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 #include "shannonrange.h"
  82
  83
  84 /********************************************************************/
  85 ValidCalculators::ValidCalculators() {
  86         try {
  87                 m = MothurOut::getInstance();
  88
  89                 initialSingle();
  90                 initialShared();
  91                 initialRarefaction();
  92                 initialSharedRarefact();
  93                 initialSummary();
  94                 initialSharedSummary();
  95                 initialVennSingle();
  96                 initialVennShared();
  97                 initialTreeGroups();
  98                 initialBoot();
  99                 initialDistance();
 100                 initialMatrix();
 101                 initialHeat();
 102
 103                 for(it = single.begin(); it != single.end(); it++) { allCalcs.insert(it->first); }
 104                 for(it = shared.begin(); it != shared.end(); it++) { allCalcs.insert(it->first); }
 105                 for(it = rarefaction.begin(); it != rarefaction.end(); it++) { allCalcs.insert(it->first); }
 106                 for(it = summary.begin(); it != summary.end(); it++) { allCalcs.insert(it->first); }
 107                 for(it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) { allCalcs.insert(it->first); }
 108                 for(it = sharedsummary.begin(); it != sharedsummary.end(); it++) { allCalcs.insert(it->first); }
 109                 for(it = vennsingle.begin(); it != vennsingle.end(); it++) { allCalcs.insert(it->first); }
 110                 for(it = vennshared.begin(); it != vennshared.end(); it++) { allCalcs.insert(it->first); }
 111                 for(it = treegroup.begin(); it != treegroup.end(); it++) { allCalcs.insert(it->first); }
 112                 for(it = matrix.begin(); it != matrix.end(); it++) { allCalcs.insert(it->first); }
 113                 for(it = heat.begin(); it != heat.end(); it++) { allCalcs.insert(it->first); }
 114                 for(it = boot.begin(); it != boot.end(); it++) { allCalcs.insert(it->first); }
 115                 for(it = distance.begin(); it != distance.end(); it++) { allCalcs.insert(it->first); }
 116
 117         }
 118         catch(exception& e) {
 119                 m->errorOut(e, "ValidCalculator", "ValidCalculator");
 120                 exit(1);
 121         }
 122 }
 123 /********************************************************************/
 124 ValidCalculators::~ValidCalculators() {}
 125 /********************************************************************/
 126 void ValidCalculators::printCitations(vector<string> Estimators) {
 127         try {
 128
 129                 for (int i = 0; i < Estimators.size(); i++) {
 130                         //is this citation, do nothing
 131                         if ((Estimators[i] == "citation") || (Estimators[i] == "default") || (Estimators[i] == "eachgap") || (Estimators[i] == "nogaps") || (Estimators[i] == "onegap")) {}
 132                         //is this a valid calculator
 133                         else if (allCalcs.count(Estimators[i]) != 0) {
 134                                 if (Estimators[i] == "sobs") { Calculator* temp = new Sobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 135                                 }else if (Estimators[i] == "chao") { Calculator* temp = new Chao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 136                                 }else if (Estimators[i] == "nseqs") { Calculator* temp = new NSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 137                                 }else if (Estimators[i] == "coverage") { Calculator* temp = new Coverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 138                                 }else if (Estimators[i] == "ace") { Calculator* temp = new Ace(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 139
 140                                 }else if (Estimators[i] == "jack") { Calculator* temp = new Jackknife(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 141                                 }else if (Estimators[i] == "shannon") { Calculator* temp = new Shannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 142                                 }else if (Estimators[i] == "shannoneven") { Calculator* temp = new ShannonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 143                 }else if (Estimators[i] == "shannonrange") { Calculator* temp = new RangeShannon(0); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 144                                 }else if (Estimators[i] == "npshannon") { Calculator* temp = new NPShannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 145                                 }else if (Estimators[i] == "heip") { Calculator* temp = new Heip(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 146
 147                                 }else if (Estimators[i] == "smithwilson") { Calculator* temp = new SmithWilson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 148                                 }else if (Estimators[i] == "simpson") { Calculator* temp = new Simpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 149                                 }else if (Estimators[i] == "simpsoneven") { Calculator* temp = new SimpsonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 150                                 }else if (Estimators[i] == "invsimpson") { Calculator* temp = new InvSimpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 151                                 }else if (Estimators[i] == "bootstrap") { Calculator* temp = new Bootstrap(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 152
 153                                 }else if (Estimators[i] == "geometric") { Calculator* temp = new Geom(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 154                                 }else if (Estimators[i] == "qstat") { Calculator* temp = new QStat(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 155                                 }else if (Estimators[i] == "logseries") { Calculator* temp = new LogSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 156                                 }else if (Estimators[i] == "bergerparker") { Calculator* temp = new BergerParker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 157                                 }else if (Estimators[i] == "bstick") { Calculator* temp = new BStick(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 158
 159                                 }else if (Estimators[i] == "goodscoverage") { Calculator* temp = new GoodsCoverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 160                                 }else if (Estimators[i] == "efron") { Calculator* temp = new Efron(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 161                                 }else if (Estimators[i] == "boneh") { Calculator* temp = new Boneh(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 162                                 }else if (Estimators[i] == "solow") { Calculator* temp = new Solow(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 163                                 }else if (Estimators[i] == "shen") { Calculator* temp = new Shen(10, 10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 164
