X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=validcalculator.cpp;h=7df7c4e28d65cb2f7853500728075e8edc161723;hp=0ffa216411077e94a02f69fada77e9421e2d378b;hb=d1c97b8c04bb75faca1e76ffad60b37a4d789d3d;hpb=25cde7ff05bbe741da1712f2c740e0bc8706e523

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 0ffa216..7df7c4e 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -8,31 +8,214 @@
  */
 
 #include "validcalculator.h"
+#include "ace.h"
+#include "sobs.h"
+#include "nseqs.h"
+#include "chao1.h"
+#include "bootstrap.h"
+#include "simpson.h"
+#include "simpsoneven.h"
+#include "invsimpson.h"
+#include "npshannon.h"
+#include "shannon.h"
+#include "smithwilson.h"
+#include "heip.h"
+#include "shannoneven.h"
+#include "jackknife.h"
+#include "geom.h"
+#include "qstat.h"
+#include "logsd.h"
+#include "bergerparker.h"
+#include "bstick.h"
+#include "goodscoverage.h"
+#include "efron.h"
+#include "boneh.h"
+#include "solow.h"
+#include "shen.h"
+#include "coverage.h"
+#include "sharedsobscollectsummary.h"
+#include "sharedchao1.h"
+#include "sharedace.h"
+#include "sharedjabund.h"
+#include "sharedsorabund.h"
+#include "sharedjclass.h"
+#include "sharedsorclass.h"
+#include "sharedjest.h"
+#include "sharedsorest.h"
+#include "sharedthetayc.h"
+#include "sharedthetan.h"
+#include "sharedkstest.h"
+#include "whittaker.h"
+#include "sharednseqs.h"
+#include "sharedochiai.h"
+#include "sharedanderbergs.h"
+#include "sharedkulczynski.h"
+#include "sharedkulczynskicody.h"
+#include "sharedlennon.h"
+#include "sharedmorisitahorn.h"
+#include "sharedbraycurtis.h"
+#include "sharedjackknife.h"
+#include "whittaker.h"
+#include "odum.h"
+#include "canberra.h"
+#include "structeuclidean.h"
+#include "structchord.h"
+#include "hellinger.h"
+#include "manhattan.h"
+#include "structpearson.h"
+#include "soergel.h"
+#include "spearman.h"
+#include "structkulczynski.h"
+#include "structchi2.h"
+#include "speciesprofile.h"
+#include "hamming.h"
+#include "gower.h"
+#include "memchi2.h"
+#include "memchord.h"
+#include "memeuclidean.h"
+#include "mempearson.h"
+#include "sharedsobs.h"
+#include "sharednseqs.h"
+
 
 /********************************************************************/
 ValidCalculators::ValidCalculators() {
 	try {
-		 initialSingle();
-		 initialShared();
-		 initialRarefaction();
-		 initialSharedRarefact();
-		 initialSummary();
-		 initialSharedSummary();
+		m = MothurOut::getInstance();
+		
+		initialSingle();  
+		initialShared();
+		initialRarefaction();
+		initialSharedRarefact();
+		initialSummary();
+		initialSharedSummary();
+		initialVennSingle();
+		initialVennShared();
+		initialTreeGroups();
+		initialBoot();
+		initialDistance();
+		initialMatrix();
+		initialHeat();
+		
+		for(it = single.begin(); it != single.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = shared.begin(); it != shared.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = rarefaction.begin(); it != rarefaction.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = summary.begin(); it != summary.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = sharedsummary.begin(); it != sharedsummary.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = vennsingle.begin(); it != vennsingle.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = vennshared.begin(); it != vennshared.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = treegroup.begin(); it != treegroup.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = matrix.begin(); it != matrix.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = heat.begin(); it != heat.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = boot.begin(); it != boot.end(); it++) { allCalcs.insert(it->first); } 
+		for(it = distance.begin(); it != distance.end(); it++) { allCalcs.insert(it->first); } 
+		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "ValidCalculator");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		 
 }
-
 /********************************************************************/
-
 ValidCalculators::~ValidCalculators() {}
-
+/********************************************************************/
+void ValidCalculators::printCitations(vector<string> Estimators) {
+	try {
+		
+		for (int i = 0; i < Estimators.size(); i++) {
+			//is this citation, do nothing
+			if ((Estimators[i] == "citation") || (Estimators[i] == "default") || (Estimators[i] == "eachgap") || (Estimators[i] == "nogaps") || (Estimators[i] == "onegap")) {}
+			//is this a valid calculator
