   = "jsd";
 464         shared["rjsd"]                  = "rjsd";
 465                 shared["default"]                   = "default";
 466         }
 467         catch(exception& e) {
 468                 m->errorOut(e, "ValidCalculator", "initialShared");
 469                 exit(1);
 470         }
 471 }
 472
 473 /********************************************************************/
 474 void ValidCalculators::initialRarefaction() {
 475         try {
 476                 rarefaction["sobs"]                     = "sobs";
 477                 rarefaction["chao"]                     = "chao";
 478                 rarefaction["ace"]                      = "ace";
 479                 rarefaction["jack"]                     = "jack";
 480                 rarefaction["shannon"]          = "shannon";
 481                 rarefaction["smithwilson"]      = "smithwilson";
 482                 rarefaction["heip"]                     = "heip";
 483                 rarefaction["npshannon"]        = "npshannon";
 484                 rarefaction["shannoneven"]      = "shannoneven";
 485                 rarefaction["simpson"]          = "simpson";
 486                 rarefaction["invsimpson"]       = "invsimpson";
 487                 rarefaction["simpsoneven"]      = "simpsoneven";
 488                 rarefaction["bootstrap"]        = "bootstrap";
 489                 rarefaction["nseqs"]            = "nseqs";
 490                 rarefaction["coverage"]         = "coverage";
 491                 rarefaction["default"]      = "default";
 492         }
 493         catch(exception& e) {
 494                 m->errorOut(e, "ValidCalculator", "initialRarefaction");
 495                 exit(1);
 496         }
 497 }
 498
 499 /********************************************************************/
 500
 501 void ValidCalculators::initialSummary() {
 502         try {
 503                 summary["sobs"]                 = "sobs";
 504                 summary["chao"]                 = "chao";
 505                 summary["ace"]                  = "ace";
 506                 summary["jack"]                 = "jack";
 507                 summary["shannon"]              = "shannon";
 508                 summary["heip"]                 = "heip";
 509                 summary["shannoneven"]  = "shannoneven";
 510                 summary["smithwilson"]  = "smithwilson";
 511                 summary["invsimpson"]   = "invsimpson";
 512                 summary["npshannon"]    = "npshannon";
 513                 summary["simpson"]              = "simpson";
 514                 summary["simpsoneven"]  = "simpsoneven";
 515                 summary["bergerparker"] = "bergerparker";
 516                 summary["geometric"]    = "geometric";
 517                 summary["bootstrap"]    = "bootstrap";
 518                 summary["logseries"]    = "logseries";
 519                 summary["qstat"]        = "qstat";
 520                 summary["bstick"]       = "bstick";
 521                 summary["nseqs"]                = "nseqs";
 522                 summary["goodscoverage"]= "goodscoverage";
 523                 summary["coverage"]             = "coverage";
 524                 summary["efron"]        = "efron";
 525                 summary["boneh"]        = "boneh";
 526                 summary["solow"]        = "solow";
 527                 summary["shen"]         = "shen";
 528                 summary["default"]          = "default";
 529         }
 530         catch(exception& e) {
 531                 m->errorOut(e, "ValidCalculator", "initialSummary");
 532                 exit(1);
 533         }
 534 }
 535
 536 /********************************************************************/
 537 void ValidCalculators::initialSharedSummary() {
 538         try {
 539                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 540                 sharedsummary["sharedchao"]                             = "sharedchao";
 541                 sharedsummary["sharedace"]                              = "sharedace";
 542                 sharedsummary["jabund"]                                 = "jabund";
 543                 sharedsummary["sorabund"]                               = "sorabund";
 544                 sharedsummary["jclass"]                                 = "jclass";
 545                 sharedsummary["sorclass"]                               = "sorclass";
 546                 sharedsummary["jest"]                                   = "jest";
 547                 sharedsummary["sorest"]                                 = "sorest";
 548                 sharedsummary["thetayc"]                                = "thetayc";
 549                 sharedsummary["thetan"]                                 = "thetan";
 550                 sharedsummary["kstest"]                                 = "kstest";
 551                 sharedsummary["whittaker"]                              = "whittaker";
 552                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 553                 sharedsummary["ochiai"]                                 = "ochiai";
 554                 sharedsummary["anderberg"]                              = "anderberg";
 555                 sharedsummary["kulczynski"]                             = "kulczynski";
 556                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 557                 sharedsummary["lennon"]                                 = "lennon";