 165                                 }else if (Estimators[i] == "sharedchao") { Calculator* temp = new SharedChao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 166                                 }else if (Estimators[i] == "sharedsobs") { Calculator* temp = new SharedSobsCS(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 167                                 }else if (Estimators[i] == "sharedace") { Calculator* temp = new SharedAce(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 168                                 }else if (Estimators[i] == "jabund") {  Calculator* temp = new JAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 169                                 }else if (Estimators[i] == "sorabund") { Calculator* temp = new SorAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 170
 171                                 }else if (Estimators[i] == "jclass") { Calculator* temp = new Jclass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 172                                 }else if (Estimators[i] == "sorclass") { Calculator* temp = new SorClass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 173                                 }else if (Estimators[i] == "jest") { Calculator* temp = new Jest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 174                                 }else if (Estimators[i] == "sorest") { Calculator* temp = new SorEst(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 175                                 }else if (Estimators[i] == "thetayc") { Calculator* temp = new ThetaYC(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 176
 177                                 }else if (Estimators[i] == "thetan") { Calculator* temp = new ThetaN(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 178                                 }else if (Estimators[i] == "kstest") { Calculator* temp = new KSTest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 179                                 }else if (Estimators[i] == "whittaker") { Calculator* temp = new Whittaker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 180                                 }else if (Estimators[i] == "sharednseqs") { Calculator* temp = new SharedNSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 181                                 }else if (Estimators[i] == "ochiai") { Calculator* temp = new Ochiai(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 182
 183                                 }else if (Estimators[i] == "anderberg") { Calculator* temp = new Anderberg(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 184                                 }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 185                                 }else if (Estimators[i] == "kulczynskicody") { Calculator* temp = new KulczynskiCody(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 186                                 }else if (Estimators[i] == "lennon") { Calculator* temp = new Lennon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 187                                 }else if (Estimators[i] == "morisitahorn") { Calculator* temp = new MorHorn(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 188
 189                                 }else if (Estimators[i] == "braycurtis") { Calculator* temp = new BrayCurtis(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 190                                 }else if (Estimators[i] == "odum") { Calculator* temp = new Odum(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 191                                 }else if (Estimators[i] == "canberra") { Calculator* temp = new Canberra(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 192                                 }else if (Estimators[i] == "structeuclidean") { Calculator* temp = new StructEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 193                                 }else if (Estimators[i] == "structchord") { Calculator* temp = new StructChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 194
 195                                 }else if (Estimators[i] == "hellinger") { Calculator* temp = new Hellinger(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 196                                 }else if (Estimators[i] == "manhattan") { Calculator* temp = new Manhattan(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 197                                 }else if (Estimators[i] == "structpearson") { Calculator* temp = new StructPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 198                                 }else if (Estimators[i] == "soergel") { Calculator* temp = new Soergel(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 199                                 }else if (Estimators[i] == "spearman") { Calculator* temp = new Spearman(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 200
 201                                 }else if (Estimators[i] == "structkulczynski") { Calculator* temp = new StructKulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 202                                 }else if (Estimators[i] == "speciesprofile") { Calculator* temp = new SpeciesProfile(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 203                                 }else if (Estimators[i] == "hamming") { Calculator* temp = new Hamming(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 204                                 }else if (Estimators[i] == "structchi2") { Calculator* temp = new StructChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 205                                 }else if (Estimators[i] == "gower") { Calculator* temp = new Gower(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 206
 207                                 }else if (Estimators[i] == "memchi2") { Calculator* temp = new MemChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 208                                 }else if (Estimators[i] == "memchord") { Calculator* temp = new MemChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 209                                 }else if (Estimators[i] == "memeuclidean") { Calculator* temp = new MemEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 210                                 }else if (Estimators[i] == "mempearson") { Calculator* temp = new MemPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 211                                 }else if (Estimators[i] == "sharedobserved") { Calculator* temp = new SharedSobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 212                                 }else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 213                 }else if (Estimators[i] == "jsd") { Calculator* temp = new JSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 214                 }else if (Estimators[i] == "rjsd") { Calculator* temp = new RJSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
 215                                 }else { m->mothurOut("[ERROR]: Missing else if for " + Estimators[i] + " in printCitations."); m->mothurOutEndLine(); }
 216                         }else { m->mothurOut(Estimators[i] + " is not a valid calculator, no citation will be given."); m->mothurOutEndLine(); }