+			else if (allCalcs.count(Estimators[i]) != 0) {
+				if (Estimators[i] == "sobs") { Calculator* temp = new Sobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "chao") { Calculator* temp = new Chao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "nseqs") { Calculator* temp = new NSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "coverage") { Calculator* temp = new Coverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "ace") { Calculator* temp = new Ace(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				
+				}else if (Estimators[i] == "jack") { Calculator* temp = new Jackknife(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "shannon") { Calculator* temp = new Shannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "shannoneven") { Calculator* temp = new ShannonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "npshannon") { Calculator* temp = new NPShannon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "heip") { Calculator* temp = new Heip(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "smithwilson") { Calculator* temp = new SmithWilson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "simpson") { Calculator* temp = new Simpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "simpsoneven") { Calculator* temp = new SimpsonEven(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "invsimpson") { Calculator* temp = new InvSimpson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "bootstrap") { Calculator* temp = new Bootstrap(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "geometric") { Calculator* temp = new Geom(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "qstat") { Calculator* temp = new QStat(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "logseries") { Calculator* temp = new LogSD(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "bergerparker") { Calculator* temp = new BergerParker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "bstick") { Calculator* temp = new BStick(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "goodscoverage") { Calculator* temp = new GoodsCoverage(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "efron") { Calculator* temp = new Efron(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "boneh") { Calculator* temp = new Boneh(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;  
+				}else if (Estimators[i] == "solow") { Calculator* temp = new Solow(10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "shen") { Calculator* temp = new Shen(10, 10); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "sharedchao") { Calculator* temp = new SharedChao1(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "sharedsobs") { Calculator* temp = new SharedSobsCS(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "sharedace") { Calculator* temp = new SharedAce(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "jabund") { 	Calculator* temp = new JAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "sorabund") { Calculator* temp = new SorAbund(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "jclass") { Calculator* temp = new Jclass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "sorclass") { Calculator* temp = new SorClass(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;  
+				}else if (Estimators[i] == "jest") { Calculator* temp = new Jest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "sorest") { Calculator* temp = new SorEst(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "thetayc") { Calculator* temp = new ThetaYC(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "thetan") { Calculator* temp = new ThetaN(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "kstest") { Calculator* temp = new KSTest(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "whittaker") { Calculator* temp = new Whittaker(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "sharednseqs") { Calculator* temp = new SharedNSeqs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;  
+				}else if (Estimators[i] == "ochiai") { Calculator* temp = new Ochiai(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				
+				}else if (Estimators[i] == "anderberg") { Calculator* temp = new Anderberg(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "kulczynskicody") { Calculator* temp = new KulczynskiCody(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp; 
+				}else if (Estimators[i] == "lennon") { Calculator* temp = new Lennon(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "morisitahorn") { Calculator* temp = new MorHorn(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				