 558                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 559                 sharedsummary["braycurtis"]                             = "braycurtis";
 560                 sharedsummary["odum"]                                   = "odum";
 561                 sharedsummary["canberra"]                               = "canberra";
 562                 sharedsummary["structeuclidean"]                = "structeuclidean";
 563                 sharedsummary["structchord"]                    = "structchord";
 564                 sharedsummary["hellinger"]                              = "hellinger";
 565                 sharedsummary["manhattan"]                              = "manhattan";
 566                 sharedsummary["structpearson"]                  = "structpearson";
 567                 sharedsummary["structkulczynski"]               = "structkulczynski";
 568                 sharedsummary["structchi2"]                             = "structchi2";
 569                 sharedsummary["soergel"]                                = "soergel";
 570                 sharedsummary["spearman"]                               = "spearman";
 571                 sharedsummary["speciesprofile"]                 = "speciesprofile";
 572                 sharedsummary["hamming"]                                = "hamming";
 573                 sharedsummary["gower"]                                  = "gower";
 574                 sharedsummary["memchi2"]                                = "memchi2";
 575                 sharedsummary["memchord"]                               = "memchord";
 576                 sharedsummary["memeuclidean"]                   = "memeuclidean";
 577                 sharedsummary["mempearson"]                             = "mempearson";
 578         sharedsummary["jsd"]                    = "jsd";
 579         sharedsummary["rjsd"]                   = "rjsd";
 580                 sharedsummary["default"]                                = "default";
 581         }
 582         catch(exception& e) {
 583                 m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 584                 exit(1);
 585         }
 586 }
 587
 588
 589 /********************************************************************/
 590
 591 void ValidCalculators::initialSharedRarefact() {
 592         try {
 593                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 594                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 595                 sharedrarefaction["default"]        = "default";
 596         }
 597         catch(exception& e) {
 598                 m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 599                 exit(1);
 600         }
 601 }
 602
 603
 604 /********************************************************************/
 605 void ValidCalculators::initialVennSingle() {
 606         try {
 607                 vennsingle["sobs"]              = "sobs";
 608                 vennsingle["chao"]                  = "chao";
 609                 vennsingle["ace"]                       = "ace";
 610                 vennsingle["jack"]                  = "jack";
 611                 vennsingle["default"]           = "default";
 612         }
 613         catch(exception& e) {
 614                 m->errorOut(e, "ValidCalculator", "initialVennSingle");
 615                 exit(1);
 616         }
 617 }
 618
 619 /********************************************************************/
 620 void ValidCalculators::initialVennShared() {
 621         try {
 622                 vennshared["sharedsobs"]        = "sharedsobs";
 623                 vennshared["sharedchao"]        = "sharedchao";
 624                 vennshared["sharedace"]         = "sharedace";
 625                 vennshared["default"]           = "default";
 626         }
 627         catch(exception& e) {
 628                 m->errorOut(e, "ValidCalculator", "initialVennShared");
 629                 exit(1);
 630         }
 631 }
 632
 633 /********************************************************************/
 634 void ValidCalculators::initialTreeGroups() {
 635         try {
 636                 treegroup["sharedsobs"]                         = "sharedsobs";
 637                 treegroup["sharedchao"]                         = "sharedchao";
 638                 treegroup["sharedace"]                          = "sharedace";
 639                 treegroup["jabund"]                                     = "jabund";
 640                 treegroup["sorabund"]                           = "sorabund";
 641                 treegroup["jclass"]                                     = "jclass";
 642                 treegroup["sorclass"]                           = "sorclass";
 643                 treegroup["jest"]                                       = "jest";
 644                 treegroup["sorest"]                                     = "sorest";
 645                 treegroup["thetayc"]                            = "thetayc";
 646                 treegroup["thetan"]                                     = "thetan";
 647                 treegroup["kstest"]                                     = "kstest";
 648                 treegroup["whittaker"]                          = "whittaker";
 649                 treegroup["sharednseqs"]                        = "sharednseqs";
 650                 treegroup["ochiai"]                                     = "ochiai";
 651                 treegroup["anderberg"]                          = "anderberg";