 217                 }
 218
 219         }
 220         catch(exception& e) {
 221                 m->errorOut(e, "ValidCalculator", "printCitations");
 222                 exit(1);
 223         }
 224 }
 225 /********************************************************************/
 226
 227 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 228         try {
 229                 //are you looking for a calculator for a single parameter
 230                 if (parameter == "single") {
 231                         //is it valid
 232                         if ((single.find(calculator)) != (single.end())) {
 233                                 return true;
 234                         }else {
 235                                 m->mothurOut(calculator + " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ");
 236                                 for (it = single.begin(); it != single.end(); it++) {
 237                                         m->mothurOut(it->first + ", ");
 238                                 }
 239                                 m->mothurOutEndLine();
 240                                 return false; }
 241                 //are you looking for a calculator for a shared parameter
 242                 }else if (parameter == "shared") {
 243                         //is it valid
 244                         if ((shared.find(calculator)) != (shared.end())) {
 245                                 return true;
 246                         }else {
 247                                 m->mothurOut(calculator +  " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ");
 248                                 for (it = shared.begin(); it != shared.end(); it++) {
 249                                         m->mothurOut(it->first + ", ");
 250                                 }
 251                                 m->mothurOutEndLine();
 252                                 return false; }
 253                 //are you looking for a calculator for a rarefaction parameter
 254                 }else if (parameter == "rarefaction") {
 255                         //is it valid
 256                         if ((rarefaction.find(calculator)) != (rarefaction.end())) {
 257                                 return true;
 258                         }else {
 259                                 m->mothurOut(calculator + " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ");
 260                                 for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 261                                         m->mothurOut(it->first + ", ");
 262                                 }
 263                                 m->mothurOutEndLine();
 264                                 return false; }
 265                 //are you looking for a calculator for a summary parameter
 266                 }else if (parameter == "summary") {
 267                         //is it valid
 268                         if ((summary.find(calculator)) != (summary.end())) {
 269                                 return true;
 270                         }else {
 271                                 m->mothurOut(calculator + " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
 272                                 for (it = summary.begin(); it != summary.end(); it++) {
 273                                         m->mothurOut(it->first + ", ");
 274                                 }
 275                                 m->mothurOutEndLine();
 276                                 return false; }
 277                 //are you looking for a calculator for a sharedsummary parameter
 278                 }else if (parameter == "sharedsummary") {
 279                         //is it valid
 280                         if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
 281                                 return true;
 282                         }else {
 283                                 m->mothurOut(calculator +  " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
 284                                 for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 285                                         m->mothurOut(it->first + ", ");
 286                                 }
 287                                 m->mothurOutEndLine();
 288                                 return false; }
 289                 }else if (parameter == "sharedrarefaction") {
 290                         //is it valid
 291                         if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 292                                 return true;
 293                         }else {
 294                                 m->mothurOut(calculator + " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ");
 295                                 for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 296                                         m->mothurOut(it->first + ", ");
 297                                 }
 298                                 m->mothurOutEndLine();
 299                                 return false; }
 300                 }else if (parameter == "vennsingle") {
 301                         //is it valid
 302                         if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 303                                 return true;
 304                         }else {
 305                                 m->mothurOut(calculator + " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ");
 306                                 for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 307                                         m->mothurOut(it->first + ", ");
 308                                 }
 309                                 m->mothurOutEndLine();
 310                                 return false; }
 311                 }else if (parameter == "vennshared") {
 312                         //is it valid
 313                         if ((vennshared.find(calculator)) != (vennshared.end())) {
 314                                 return true;
 315                         }else {
 316                                 m->mothurOut(calculator + " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ");
 317                                 for (it = vennshared.begin(); it != vennshared.end(); it++) {
 318                                         m->mothurOut(it->first + ", ");
 319                                 }
 320                                 m->mothurOutEndLine();
 321                                 return false; }
 322                 }else if (parameter == "treegroup") {
 323                         //is it valid
 324                         if ((treegroup.find(calculator)) != (treegroup.end())) {
 325                                 return true;
 326                         }else {
 327                                 m->mothurOut(calculator + " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ");
 328                                 for (it = treegroup.begin(); it != treegroup.end(); it++) {
 329                                         m->mothurOut(it->first + ", ");
 330                                 }
 331                                 m->mothurOutEndLine();