+				}else if (Estimators[i] == "braycurtis") { Calculator* temp = new BrayCurtis(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "odum") { Calculator* temp = new Odum(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "canberra") { Calculator* temp = new Canberra(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "structeuclidean") { Calculator* temp = new StructEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "structchord") { Calculator* temp = new StructChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				
+				}else if (Estimators[i] == "hellinger") { Calculator* temp = new Hellinger(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "manhattan") { Calculator* temp = new Manhattan(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "structpearson") { Calculator* temp = new StructPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "soergel") { Calculator* temp = new Soergel(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "spearman") { Calculator* temp = new Spearman(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				
+				}else if (Estimators[i] == "structkulczynski") { Calculator* temp = new StructKulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "speciesprofile") { Calculator* temp = new SpeciesProfile(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "hamming") { Calculator* temp = new Hamming(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "structchi2") { Calculator* temp = new StructChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "gower") { Calculator* temp = new Gower(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				
+				}else if (Estimators[i] == "memchi2") { Calculator* temp = new MemChi2(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "memchord") { Calculator* temp = new MemChord(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "memeuclidean") { Calculator* temp = new MemEuclidean(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "mempearson") { Calculator* temp = new MemPearson(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "sharedobserved") { Calculator* temp = new SharedSobs(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else if (Estimators[i] == "kulczynski") { Calculator* temp = new Kulczynski(); m->mothurOut(temp->getName() + ": "); temp->citation(); delete temp;
+				}else { m->mothurOut("[ERROR]: Missing else if for " + Estimators[i] + " in printCitations."); m->mothurOutEndLine(); }
+			}else { m->mothurOut(Estimators[i] + " is not a valid calculator, no citation will be given."); m->mothurOutEndLine(); }
+		}
+			
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "printCitations");
+		exit(1);
+	}
+}
 /********************************************************************/
 
 bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
@@ -43,11 +226,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((single.find(calculator)) != (single.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
+				m->mothurOut(calculator + " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ");
 				for (it = single.begin(); it != single.end(); it++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a shared parameter
 		}else if (parameter == "shared") {
@@ -55,11 +238,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((shared.find(calculator)) != (shared.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
+				m->mothurOut(calculator +  " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ");
 				for (it = shared.begin(); it != shared.end(); it++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a rarefaction parameter
 		}else if (parameter == "rarefaction") {
@@ -67,11 +250,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((rarefaction.find(calculator)) != (rarefaction.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
+				m->mothurOut(calculator + " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ");
 				for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a summary parameter
 		}else if (parameter == "summary") {
@@ -79,11 +262,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((summary.find(calculator)) != (summary.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+				m->mothurOut(calculator + " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
 				for (it = summary.begin(); it != summary.end(); it++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a sharedsummary parameter