 652                 treegroup["kulczynski"]                         = "kulczynski";
 653                 treegroup["kulczynskicody"]                     = "kulczynskicody";
 654                 treegroup["lennon"]                                     = "lennon";
 655                 treegroup["morisitahorn"]                       = "morisitahorn";
 656                 treegroup["braycurtis"]                         = "braycurtis";
 657                 treegroup["odum"]                                       = "odum";
 658                 treegroup["canberra"]                           = "canberra";
 659                 treegroup["structeuclidean"]            = "structeuclidean";
 660                 treegroup["structchord"]                        = "structchord";
 661                 treegroup["hellinger"]                          = "hellinger";
 662                 treegroup["manhattan"]                          = "manhattan";
 663                 treegroup["structpearson"]                      = "structpearson";
 664                 treegroup["structkulczynski"]           = "structkulczynski";
 665                 treegroup["structchi2"]                         = "structchi2";
 666                 treegroup["soergel"]                            = "soergel";
 667                 treegroup["spearman"]                           = "spearman";
 668                 treegroup["speciesprofile"]                     = "speciesprofile";
 669                 treegroup["hamming"]                            = "hamming";
 670                 treegroup["gower"]                                      = "gower";
 671                 treegroup["memchi2"]                            = "memchi2";
 672                 treegroup["memchord"]                           = "memchord";
 673                 treegroup["memeuclidean"]                       = "memeuclidean";
 674                 treegroup["mempearson"]                         = "mempearson";
 675
 676         }
 677         catch(exception& e) {
 678                 m->errorOut(e, "ValidCalculator", "initialTreeGroups");
 679                 exit(1);
 680         }
 681 }
 682 /********************************************************************/
 683 void ValidCalculators::initialHeat() {
 684         try {
 685                 heat["jabund"]                          = "jabund";
 686                 heat["sorabund"]                        = "sorabund";
 687                 heat["jclass"]                          = "jclass";
 688                 heat["sorclass"]                        = "sorclass";
 689                 heat["jest"]                            = "jest";
 690                 heat["sorest"]                          = "sorest";
 691                 heat["thetayc"]                         = "thetayc";
 692                 heat["thetan"]                          = "thetan";
 693                 heat["morisitahorn"]            = "morisitahorn";
 694                 heat["braycurtis"]                      = "braycurtis";
 695         }
 696         catch(exception& e) {
 697                 m->errorOut(e, "ValidCalculator", "initialHeat");
 698                 exit(1);
 699         }
 700 }
 701
 702 /********************************************************************/
 703 void ValidCalculators::initialMatrix() {
 704         try {
 705                 matrix["sharedsobs"]                            = "sharedsobs";
 706                 matrix["sharedchao"]                            = "sharedchao";
 707                 matrix["sharedace"]                             = "sharedace";
 708                 matrix["jabund"]                                        = "jabund";
 709                 matrix["sorabund"]                              = "sorabund";
 710                 matrix["jclass"]                                        = "jclass";
 711                 matrix["sorclass"]                              = "sorclass";
 712                 matrix["jest"]                                  = "jest";
 713                 matrix["sorest"]                                        = "sorest";
 714                 matrix["thetayc"]                               = "thetayc";
 715                 matrix["thetan"]                                        = "thetan";
 716                 matrix["kstest"]                                        = "kstest";
 717                 matrix["whittaker"]                             = "whittaker";
 718                 matrix["sharednseqs"]                   = "sharednseqs";
 719                 matrix["ochiai"]                                        = "ochiai";
 720                 matrix["anderberg"]                             = "anderberg";
 721                 matrix["kulczynski"]                            = "kulczynski";
 722                 matrix["kulczynskicody"]                        = "kulczynskicody";
 723                 matrix["lennon"]                                        = "lennon";
 724                 matrix["morisitahorn"]                  = "morisitahorn";
 725                 matrix["braycurtis"]                            = "braycurtis";
 726                 matrix["odum"]                                  = "odum";
 727                 matrix["canberra"]                              = "canberra";
 728                 matrix["structeuclidean"]               = "structeuclidean";
 729                 matrix["structchord"]                   = "structchord";
 730                 matrix["hellinger"]                             = "hellinger";
