X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=3e698bf19c67bfe46819df2a1bd10de2a0299b5b;hb=df82ee669d7eb9ae9a1a334339dfab7961cb16c6;hp=70299cb23dca8910e47c9fc8589e8f3d7543f18a;hpb=fd00cd216d3a38ccea22eae258e601df64218b05;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 70299cb..3e698bf 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -22,6 +22,9 @@ 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";
@@ -139,23 +142,56 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			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 ";
+				cout << 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 << ", ";
 				}
 				cout << endl;
 				return false; }
+		}else if (parameter == "matrix") {
+			//is it valid
+			if ((matrix.find(calculator)) != (matrix.end())) {
+				return true;
+			}else { 
+				cout << 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++) {
+					cout << it->first << ", ";
+				}
+				cout << endl;
+				return false; }
+		}else if (parameter == "heat") {
+			//is it valid
+			if ((heat.find(calculator)) != (heat.end())) {
+				return true;
+			}else { 
+				cout << 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++) {
+					cout << it->first << ", ";
+				}
+				cout << endl;
+				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 ";
+				cout << 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 << ", ";
 				}
 				cout << endl;
 				return false; }
+		}else if (parameter == "distance") {
+			//is it valid
+			if ((distance.find(calculator)) != (distance.end())) {
+				return true;
+			}else { 
+				cout << 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++) {
+					cout << it->first << ", ";
+				}
+				cout << endl;
+				return false; }
 		//not a valid parameter
 		}else { return false; }
 		
@@ -186,9 +222,13 @@ void ValidCalculators::initialSingle() {
 		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) {
@@ -208,7 +248,7 @@ void ValidCalculators::initialShared() {
 		shared["sharedchao"]			= "sharedchao";
 		shared["sharedace"]				= "sharedace";
 		shared["jabund"]				= "jabund";
-		shared["sorabund"]			= "sorabund";
+		shared["sorabund"]				= "sorabund";
 		shared["jclass"]				= "jclass";
 		shared["sorclass"]				= "sorclass";
 		shared["jest"]					= "jest";
@@ -280,7 +320,12 @@ void ValidCalculators::initialSummary() {
 		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) {
@@ -390,7 +435,7 @@ void ValidCalculators::initialVennShared() {
 void ValidCalculators::initialTreeGroups() {
 	try {	
 		treegroup["jabund"]					= "jabund";
-		treegroup["sorabund"]			= "sorabund";
+		treegroup["sorabund"]				= "sorabund";
 		treegroup["jclass"]					= "jclass";
 		treegroup["sorclass"]				= "sorclass";
 		treegroup["jest"]					= "jest";
@@ -398,7 +443,7 @@ void ValidCalculators::initialTreeGroups() {
 		treegroup["thetayc"]				= "thetayc";
 		treegroup["thetan"]					= "thetan";
 		treegroup["morisitahorn"]			= "morisitahorn";
-		treegroup["braycurtis"]			= "braycurtis";
+		treegroup["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";
@@ -409,11 +454,59 @@ void ValidCalculators::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 initialHeat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ValidCalculator class function initialHeat. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
+/********************************************************************/
+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) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ValidCalculator class function initialMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
+
 /********************************************************************/
 void ValidCalculators::initialBoot() {
 	try {	
 		boot["jabund"]				= "jabund";
-		boot["sorabund"]		= "sorabund";
+		boot["sorabund"]			= "sorabund";
 		boot["jclass"]				= "jclass";
 		boot["sorclass"]			= "orclass";
 		boot["jest"]				= "jest";
@@ -432,6 +525,22 @@ void ValidCalculators::initialBoot() {
 		exit(1);
 	}	
 }
+/********************************************************************/
+void ValidCalculators::initialDistance() {
+	try {	
+		distance["nogaps"]		= "nogaps";
+		distance["eachgap"]		= "eachgap";
+		distance["onegap"]		= "onegap";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ValidCalculator class function initialDistance. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
 
 /********************************************************************/
 void ValidCalculators::printCalc(string parameter, ostream& out) {
@@ -478,11 +587,24 @@ 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) {