 		}else if (parameter == "sharedsummary") {
@@ -91,60 +274,144 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+				m->mothurOut(calculator +  " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ");
 				for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		}else if (parameter == "sharedrarefaction") {
 			//is it valid
 			if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
+				m->mothurOut(calculator + " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ");
 				for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
-		//not a valid paramter
+		}else if (parameter == "vennsingle") {
+			//is it valid
+			if ((vennsingle.find(calculator)) != (vennsingle.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator + " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ");
+				for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "vennshared") {
+			//is it valid
+			if ((vennshared.find(calculator)) != (vennshared.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator + " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ");
+				for (it = vennshared.begin(); it != vennshared.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "treegroup") {
+			//is it valid
+			if ((treegroup.find(calculator)) != (treegroup.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator + " is not a valid estimator for the tree.shared command and will be disregarded. Valid estimators are ");
+				for (it = treegroup.begin(); it != treegroup.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "matrix") {
+			//is it valid
+			if ((matrix.find(calculator)) != (matrix.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator +  " is not a valid estimator for the matrix.output command and will be disregarded. Valid estimators are ");
+				for (it = matrix.begin(); it != matrix.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "heat") {
+			//is it valid
+			if ((heat.find(calculator)) != (heat.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator + " is not a valid estimator for the heatmap.sim command and will be disregarded. Valid estimators are ");
+				for (it = heat.begin(); it != heat.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "boot") {
+			//is it valid
+			if ((boot.find(calculator)) != (boot.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator + " is not a valid estimator for the bootstrap.shared command and will be disregarded. Valid estimators are ");
+				for (it = boot.begin(); it != boot.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "distance") {
+			//is it valid
+			if ((distance.find(calculator)) != (distance.end())) {
+				return true;
+			}else { 
+				m->mothurOut(calculator +  " is not a valid estimator for the distance command and will be disregarded. Valid calculators are ");
+				for (it = distance.begin(); it != distance.end(); it++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		//not a valid parameter
 		}else { return false; }
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "isValidCalculator");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
 void ValidCalculators::initialSingle() {
 	try {	
-	
-		single["sobs"]		= "sobs";
-		single["chao"]		= "chao";
-		single["ace"]		= "ace";
-		single["jack"]		= "jack";
-		single["shannon"]	= "shannon";
-		single["npshannon"]	= "npshannon";
-		single["simpson"]	= "simpson";
-		single["bootstrap"]	= "bootstrap";
-		single["default"]	= "default";
-		single["nseqs"]		= "nseqs";
+		single["sobs"]	        = "sobs";
+		single["chao"]		    = "chao";
+		single["ace"]		    = "ace";
+		single["jack"]		    = "jack";
+		single["shannon"]	    = "shannon";
+		single["npshannon"]    	= "npshannon";
+		single["shannoneven"]	= "shannoneven";
+		single["smithwilson"]	= "smithwilson";
+		single["heip"]			= "heip";
+		single["simpson"]	    = "simpson";
+		single["simpsoneven"]   = "simpsoneven";
+		single["invsimpson"]	= "invsimpson";
+		single["bergerparker"]  = "bergerparker";
+		single["bootstrap"]    	= "bootstrap";
+		single["geometric"]     = "geometric";
+		single["logseries"]		= "logseries";
+		single["qstat"]         = "qstat";
+		single["bstick"]        = "bstick";
+		single["goodscoverage"] = "goodscoverage";
+		single["nseqs"]			= "nseqs";
+		single["coverage"]		= "coverage";
+		single["efron"]         = "efron";
+		single["boneh"]         = "boneh";
+		single["solow"]         = "solow";
+		single["shen"]          = "shen";
