X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=3e698bf19c67bfe46819df2a1bd10de2a0299b5b;hb=b7cce6e0a45013919e76a266533fcca4052cf157;hp=14fa775e7398d4be2b5b13a02f111303093c9e9d;hpb=3117b1c3109121dff476997d3c5db5b47a77729b;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 14fa775..3e698bf 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -23,6 +23,8 @@ ValidCalculators::ValidCalculators() {
 		 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";
@@ -146,6 +148,28 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 				}
 				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())) {
@@ -201,6 +225,10 @@ void ValidCalculators::initialSingle() {
 		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) {
@@ -294,6 +322,10 @@ void ValidCalculators::initialSummary() {
 		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) {
@@ -422,6 +454,54 @@ 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 {	
@@ -507,6 +587,14 @@ 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 << ", ";