 332                                 return false; }
 333                 }else if (parameter == "matrix") {
 334                         //is it valid
 335                         if ((matrix.find(calculator)) != (matrix.end())) {
 336                                 return true;
 337                         }else {
 338                                 m->mothurOut(calculator +  " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ");
 339                                 for (it = matrix.begin(); it != matrix.end(); it++) {
 340                                         m->mothurOut(it->first + ", ");
 341                                 }
 342                                 m->mothurOutEndLine();
 343                                 return false; }
 344                 }else if (parameter == "heat") {
 345                         //is it valid
 346                         if ((heat.find(calculator)) != (heat.end())) {
 347                                 return true;
 348                         }else {
 349                                 m->mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
 350                                 for (it = heat.begin(); it != heat.end(); it++) {
 351                                         m->mothurOut(it->first + ", ");
 352                                 }
 353                                 m->mothurOutEndLine();
 354                                 return false; }
 355                 }else if (parameter == "boot") {
 356                         //is it valid
 357                         if ((boot.find(calculator)) != (boot.end())) {
 358                                 return true;
 359                         }else {
 360                                 m->mothurOut(calculator + " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ");
 361                                 for (it = boot.begin(); it != boot.end(); it++) {
 362                                         m->mothurOut(it->first + ", ");
 363                                 }
 364                                 m->mothurOutEndLine();
 365                                 return false; }
 366                 }else if (parameter == "distance") {
 367                         //is it valid
 368                         if ((distance.find(calculator)) != (distance.end())) {
 369                                 return true;
 370                         }else {
 371                                 m->mothurOut(calculator +  " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ");
 372                                 for (it = distance.begin(); it != distance.end(); it++) {
 373                                         m->mothurOut(it->first + ", ");
 374                                 }
 375                                 m->mothurOutEndLine();
 376                                 return false; }
 377                 //not a valid parameter
 378                 }else { return false; }
 379
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "ValidCalculator", "isValidCalculator");
 383                 exit(1);
 384         }
 385 }
 386
 387 /********************************************************************/
 388 void ValidCalculators::initialSingle() {
 389         try {
 390                 single["sobs"]          = "sobs";
 391                 single["chao"]              = "chao";
 392                 single["ace"]               = "ace";
 393                 single["jack"]              = "jack";
 394                 single["shannon"]           = "shannon";
 395                 single["npshannon"]     = "npshannon";
 396                 single["shannoneven"]   = "shannoneven";
 397         single["shannonrange"]  = "shannonrange";
 398                 single["smithwilson"]   = "smithwilson";
 399                 single["heip"]                  = "heip";
 400                 single["simpson"]           = "simpson";
 401                 single["simpsoneven"]   = "simpsoneven";
 402                 single["invsimpson"]    = "invsimpson";
 403                 single["bergerparker"]  = "bergerparker";
 404                 single["bootstrap"]     = "bootstrap";
 405                 single["geometric"]     = "geometric";
 406                 single["logseries"]             = "logseries";
 407                 single["qstat"]         = "qstat";
 408                 single["bstick"]        = "bstick";
 409                 single["goodscoverage"] = "goodscoverage";
 410                 single["nseqs"]                 = "nseqs";
 411                 single["coverage"]              = "coverage";
 412                 single["efron"]         = "efron";
 413                 single["boneh"]         = "boneh";
 414                 single["solow"]         = "solow";
 415                 single["shen"]          = "shen";
 416                 single["default"]           = "default";
 417         }
 418         catch(exception& e) {
 419                 m->errorOut(e, "ValidCalculator", "initialSingle");
 420                 exit(1);
 421         }
 422 }
 423
 424 /********************************************************************/
 425 void ValidCalculators::initialShared() {
 426         try {
 427                 shared["sharedsobs"]                    = "sharedsobs";
 428                 shared["sharedchao"]                    = "sharedchao";
 429                 shared["sharedace"]                             = "sharedace";
 430                 shared["jabund"]                                = "jabund";
 431                 shared["sorabund"]                              = "sorabund";
 432                 shared["jclass"]                                = "jclass";
 433                 shared["sorclass"]                              = "sorclass";
 434                 shared["jest"]                                  = "jest";
 435                 shared["sorest"]                                = "sorest";
 436                 shared["thetayc"]                               = "thetayc";
 437                 shared["thetan"]                                = "thetan";
 438                 shared["kstest"]                                = "kstest";
 439                 shared["whittaker"]                         = "whittaker";
 440                 shared["sharednseqs"]                   = "sharednseqs";
 441                 shared["ochiai"]                                = "ochiai";
 442                 shared["anderberg"]                             = "anderberg";
 443                 shared["kulczynski"]                    = "kulczynski";
 444                 shared["kulczynskicody"]                = "kulczynskicody";
 445                 shared["lennon"]                                = "lennon";
 446                 shared["morisitahorn"]                  = "morisitahorn";
 447                 shared["braycurtis"]                    = "braycurtis";
 448                 shared["odum"]                                  = "odum";
 449                 shared["canberra"]                              = "canberra";
 450                 shared["structeuclidean"]               = "structeuclidean";
 451                 shared["structchord"]                   = "structchord";