+		single["default"]	    = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSingle");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -153,32 +420,48 @@ void ValidCalculators::initialShared() {
 		shared["sharedsobs"]			= "sharedsobs";
 		shared["sharedchao"]			= "sharedchao";
 		shared["sharedace"]				= "sharedace";
-		shared["sharedjabund"]			= "sharedjabund";
-		shared["sharedsorensonabund"]	= "sharedsorensonabund";
-		shared["sharedjclass"]			= "sharedjclass";
-		shared["sharedsorclass"]		= "sharedsorclass";
-		shared["sharedjest"]			= "sharedjest";
-		shared["sharedsorest"]			= "sharedsorest";
-		shared["sharedthetayc"]			= "sharedthetayc";
-		shared["sharedthetan"]			= "sharedthetan";
+		shared["jabund"]				= "jabund";
+		shared["sorabund"]				= "sorabund";
+		shared["jclass"]				= "jclass";
+		shared["sorclass"]				= "sorclass";
+		shared["jest"]					= "jest";
+		shared["sorest"]				= "sorest";
+		shared["thetayc"]				= "thetayc";
+		shared["thetan"]				= "thetan";
+		shared["kstest"]				= "kstest";
+		shared["whittaker"]			    = "whittaker";
 		shared["sharednseqs"]			= "sharednseqs";
-		shared["sharedochiai"]			= "sharedochiai";
-		shared["sharedanderberg"]		= "sharedanderberg";
-		shared["sharedkulczynski"]		= "sharedkulczynski";
-		shared["sharedkulczynskicody"]	= "sharedkulczynskicody";
-		shared["sharedlennon"]			= "sharedlennon";
-		shared["sharedmorisitahorn"]	= "sharedmorisitahorn";
-		shared["sharedbraycurtis"]		= "sharedbraycurtis";
+		shared["ochiai"]				= "ochiai";
+		shared["anderberg"]				= "anderberg";
+		shared["kulczynski"]			= "kulczynski";
+		shared["kulczynskicody"]		= "kulczynskicody";
+		shared["lennon"]				= "lennon";
+		shared["morisitahorn"]			= "morisitahorn";
+		shared["braycurtis"]			= "braycurtis";
+		shared["odum"]					= "odum";
+		shared["canberra"]				= "canberra";
+		shared["structeuclidean"]		= "structeuclidean";
+		shared["structchord"]			= "structchord";
+		shared["hellinger"]				= "hellinger";
+		shared["manhattan"]				= "manhattan";
+		shared["structpearson"]			= "structpearson";
+		shared["soergel"]				= "soergel";
+		shared["spearman"]				= "spearman";
+		shared["structkulczynski"]		= "structkulczynski";
+		shared["structchi2"]			= "structchi2";
+		shared["speciesprofile"]		= "speciesprofile";
+		shared["hamming"]				= "hamming";
+		shared["gower"]					= "gower";
+		shared["memchi2"]				= "memchi2";
+		shared["memchord"]				= "memchord";
+		shared["memeuclidean"]			= "memeuclidean";
+		shared["mempearson"]			= "mempearson";
 		shared["default"]	            = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialShared");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -189,20 +472,22 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["ace"]			= "ace";
 		rarefaction["jack"]			= "jack";
 		rarefaction["shannon"]		= "shannon";
+		rarefaction["smithwilson"]	= "smithwilson";
+		rarefaction["heip"]			= "heip";
 		rarefaction["npshannon"]	= "npshannon";
+		rarefaction["shannoneven"]	= "shannoneven";
 		rarefaction["simpson"]		= "simpson";
+		rarefaction["invsimpson"]	= "invsimpson";
+		rarefaction["simpsoneven"]	= "simpsoneven";
 		rarefaction["bootstrap"]	= "bootstrap";
 		rarefaction["nseqs"]		= "nseqs";
+		rarefaction["coverage"]		= "coverage";
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialRarefaction");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -214,20 +499,32 @@ void ValidCalculators::initialSummary() {
 		summary["ace"]			= "ace";
 		summary["jack"]			= "jack";
 		summary["shannon"]		= "shannon";
+		summary["heip"]			= "heip";
+		summary["shannoneven"]	= "shannoneven";
+		summary["smithwilson"]	= "smithwilson";
+		summary["invsimpson"]	= "invsimpson";
 		summary["npshannon"]	= "npshannon";
 		summary["simpson"]		= "simpson";
+		summary["simpsoneven"]	= "simpsoneven";
+		summary["bergerparker"] = "bergerparker";
+		summary["geometric"]    = "geometric";
 		summary["bootstrap"]	= "bootstrap";
+		summary["logseries"]    = "logseries";
+		summary["qstat"]        = "qstat";
+		summary["bstick"]       = "bstick";
 		summary["nseqs"]		= "nseqs";
+		summary["goodscoverage"]= "goodscoverage";
+		summary["coverage"]		= "coverage";
+		summary["efron"]        = "efron";
+		summary["boneh"]        = "boneh";
+		summary["solow"]        = "solow";
+		summary["shen"]         = "shen";
 		summary["default"]	    = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSummary");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -236,32 +533,48 @@ void ValidCalculators::initialSharedSummary() {