 731                 matrix["manhattan"]                             = "manhattan";
 732                 matrix["structpearson"]                 = "structpearson";
 733                 matrix["structkulczynski"]              = "structkulczynski";
 734                 matrix["structchi2"]                            = "structchi2";
 735                 matrix["soergel"]                               = "soergel";
 736                 matrix["spearman"]                              = "spearman";
 737                 matrix["speciesprofile"]                = "speciesprofile";
 738                 matrix["hamming"]                               = "hamming";
 739                 matrix["gower"]                                 = "gower";
 740                 matrix["memchi2"]                               = "memchi2";
 741                 matrix["memchord"]                              = "memchord";
 742                 matrix["memeuclidean"]                  = "memeuclidean";
 743                 matrix["mempearson"]                    = "mempearson";
 744         matrix["rjsd"]                   = "rjsd";
 745         matrix["jsd"]                   = "jsd";
 746
 747         }
 748         catch(exception& e) {
 749                 m->errorOut(e, "ValidCalculator", "initialMatrix");
 750                 exit(1);
 751         }
 752 }
 753
 754 /********************************************************************/
 755 void ValidCalculators::initialBoot() {
 756         try {
 757                 boot["jabund"]                          = "jabund";
 758                 boot["sorabund"]                        = "sorabund";
 759                 boot["jclass"]                          = "jclass";
 760                 boot["sorclass"]                        = "orclass";
 761                 boot["jest"]                            = "jest";
 762                 boot["sorest"]                          = "sorest";
 763                 boot["thetayc"]                         = "thetayc";
 764                 boot["thetan"]                          = "thetan";
 765                 boot["morisitahorn"]            = "morisitahorn";
 766                 boot["braycurtis"]                      = "braycurtis";
 767         }
 768         catch(exception& e) {
 769                 m->errorOut(e, "ValidCalculator", "initialBoot");
 770                 exit(1);
 771         }
 772 }
 773 /********************************************************************/
 774 void ValidCalculators::initialDistance() {
 775         try {
 776                 distance["nogaps"]              = "nogaps";
 777                 distance["eachgap"]             = "eachgap";
 778                 distance["onegap"]              = "onegap";
 779         }
 780         catch(exception& e) {
 781                 m->errorOut(e, "ValidCalculator", "initialDistance");
 782                 exit(1);
 783         }
 784 }
 785
 786 /********************************************************************/
 787 void ValidCalculators::printCalc(string parameter, ostream& out) {
 788         try{
 789                 out << "The available estimators for calc are ";
 790                 //are you looking for a calculator for a single parameter
 791                 if (parameter == "single") {
 792                         for (it = single.begin(); it != single.end(); it++) {
 793                                 out << it->first << ", ";
 794                         }
 795                 //are you looking for a calculator for a shared parameter
 796                 }else if (parameter == "shared") {
 797                         for (it = shared.begin(); it != shared.end(); it++) {
 798                                 out << it->first << ", ";
 799                         }
 800                 //are you looking for a calculator for a rarefaction parameter
 801                 }else if (parameter == "rarefaction") {
 802                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 803                                 out << it->first << ", ";
 804                         }
 805                 //are you looking for a calculator for a summary parameter
 806                 }else if (parameter == "summary") {
 807                         for (it = summary.begin(); it != summary.end(); it++) {
 808                                 out << it->first << ", ";
 809                         }
 810                 //are you looking for a calculator for a sharedsummary parameter
 811                 }else if (parameter == "sharedsummary") {
 812                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 813                                 out << it->first << ", ";
 814                         }
 815                 }else if (parameter == "sharedrarefaction") {
 816                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 817                                 out << it->first << ", ";
 818                         }
 819                 }else if (parameter == "vennsingle") {
 820                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 821                                 out << it->first << ", ";
 822                         }
 823                 }else if (parameter == "vennshared") {
 824                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 825                                 out << it->first << ", ";
 826                         }
 827                 }else if (parameter == "treegroup") {
