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