 		sharedsummary["sharedsobs"]				= "sharedsobs";
 		sharedsummary["sharedchao"]				= "sharedchao";
 		sharedsummary["sharedace"]				= "sharedace";
-		sharedsummary["sharedjabund"]			= "sharedjabund";
-		sharedsummary["sharedsorensonabund"]	= "sharedsorensonabund";
-		sharedsummary["sharedjclass"]			= "sharedjclass";
-		sharedsummary["sharedsorclass"]			= "sharedsorclass";
-		sharedsummary["sharedjest"]				= "sharedjest";
-		sharedsummary["sharedsorest"]			= "sharedsorest";
-		sharedsummary["sharedthetayc"]			= "sharedthetayc";
-		sharedsummary["sharedthetan"]			= "sharedthetan";
+		sharedsummary["jabund"]					= "jabund";
+		sharedsummary["sorabund"]				= "sorabund";
+		sharedsummary["jclass"]					= "jclass";
+		sharedsummary["sorclass"]				= "sorclass";
+		sharedsummary["jest"]					= "jest";
+		sharedsummary["sorest"]					= "sorest";
+		sharedsummary["thetayc"]				= "thetayc";
+		sharedsummary["thetan"]					= "thetan";
+		sharedsummary["kstest"]					= "kstest";
+		sharedsummary["whittaker"]				= "whittaker";
 		sharedsummary["sharednseqs"]			= "sharednseqs";
-		sharedsummary["sharedochiai"]			= "sharedochiai";
-		sharedsummary["sharedanderberg"]		= "sharedanderberg";
-		sharedsummary["sharedkulczynski"]		= "sharedkulczynski";
-		sharedsummary["sharedkulczynskicody"]	= "sharedkulczynskicody";
-		sharedsummary["sharedlennon"]			= "sharedlennon";
-		sharedsummary["sharedmorisitahorn"]		= "sharedmorisitahorn";
-		sharedsummary["sharedbraycurtis"]		= "sharedbraycurtis";
+		sharedsummary["ochiai"]					= "ochiai";
+		sharedsummary["anderberg"]				= "anderberg";
+		sharedsummary["kulczynski"]				= "kulczynski";
+		sharedsummary["kulczynskicody"]			= "kulczynskicody";
+		sharedsummary["lennon"]					= "lennon";
+		sharedsummary["morisitahorn"]			= "morisitahorn";
+		sharedsummary["braycurtis"]				= "braycurtis";
+		sharedsummary["odum"]					= "odum";
+		sharedsummary["canberra"]				= "canberra";
+		sharedsummary["structeuclidean"]		= "structeuclidean";
+		sharedsummary["structchord"]			= "structchord";
+		sharedsummary["hellinger"]				= "hellinger";
+		sharedsummary["manhattan"]				= "manhattan";
+		sharedsummary["structpearson"]			= "structpearson";
+		sharedsummary["structkulczynski"]		= "structkulczynski";
+		sharedsummary["structchi2"]				= "structchi2";
+		sharedsummary["soergel"]				= "soergel";
+		sharedsummary["spearman"]				= "spearman";
+		sharedsummary["speciesprofile"]			= "speciesprofile";
+		sharedsummary["hamming"]				= "hamming";
+		sharedsummary["gower"]					= "gower";
+		sharedsummary["memchi2"]				= "memchi2";
+		sharedsummary["memchord"]				= "memchord";
+		sharedsummary["memeuclidean"]			= "memeuclidean";
+		sharedsummary["mempearson"]				= "mempearson";
 		sharedsummary["default"]				= "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 
@@ -274,16 +587,336 @@ void ValidCalculators::initialSharedRarefact() {
 		sharedrarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+
+/********************************************************************/
+void ValidCalculators::initialVennSingle() {
+	try {
+		vennsingle["sobs"]	        = "sobs";
+		vennsingle["chao"]		    = "chao";
+		vennsingle["ace"]			= "ace";
+		vennsingle["jack"]		    = "jack";
+		vennsingle["default"]		= "default";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialVennSingle");
 		exit(1);
-	}	
+	}
 }
 
 /********************************************************************/
+void ValidCalculators::initialVennShared() {
+	try {
+		vennshared["sharedsobs"]	= "sharedsobs";
+		vennshared["sharedchao"]	= "sharedchao";
+		vennshared["sharedace"]		= "sharedace";
+		vennshared["default"]		= "default";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialVennShared");
+		exit(1);
+	}
+}
 
+/********************************************************************/
+void ValidCalculators::initialTreeGroups() {
+	try {	
+		treegroup["sharedsobs"]				= "sharedsobs";
+		treegroup["sharedchao"]				= "sharedchao";
+		treegroup["sharedace"]				= "sharedace";
+		treegroup["jabund"]					= "jabund";
+		treegroup["sorabund"]				= "sorabund";
+		treegroup["jclass"]					= "jclass";
+		treegroup["sorclass"]				= "sorclass";
+		treegroup["jest"]					= "jest";
+		treegroup["sorest"]					= "sorest";
+		treegroup["thetayc"]				= "thetayc";
+		treegroup["thetan"]					= "thetan";
+		treegroup["kstest"]					= "kstest";
+		treegroup["whittaker"]				= "whittaker";
+		treegroup["sharednseqs"]			= "sharednseqs";