 452                 shared["hellinger"]                             = "hellinger";
 453                 shared["manhattan"]                             = "manhattan";
 454                 shared["structpearson"]                 = "structpearson";
 455                 shared["soergel"]                               = "soergel";
 456                 shared["spearman"]                              = "spearman";
 457                 shared["structkulczynski"]              = "structkulczynski";
 458                 shared["structchi2"]                    = "structchi2";
 459                 shared["speciesprofile"]                = "speciesprofile";
 460                 shared["hamming"]                               = "hamming";
 461                 shared["gower"]                                 = "gower";
 462                 shared["memchi2"]                               = "memchi2";
 463                 shared["memchord"]                              = "memchord";
 464                 shared["memeuclidean"]                  = "memeuclidean";
 465                 shared["mempearson"]                    = "mempearson";
 466         shared["jsd"]                   = "jsd";
 467         shared["rjsd"]                  = "rjsd";
 468                 shared["default"]                   = "default";
 469         }
 470         catch(exception& e) {
 471                 m->errorOut(e, "ValidCalculator", "initialShared");
 472                 exit(1);
 473         }
 474 }
 475
 476 /********************************************************************/
 477 void ValidCalculators::initialRarefaction() {
 478         try {
 479                 rarefaction["sobs"]                     = "sobs";
 480                 rarefaction["chao"]                     = "chao";
 481                 rarefaction["ace"]                      = "ace";
 482                 rarefaction["jack"]                     = "jack";
 483                 rarefaction["shannon"]          = "shannon";
 484                 rarefaction["smithwilson"]      = "smithwilson";
 485                 rarefaction["heip"]                     = "heip";
 486                 rarefaction["npshannon"]        = "npshannon";
 487                 rarefaction["shannoneven"]      = "shannoneven";
 488         rarefaction["shannonrange"]     = "shannonrange";
 489                 rarefaction["simpson"]          = "simpson";
 490                 rarefaction["invsimpson"]       = "invsimpson";
 491                 rarefaction["simpsoneven"]      = "simpsoneven";
 492                 rarefaction["bootstrap"]        = "bootstrap";
 493                 rarefaction["nseqs"]            = "nseqs";
 494                 rarefaction["coverage"]         = "coverage";
 495                 rarefaction["default"]      = "default";
 496         }
 497         catch(exception& e) {
 498                 m->errorOut(e, "ValidCalculator", "initialRarefaction");
 499                 exit(1);
 500         }
 501 }
 502
 503 /********************************************************************/
 504
 505 void ValidCalculators::initialSummary() {
 506         try {
 507                 summary["sobs"]                 = "sobs";
 508                 summary["chao"]                 = "chao";
 509                 summary["ace"]                  = "ace";
 510                 summary["jack"]                 = "jack";
 511                 summary["shannon"]              = "shannon";
 512                 summary["heip"]                 = "heip";
 513                 summary["shannoneven"]  = "shannoneven";
 514                 summary["smithwilson"]  = "smithwilson";
 515                 summary["invsimpson"]   = "invsimpson";
 516                 summary["npshannon"]    = "npshannon";
 517         summary["shannonrange"] = "shannonrange";
 518                 summary["simpson"]              = "simpson";
 519                 summary["simpsoneven"]  = "simpsoneven";
 520                 summary["bergerparker"] = "bergerparker";
 521                 summary["geometric"]    = "geometric";
 522                 summary["bootstrap"]    = "bootstrap";
 523                 summary["logseries"]    = "logseries";
 524                 summary["qstat"]        = "qstat";
 525                 summary["bstick"]       = "bstick";
 526                 summary["nseqs"]                = "nseqs";
 527                 summary["goodscoverage"]= "goodscoverage";
 528                 summary["coverage"]             = "coverage";
 529                 summary["efron"]        = "efron";
 530                 summary["boneh"]        = "boneh";
 531                 summary["solow"]        = "solow";
 532                 summary["shen"]         = "shen";
 533                 summary["default"]          = "default";
 534         }
 535         catch(exception& e) {
 536                 m->errorOut(e, "ValidCalculator", "initialSummary");
 537                 exit(1);
 538         }
 539 }
 540
 541 /********************************************************************/
 542 void ValidCalculators::initialSharedSummary() {
 543         try {
 544                 sharedsummary["sharedsobs"]                             = "sharedsobs";
 545                 sharedsummary["sharedchao"]                             = "sharedchao";
 546                 sharedsummary["sharedace"]                              = "sharedace";
 547                 sharedsummary["jabund"]                                 = "jabund";
 548                 sharedsummary["sorabund"]                               = "sorabund";
 549                 sharedsummary["jclass"]                                 = "jclass";
 550                 sharedsummary["sorclass"]                               = "sorclass";
 551                 sharedsummary["jest"]                                   = "jest";
 552                 sharedsummary["sorest"]                                 = "sorest";
 553                 sharedsummary["thetayc"]                                = "thetayc";
 554                 sharedsummary["thetan"]                                 = "thetan";
 555                 sharedsummary["kstest"]                                 = "kstest";
 556                 sharedsummary["whittaker"]                              = "whittaker";
 557                 sharedsummary["sharednseqs"]                    = "sharednseqs";
 558                 sharedsummary["ochiai"]                                 = "ochiai";
 559                 sharedsummary["anderberg"]                              = "anderberg";
 560                 sharedsummary["kulczynski"]                             = "kulczynski";
 561                 sharedsummary["kulczynskicody"]                 = "kulczynskicody";
 562                 sharedsummary["lennon"]                                 = "lennon";
 563                 sharedsummary["morisitahorn"]                   = "morisitahorn";
 564                 sharedsummary["braycurtis"]                             = "braycurtis";
 565                 sharedsummary["odum"]                                   = "odum";
 566                 sharedsummary["canberra"]                               = "canberra";
 567                 sharedsummary["structeuclidean"]                = "structeuclidean";
