X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=6242d5aaf5c7e49eb54a75b26a0eb48425302123;hb=45b880733289694b2a23c9dc8a774aa626458f81;hp=7d3477f68c2c8eb71c5c42ab27b1aceb7eb81472;hpb=51cf89e90eef8b300c2786eb1560dd89e6e83445;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 7d3477f..6242d5a 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -12,6 +12,8 @@
 /********************************************************************/
 ValidCalculators::ValidCalculators() {
 	try {
+		 m = MothurOut::getInstance();
+		
 		 initialSingle();
 		 initialShared();
 		 initialRarefaction();
@@ -22,15 +24,14 @@ ValidCalculators::ValidCalculators() {
 		 initialVennShared();
 		 initialTreeGroups();
 		 initialBoot();
+		 initialDistance();
+		 initialMatrix();
+		 initialHeat();
 	}
 	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);
-	}		 
 }
 
 /********************************************************************/
@@ -47,11 +48,11 @@ 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") {
@@ -59,11 +60,11 @@ 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") {
@@ -71,11 +72,11 @@ 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") {
@@ -83,11 +84,11 @@ 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") {
@@ -95,79 +96,108 @@ 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; }
 		}else if (parameter == "vennsingle") {
 			//is it valid
 			if ((vennsingle.find(calculator)) != (vennsingle.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the venn command in single mode and will be disregarded. Valid estimators are ";
+				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++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		}else if (parameter == "vennshared") {
 			//is it valid
 			if ((vennshared.find(calculator)) != (vennshared.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the venn command in shared mode and will be disregarded. Valid estimators are ";
+				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++) {
-					cout << it->first << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		}else if (parameter == "treegroup") {
 			//is it valid
 			if ((treegroup.find(calculator)) != (treegroup.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the tree.shared command in shared mode and will be disregarded. Valid estimators are ";
+				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++) {
-					cout << it->first << ", ";
+					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 + ", ");
 				}
-				cout << endl;
+				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 { 
-				cout << calculator << " is not a valid estimator for the bootstrap.shared command in shared mode and will be disregarded. Valid estimators are ";
+				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++) {
-					cout << it->first << ", ";
+					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 + ", ");
 				}
-				cout << endl;
+				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);
-	}	
 }
 
 /********************************************************************/
@@ -179,24 +209,31 @@ void ValidCalculators::initialSingle() {
 		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["geom"]          = "geom";
-		single["logsd"]         = "logsd";
+		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);
-	}	
 }
 
 /********************************************************************/
@@ -206,7 +243,7 @@ void ValidCalculators::initialShared() {
 		shared["sharedchao"]			= "sharedchao";
 		shared["sharedace"]				= "sharedace";
 		shared["jabund"]				= "jabund";
-		shared["sorensonabund"]			= "sorensonabund";
+		shared["sorabund"]				= "sorabund";
 		shared["jclass"]				= "jclass";
 		shared["sorclass"]				= "sorclass";
 		shared["jest"]					= "jest";
@@ -214,7 +251,7 @@ void ValidCalculators::initialShared() {
 		shared["thetayc"]				= "thetayc";
 		shared["thetan"]				= "thetan";
 		shared["kstest"]				= "kstest";
-		shared["bdiversity"]			= "bdiversity";
+		shared["whittaker"]			    = "whittaker";
 		shared["sharednseqs"]			= "sharednseqs";
 		shared["ochiai"]				= "ochiai";
 		shared["anderberg"]				= "anderberg";
@@ -223,16 +260,30 @@ void ValidCalculators::initialShared() {
 		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);
-	}	
 }
 
 /********************************************************************/
@@ -243,20 +294,22 @@ 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);
-	}	
 }
 
 /********************************************************************/
@@ -268,25 +321,32 @@ 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["geom"]         = "geom";
+		summary["geometric"]    = "geometric";
 		summary["bootstrap"]	= "bootstrap";
-		summary["logsd"]        = "logsd";
+		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);
-	}	
 }
 