+		treegroup["ochiai"]					= "ochiai";
+		treegroup["anderberg"]				= "anderberg";
+		treegroup["kulczynski"]				= "kulczynski";
+		treegroup["kulczynskicody"]			= "kulczynskicody";
+		treegroup["lennon"]					= "lennon";
+		treegroup["morisitahorn"]			= "morisitahorn";
+		treegroup["braycurtis"]				= "braycurtis";
+		treegroup["odum"]					= "odum";
+		treegroup["canberra"]				= "canberra";
+		treegroup["structeuclidean"]		= "structeuclidean";
+		treegroup["structchord"]			= "structchord";
+		treegroup["hellinger"]				= "hellinger";
+		treegroup["manhattan"]				= "manhattan";
+		treegroup["structpearson"]			= "structpearson";
+		treegroup["structkulczynski"]		= "structkulczynski";
+		treegroup["structchi2"]				= "structchi2";
+		treegroup["soergel"]				= "soergel";
+		treegroup["spearman"]				= "spearman";
+		treegroup["speciesprofile"]			= "speciesprofile";
+		treegroup["hamming"]				= "hamming";
+		treegroup["gower"]					= "gower";
+		treegroup["memchi2"]				= "memchi2";
+		treegroup["memchord"]				= "memchord";
+		treegroup["memeuclidean"]			= "memeuclidean";
+		treegroup["mempearson"]				= "mempearson";
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialTreeGroups");
+		exit(1);
+	}
+}
+/********************************************************************/
+void ValidCalculators::initialHeat() {
+	try {	
+		heat["jabund"]				= "jabund";
+		heat["sorabund"]			= "sorabund";
+		heat["jclass"]				= "jclass";
+		heat["sorclass"]			= "sorclass";
+		heat["jest"]				= "jest";
+		heat["sorest"]				= "sorest";
+		heat["thetayc"]				= "thetayc";
+		heat["thetan"]				= "thetan";
+		heat["morisitahorn"]		= "morisitahorn";
+		heat["braycurtis"]			= "braycurtis";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialHeat");
+		exit(1);
+	}
+}
+
+/********************************************************************/
+void ValidCalculators::initialMatrix() {
+	try {	
+		matrix["sharedsobs"]				= "sharedsobs";
+		matrix["sharedchao"]				= "sharedchao";
+		matrix["sharedace"]				= "sharedace";
+		matrix["jabund"]					= "jabund";
+		matrix["sorabund"]				= "sorabund";
+		matrix["jclass"]					= "jclass";
+		matrix["sorclass"]				= "sorclass";
+		matrix["jest"]					= "jest";
+		matrix["sorest"]					= "sorest";
+		matrix["thetayc"]				= "thetayc";
+		matrix["thetan"]					= "thetan";
+		matrix["kstest"]					= "kstest";
+		matrix["whittaker"]				= "whittaker";
+		matrix["sharednseqs"]			= "sharednseqs";
+		matrix["ochiai"]					= "ochiai";
+		matrix["anderberg"]				= "anderberg";
+		matrix["kulczynski"]				= "kulczynski";
+		matrix["kulczynskicody"]			= "kulczynskicody";
+		matrix["lennon"]					= "lennon";
+		matrix["morisitahorn"]			= "morisitahorn";
+		matrix["braycurtis"]				= "braycurtis";
+		matrix["odum"]					= "odum";
+		matrix["canberra"]				= "canberra";
+		matrix["structeuclidean"]		= "structeuclidean";
+		matrix["structchord"]			= "structchord";
+		matrix["hellinger"]				= "hellinger";
+		matrix["manhattan"]				= "manhattan";
+		matrix["structpearson"]			= "structpearson";
+		matrix["structkulczynski"]		= "structkulczynski";
+		matrix["structchi2"]				= "structchi2";
+		matrix["soergel"]				= "soergel";
+		matrix["spearman"]				= "spearman";
+		matrix["speciesprofile"]			= "speciesprofile";
+		matrix["hamming"]				= "hamming";
+		matrix["gower"]					= "gower";
+		matrix["memchi2"]				= "memchi2";
+		matrix["memchord"]				= "memchord";
+		matrix["memeuclidean"]			= "memeuclidean";
+		matrix["mempearson"]				= "mempearson";
+		
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialMatrix");
+		exit(1);
+	}
+}
+
+/********************************************************************/
+void ValidCalculators::initialBoot() {
+	try {	
+		boot["jabund"]				= "jabund";
+		boot["sorabund"]			= "sorabund";
+		boot["jclass"]				= "jclass";
+		boot["sorclass"]			= "orclass";
+		boot["jest"]				= "jest";
+		boot["sorest"]				= "sorest";
+		boot["thetayc"]				= "thetayc";
+		boot["thetan"]				= "thetan";
+		boot["morisitahorn"]		= "morisitahorn";
+		boot["braycurtis"]			= "braycurtis";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialBoot");
+		exit(1);
+	}
+}
+/********************************************************************/
+void ValidCalculators::initialDistance() {
+	try {	
+		distance["nogaps"]		= "nogaps";
+		distance["eachgap"]		= "eachgap";
+		distance["onegap"]		= "onegap";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialDistance");
+		exit(1);
+	}
+}
+
+/********************************************************************/