 568                 sharedsummary["structchord"]                    = "structchord";
 569                 sharedsummary["hellinger"]                              = "hellinger";
 570                 sharedsummary["manhattan"]                              = "manhattan";
 571                 sharedsummary["structpearson"]                  = "structpearson";
 572                 sharedsummary["structkulczynski"]               = "structkulczynski";
 573                 sharedsummary["structchi2"]                             = "structchi2";
 574                 sharedsummary["soergel"]                                = "soergel";
 575                 sharedsummary["spearman"]                               = "spearman";
 576                 sharedsummary["speciesprofile"]                 = "speciesprofile";
 577                 sharedsummary["hamming"]                                = "hamming";
 578                 sharedsummary["gower"]                                  = "gower";
 579                 sharedsummary["memchi2"]                                = "memchi2";
 580                 sharedsummary["memchord"]                               = "memchord";
 581                 sharedsummary["memeuclidean"]                   = "memeuclidean";
 582                 sharedsummary["mempearson"]                             = "mempearson";
 583         sharedsummary["jsd"]                    = "jsd";
 584         sharedsummary["rjsd"]                   = "rjsd";
 585                 sharedsummary["default"]                                = "default";
 586         }
 587         catch(exception& e) {
 588                 m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 589                 exit(1);
 590         }
 591 }
 592
 593
 594 /********************************************************************/
 595
 596 void ValidCalculators::initialSharedRarefact() {
 597         try {
 598                 sharedrarefaction["sharedobserved"]     = "sharedobserved";
 599                 sharedrarefaction["sharednseqs"]        = "sharednseqs";
 600                 sharedrarefaction["default"]        = "default";
 601         }
 602         catch(exception& e) {
 603                 m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 604                 exit(1);
 605         }
 606 }
 607
 608
 609 /********************************************************************/
 610 void ValidCalculators::initialVennSingle() {
 611         try {
 612                 vennsingle["sobs"]              = "sobs";
 613                 vennsingle["chao"]                  = "chao";
 614                 vennsingle["ace"]                       = "ace";
 615                 vennsingle["jack"]                  = "jack";
 616                 vennsingle["default"]           = "default";
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "ValidCalculator", "initialVennSingle");
 620                 exit(1);
 621         }
 622 }
 623
 624 /********************************************************************/
 625 void ValidCalculators::initialVennShared() {
 626         try {
 627                 vennshared["sharedsobs"]        = "sharedsobs";
 628                 vennshared["sharedchao"]        = "sharedchao";
 629                 vennshared["sharedace"]         = "sharedace";
 630                 vennshared["default"]           = "default";
 631         }
 632         catch(exception& e) {
 633                 m->errorOut(e, "ValidCalculator", "initialVennShared");
 634                 exit(1);
 635         }
 636 }
 637
 638 /********************************************************************/
 639 void ValidCalculators::initialTreeGroups() {
 640         try {
 641                 treegroup["sharedsobs"]                         = "sharedsobs";
 642                 treegroup["sharedchao"]                         = "sharedchao";
 643                 treegroup["sharedace"]                          = "sharedace";
 644                 treegroup["jabund"]                                     = "jabund";
 645                 treegroup["sorabund"]                           = "sorabund";
 646                 treegroup["jclass"]                                     = "jclass";
 647                 treegroup["sorclass"]                           = "sorclass";
 648                 treegroup["jest"]                                       = "jest";
 649                 treegroup["sorest"]                                     = "sorest";
 650                 treegroup["thetayc"]                            = "thetayc";
 651                 treegroup["thetan"]                                     = "thetan";
 652                 treegroup["kstest"]                                     = "kstest";
 653                 treegroup["whittaker"]                          = "whittaker";
 654                 treegroup["sharednseqs"]                        = "sharednseqs";
 655                 treegroup["ochiai"]                                     = "ochiai";
 656                 treegroup["anderberg"]                          = "anderberg";
 657                 treegroup["kulczynski"]                         = "kulczynski";
 658                 treegroup["kulczynskicody"]                     = "kulczynskicody";
 659                 treegroup["lennon"]                                     = "lennon";
 660                 treegroup["morisitahorn"]                       = "morisitahorn";
 661                 treegroup["braycurtis"]                         = "braycurtis";
 662                 treegroup["odum"]                                       = "odum";
 663                 treegroup["canberra"]                           = "canberra";
 664                 treegroup["structeuclidean"]            = "structeuclidean";
 665                 treegroup["structchord"]                        = "structchord";
 666                 treegroup["hellinger"]                          = "hellinger";
 667                 treegroup["manhattan"]                          = "manhattan";
 668                 treegroup["structpearson"]                      = "structpearson";
 669                 treegroup["structkulczynski"]           = "structkulczynski";
 670                 treegroup["structchi2"]                         = "structchi2";
 671                 treegroup["soergel"]                            = "soergel";
 672                 treegroup["spearman"]                           = "spearman";
 673                 treegroup["speciesprofile"]                     = "speciesprofile";
 674                 treegroup["hamming"]                            = "hamming";
 675                 treegroup["gower"]                                      = "gower";
 676                 treegroup["memchi2"]                            = "memchi2";
 677                 treegroup["memchord"]                           = "memchord";
 678                 treegroup["memeuclidean"]                       = "memeuclidean";
 679                 treegroup["mempearson"]                         = "mempearson";
 680
 681         }
 682         catch(exception& e) {
 683                 m->errorOut(e, "ValidCalculator", "initialTreeGroups");
 684                 exit(1);
 685         }