 828                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 829                                 out << it->first << ", ";
 830                         }
 831                 }else if (parameter == "matrix") {
 832                         for (it = matrix.begin(); it != matrix.end(); it++) {
 833                                 out << it->first << ", ";
 834                         }
 835                 }else if (parameter == "heat") {
 836                         for (it = heat.begin(); it != heat.end(); it++) {
 837                                 out << it->first << ", ";
 838                         }
 839                 }else if (parameter == "boot") {
 840                         for (it = boot.begin(); it != boot.end(); it++) {
 841                                 out << it->first << ", ";
 842                         }
 843                 }else if (parameter == "distance") {
 844                         for (it = distance.begin(); it != distance.end(); it++) {
 845                                 out << it->first << ", ";
 846                         }
 847                 }
 848
 849                 out << endl;
 850         }
 851         catch(exception& e) {
 852                 m->errorOut(e, "ValidCalculator", "printCalc");
 853                 exit(1);
 854         }
 855 }
 856 /********************************************************************/
 857 string ValidCalculators::printCalc(string parameter) {
 858         try{
 859                 string output = "The available estimators for calc are ";
 860                 //are you looking for a calculator for a single parameter
 861                 if (parameter == "single") {
 862                         for (it = single.begin(); it != single.end(); it++) {
 863                                 output += it->first + ", ";
 864                         }
 865                         //are you looking for a calculator for a shared parameter
 866                 }else if (parameter == "shared") {
 867                         for (it = shared.begin(); it != shared.end(); it++) {
 868                                 output += it->first + ", ";
 869                         }
 870                         //are you looking for a calculator for a rarefaction parameter
 871                 }else if (parameter == "rarefaction") {
 872                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 873                                 output += it->first + ", ";
 874                         }
 875                         //are you looking for a calculator for a summary parameter
 876                 }else if (parameter == "summary") {
 877                         for (it = summary.begin(); it != summary.end(); it++) {
 878                                 output += it->first + ", ";
 879                         }
 880                         //are you looking for a calculator for a sharedsummary parameter
 881                 }else if (parameter == "sharedsummary") {
 882                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 883                                 output += it->first + ", ";
 884                         }
 885                 }else if (parameter == "sharedrarefaction") {
 886                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 887                                 output += it->first + ", ";
 888                         }
 889                 }else if (parameter == "vennsingle") {
 890                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 891                                 output += it->first + ", ";
 892                         }
 893                 }else if (parameter == "vennshared") {
 894                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 895                                 output += it->first + ", ";
 896                         }
 897                 }else if (parameter == "treegroup") {
 898                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 899                                 output += it->first + ", ";
 900                         }
 901                 }else if (parameter == "matrix") {
 902                         for (it = matrix.begin(); it != matrix.end(); it++) {
 903                                 output += it->first + ", ";
 904                         }
 905                 }else if (parameter == "heat") {
 906                         for (it = heat.begin(); it != heat.end(); it++) {
 907                                 output += it->first + ", ";
 908                         }
 909                 }else if (parameter == "boot") {
 910                         for (it = boot.begin(); it != boot.end(); it++) {
 911                                 output += it->first + ", ";
 912                         }
 913                 }else if (parameter == "distance") {
 914                         for (it = distance.begin(); it != distance.end(); it++) {
 915                                 output += it->first + ", ";
 916                         }
 917                 }
 918
 919                 //rip off comma
 920                 output = output.substr(0, output.length()-1);
 921                 output += "\n";
 922
 923                 return output;
 924         }
 925         catch(exception& e) {
 926                 m->errorOut(e, "ValidCalculator", "printCalc");
 927                 exit(1);
 928         }
 929 }
 930 /********************************************************************/
 931
 932