+void ValidCalculators::printCalc(string parameter, ostream& out) {
+	try{
+		out << "The available estimators for calc are ";
+		//are you looking for a calculator for a single parameter
+		if (parameter == "single") {
+			for (it = single.begin(); it != single.end(); it++) {
+				out << it->first << ", ";
+			}
+		//are you looking for a calculator for a shared parameter
+		}else if (parameter == "shared") {
+			for (it = shared.begin(); it != shared.end(); it++) {
+				out << it->first << ", ";
+			}
+		//are you looking for a calculator for a rarefaction parameter
+		}else if (parameter == "rarefaction") {
+			for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+				out << it->first << ", ";
+			}
+		//are you looking for a calculator for a summary parameter
+		}else if (parameter == "summary") {
+			for (it = summary.begin(); it != summary.end(); it++) {
+				out << it->first << ", ";
+			}
+		//are you looking for a calculator for a sharedsummary parameter
+		}else if (parameter == "sharedsummary") {
+			for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "sharedrarefaction") {
+			for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "vennsingle") {
+			for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "vennshared") {
+			for (it = vennshared.begin(); it != vennshared.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "treegroup") {
+			for (it = treegroup.begin(); it != treegroup.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "matrix") {
+			for (it = matrix.begin(); it != matrix.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "heat") {
+			for (it = heat.begin(); it != heat.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "boot") {
+			for (it = boot.begin(); it != boot.end(); it++) {
+				out << it->first << ", ";
+			}
+		}else if (parameter == "distance") {
+			for (it = distance.begin(); it != distance.end(); it++) {
+				out << it->first << ", ";
+			}
+		}
+
+		out << endl;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "printCalc");
+		exit(1);
+	}
+}
+/********************************************************************/
+string ValidCalculators::printCalc(string parameter) {
+	try{
+		string output = "The available estimators for calc are ";
+		//are you looking for a calculator for a single parameter
+		if (parameter == "single") {
+			for (it = single.begin(); it != single.end(); it++) {
+				output += it->first + ", ";
+			}
+			//are you looking for a calculator for a shared parameter
+		}else if (parameter == "shared") {
+			for (it = shared.begin(); it != shared.end(); it++) {
+				output += it->first + ", ";
+			}
+			//are you looking for a calculator for a rarefaction parameter
+		}else if (parameter == "rarefaction") {
+			for (it = rarefaction.begin(); it != rarefaction.end(); it++) {
+				output += it->first + ", ";
+			}
+			//are you looking for a calculator for a summary parameter
+		}else if (parameter == "summary") {
+			for (it = summary.begin(); it != summary.end(); it++) {
+				output += it->first + ", ";
+			}
+			//are you looking for a calculator for a sharedsummary parameter
+		}else if (parameter == "sharedsummary") {
+			for (it = sharedsummary.begin(); it != sharedsummary.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "sharedrarefaction") {
+			for (it = sharedrarefaction.begin(); it != sharedrarefaction.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "vennsingle") {
+			for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "vennshared") {
+			for (it = vennshared.begin(); it != vennshared.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "treegroup") {
+			for (it = treegroup.begin(); it != treegroup.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "matrix") {
+			for (it = matrix.begin(); it != matrix.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "heat") {
+			for (it = heat.begin(); it != heat.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "boot") {
+			for (it = boot.begin(); it != boot.end(); it++) {
+				output += it->first + ", ";
+			}
+		}else if (parameter == "distance") {
+			for (it = distance.begin(); it != distance.end(); it++) {
+				output += it->first + ", ";
+			}
+		}
+		
+		//rip off comma
+		output = output.substr(0, output.length()-1);
+		output += "\n";
+		
+		return output;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "printCalc");
+		exit(1);
+	}
+}
+/********************************************************************/