 686 }
 687 /********************************************************************/
 688 void ValidCalculators::initialHeat() {
 689         try {
 690                 heat["jabund"]                          = "jabund";
 691                 heat["sorabund"]                        = "sorabund";
 692                 heat["jclass"]                          = "jclass";
 693                 heat["sorclass"]                        = "sorclass";
 694                 heat["jest"]                            = "jest";
 695                 heat["sorest"]                          = "sorest";
 696                 heat["thetayc"]                         = "thetayc";
 697                 heat["thetan"]                          = "thetan";
 698                 heat["morisitahorn"]            = "morisitahorn";
 699                 heat["braycurtis"]                      = "braycurtis";
 700         }
 701         catch(exception& e) {
 702                 m->errorOut(e, "ValidCalculator", "initialHeat");
 703                 exit(1);
 704         }
 705 }
 706
 707 /********************************************************************/
 708 void ValidCalculators::initialMatrix() {
 709         try {
 710                 matrix["sharedsobs"]                            = "sharedsobs";
 711                 matrix["sharedchao"]                            = "sharedchao";
 712                 matrix["sharedace"]                             = "sharedace";
 713                 matrix["jabund"]                                        = "jabund";
 714                 matrix["sorabund"]                              = "sorabund";
 715                 matrix["jclass"]                                        = "jclass";
 716                 matrix["sorclass"]                              = "sorclass";
 717                 matrix["jest"]                                  = "jest";
 718                 matrix["sorest"]                                        = "sorest";
 719                 matrix["thetayc"]                               = "thetayc";
 720                 matrix["thetan"]                                        = "thetan";
 721                 matrix["kstest"]                                        = "kstest";
 722                 matrix["whittaker"]                             = "whittaker";
 723                 matrix["sharednseqs"]                   = "sharednseqs";
 724                 matrix["ochiai"]                                        = "ochiai";
 725                 matrix["anderberg"]                             = "anderberg";
 726                 matrix["kulczynski"]                            = "kulczynski";
 727                 matrix["kulczynskicody"]                        = "kulczynskicody";
 728                 matrix["lennon"]                                        = "lennon";
 729                 matrix["morisitahorn"]                  = "morisitahorn";
 730                 matrix["braycurtis"]                            = "braycurtis";
 731                 matrix["odum"]                                  = "odum";
 732                 matrix["canberra"]                              = "canberra";
 733                 matrix["structeuclidean"]               = "structeuclidean";
 734                 matrix["structchord"]                   = "structchord";
 735                 matrix["hellinger"]                             = "hellinger";
 736                 matrix["manhattan"]                             = "manhattan";
 737                 matrix["structpearson"]                 = "structpearson";
 738                 matrix["structkulczynski"]              = "structkulczynski";
 739                 matrix["structchi2"]                            = "structchi2";
 740                 matrix["soergel"]                               = "soergel";
 741                 matrix["spearman"]                              = "spearman";
 742                 matrix["speciesprofile"]                = "speciesprofile";
 743                 matrix["hamming"]                               = "hamming";
 744                 matrix["gower"]                                 = "gower";
 745                 matrix["memchi2"]                               = "memchi2";
 746                 matrix["memchord"]                              = "memchord";
 747                 matrix["memeuclidean"]                  = "memeuclidean";
 748                 matrix["mempearson"]                    = "mempearson";
 749         matrix["rjsd"]                   = "rjsd";
 750         matrix["jsd"]                   = "jsd";
 751
 752         }
 753         catch(exception& e) {
 754                 m->errorOut(e, "ValidCalculator", "initialMatrix");
 755                 exit(1);
 756         }
 757 }
 758
 759 /********************************************************************/
 760 void ValidCalculators::initialBoot() {
 761         try {
 762                 boot["jabund"]                          = "jabund";
 763                 boot["sorabund"]                        = "sorabund";
 764                 boot["jclass"]                          = "jclass";
 765                 boot["sorclass"]                        = "orclass";
 766                 boot["jest"]                            = "jest";
 767                 boot["sorest"]                          = "sorest";
 768                 boot["thetayc"]                         = "thetayc";
 769                 boot["thetan"]                          = "thetan";
 770                 boot["morisitahorn"]            = "morisitahorn";
 771                 boot["braycurtis"]                      = "braycurtis";
 772         }
 773         catch(exception& e) {
 774                 m->errorOut(e, "ValidCalculator", "initialBoot");
 775                 exit(1);
 776         }
 777 }
 778 /********************************************************************/
 779 void ValidCalculators::initialDistance() {
 780         try {
 781                 distance["nogaps"]              = "nogaps";
 782                 distance["eachgap"]             = "eachgap";
 783                 distance["onegap"]              = "onegap";
 784         }
 785         catch(exception& e) {
 786                 m->errorOut(e, "ValidCalculator", "initialDistance");
 787                 exit(1);
 788         }
 789 }
 790
 791 /********************************************************************/
 792 void ValidCalculators::printCalc(string parameter, ostream& out) {
 793         try{
 794                 out << "The available estimators for calc are ";
 795                 //are you looking for a calculator for a single parameter
 796                 if (parameter == "single") {
 797                         for (it = single.begin(); it != single.end(); it++) {
 798                                 out << it->first << ", ";
 799                         }
 800                 //are you looking for a calculator for a shared parameter
 801                 }else if (parameter == "shared") {
 802                         for (it = shared.begin(); it != shared.end(); it++) {
 803                                 out << it->first << ", ";
 804                         }
 805                 //are you looking for a calculator for a rarefaction parameter