 /********************************************************************/
@@ -296,7 +356,7 @@ void ValidCalculators::initialSharedSummary() {
 		sharedsummary["sharedchao"]				= "sharedchao";
 		sharedsummary["sharedace"]				= "sharedace";
 		sharedsummary["jabund"]					= "jabund";
-		sharedsummary["sorensonabund"]			= "sorensonabund";
+		sharedsummary["sorabund"]				= "sorabund";
 		sharedsummary["jclass"]					= "jclass";
 		sharedsummary["sorclass"]				= "sorclass";
 		sharedsummary["jest"]					= "jest";
@@ -304,7 +364,7 @@ void ValidCalculators::initialSharedSummary() {
 		sharedsummary["thetayc"]				= "thetayc";
 		sharedsummary["thetan"]					= "thetan";
 		sharedsummary["kstest"]					= "kstest";
-		sharedsummary["bdiversity"]				= "bdiversity";
+		sharedsummary["whittaker"]				= "whittaker";
 		sharedsummary["sharednseqs"]			= "sharednseqs";
 		sharedsummary["ochiai"]					= "ochiai";
 		sharedsummary["anderberg"]				= "anderberg";
@@ -313,16 +373,30 @@ void ValidCalculators::initialSharedSummary() {
 		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);
-	}	
 }
 
 
@@ -335,13 +409,9 @@ 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";
-		exit(1);
-	}	
 }
 
 
@@ -355,13 +425,9 @@ void ValidCalculators::initialVennSingle() {
 		vennsingle["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", "initialVennSingle");
 		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);
-	}	
 }
 
 /********************************************************************/
@@ -373,20 +439,16 @@ void ValidCalculators::initialVennShared() {
 		vennshared["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", "initialVennShared");
 		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);
-	}	
 }
 
 /********************************************************************/
 void ValidCalculators::initialTreeGroups() {
 	try {	
 		treegroup["jabund"]					= "jabund";
-		treegroup["sorensonabund"]			= "sorensonabund";
+		treegroup["sorabund"]				= "sorabund";
 		treegroup["jclass"]					= "jclass";
 		treegroup["sorclass"]				= "sorclass";
 		treegroup["jest"]					= "jest";
@@ -394,21 +456,58 @@ void ValidCalculators::initialTreeGroups() {
 		treegroup["thetayc"]				= "thetayc";
 		treegroup["thetan"]					= "thetan";
 		treegroup["morisitahorn"]			= "morisitahorn";
+		treegroup["braycurtis"]				= "braycurtis";
+	}
+	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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialHeat");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+/********************************************************************/
+void ValidCalculators::initialMatrix() {
+	try {	
+		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["morisitahorn"]			= "morisitahorn";
+		matrix["braycurtis"]			= "braycurtis";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialMatrix");
 		exit(1);
-	}	
+	}
 }
+
 /********************************************************************/
 void ValidCalculators::initialBoot() {
 	try {	
 		boot["jabund"]				= "jabund";
-		boot["sorensonabund"]		= "sorensonabund";
+		boot["sorabund"]			= "sorabund";
 		boot["jclass"]				= "jclass";
 		boot["sorclass"]			= "orclass";
 		boot["jest"]				= "jest";
@@ -416,15 +515,24 @@ void ValidCalculators::initialBoot() {
 		boot["thetayc"]				= "thetayc";
 		boot["thetan"]				= "thetan";
 		boot["morisitahorn"]		= "morisitahorn";
+		boot["braycurtis"]			= "braycurtis";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialBoot");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialBoot. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/********************************************************************/
+void ValidCalculators::initialDistance() {
+	try {	
+		distance["nogaps"]		= "nogaps";
+		distance["eachgap"]		= "eachgap";
+		distance["onegap"]		= "onegap";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialDistance");
 		exit(1);
-	}	
+	}
 }
 
 /********************************************************************/
@@ -472,22 +580,30 @@ void ValidCalculators::printCalc(string parameter, ostream& out) {
 			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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "printCalc");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function printCalc. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
-
 }
 /********************************************************************/