 806                 }else if (parameter == "rarefaction") {
 807                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 808                                 out << it->first << ", ";
 809                         }
 810                 //are you looking for a calculator for a summary parameter
 811                 }else if (parameter == "summary") {
 812                         for (it = summary.begin(); it != summary.end(); it++) {
 813                                 out << it->first << ", ";
 814                         }
 815                 //are you looking for a calculator for a sharedsummary parameter
 816                 }else if (parameter == "sharedsummary") {
 817                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 818                                 out << it->first << ", ";
 819                         }
 820                 }else if (parameter == "sharedrarefaction") {
 821                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 822                                 out << it->first << ", ";
 823                         }
 824                 }else if (parameter == "vennsingle") {
 825                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 826                                 out << it->first << ", ";
 827                         }
 828                 }else if (parameter == "vennshared") {
 829                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 830                                 out << it->first << ", ";
 831                         }
 832                 }else if (parameter == "treegroup") {
 833                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 834                                 out << it->first << ", ";
 835                         }
 836                 }else if (parameter == "matrix") {
 837                         for (it = matrix.begin(); it != matrix.end(); it++) {
 838                                 out << it->first << ", ";
 839                         }
 840                 }else if (parameter == "heat") {
 841                         for (it = heat.begin(); it != heat.end(); it++) {
 842                                 out << it->first << ", ";
 843                         }
 844                 }else if (parameter == "boot") {
 845                         for (it = boot.begin(); it != boot.end(); it++) {
 846                                 out << it->first << ", ";
 847                         }
 848                 }else if (parameter == "distance") {
 849                         for (it = distance.begin(); it != distance.end(); it++) {
 850                                 out << it->first << ", ";
 851                         }
 852                 }
 853
 854                 out << endl;
 855         }
 856         catch(exception& e) {
 857                 m->errorOut(e, "ValidCalculator", "printCalc");
 858                 exit(1);
 859         }
 860 }
 861 /********************************************************************/
 862 string ValidCalculators::printCalc(string parameter) {
 863         try{
 864                 string output = "The available estimators for calc are ";
 865                 //are you looking for a calculator for a single parameter
 866                 if (parameter == "single") {
 867                         for (it = single.begin(); it != single.end(); it++) {
 868                                 output += it->first + ", ";
 869                         }
 870                         //are you looking for a calculator for a shared parameter
 871                 }else if (parameter == "shared") {
 872                         for (it = shared.begin(); it != shared.end(); it++) {
 873                                 output += it->first + ", ";
 874                         }
 875                         //are you looking for a calculator for a rarefaction parameter
 876                 }else if (parameter == "rarefaction") {
 877                         for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
 878                                 output += it->first + ", ";
 879                         }
 880                         //are you looking for a calculator for a summary parameter
 881                 }else if (parameter == "summary") {
 882                         for (it = summary.begin(); it != summary.end(); it++) {
 883                                 output += it->first + ", ";
 884                         }
 885                         //are you looking for a calculator for a sharedsummary parameter
 886                 }else if (parameter == "sharedsummary") {
 887                         for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
 888                                 output += it->first + ", ";
 889                         }
 890                 }else if (parameter == "sharedrarefaction") {
 891                         for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
 892                                 output += it->first + ", ";
 893                         }
 894                 }else if (parameter == "vennsingle") {
 895                         for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
 896                                 output += it->first + ", ";
 897                         }
 898                 }else if (parameter == "vennshared") {
 899                         for (it = vennshared.begin(); it != vennshared.end(); it++) {
 900                                 output += it->first + ", ";
 901                         }
 902                 }else if (parameter == "treegroup") {
 903                         for (it = treegroup.begin(); it != treegroup.end(); it++) {
 904                                 output += it->first + ", ";
 905                         }
 906                 }else if (parameter == "matrix") {
 907                         for (it = matrix.begin(); it != matrix.end(); it++) {
 908                                 output += it->first + ", ";
 909                         }
 910                 }else if (parameter == "heat") {
 911                         for (it = heat.begin(); it != heat.end(); it++) {
 912                                 output += it->first + ", ";
 913                         }
 914                 }else if (parameter == "boot") {
 915                         for (it = boot.begin(); it != boot.end(); it++) {
 916                                 output += it->first + ", ";
 917                         }
 918                 }else if (parameter == "distance") {
 919                         for (it = distance.begin(); it != distance.end(); it++) {
 920                                 output += it->first + ", ";
 921                         }
 922                 }
 923
 924                 //rip off comma
 925                 output = output.substr(0, output.length()-1);
 926                 output += "\n";
 927
 928                 return output;
 929         }
 930         catch(exception& e) {
 931                 m->errorOut(e, "ValidCalculator", "printCalc");
 932                 exit(1);
 933         }
 934 }
 935 /********************************************************************/
 936
 937