X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=72d404147a3b71bf9a6b1efe82098f943558adf4;hb=477e76a8a79b60f6cd4253324dd830bdea25e3e9;hp=4c05e4a8e466e2a99a2628e0ca7e1cf31c5e4bfe;hpb=c537597ec5ebd47b4898da87ae03b0c2aeced354;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 4c05e4a..72d4041 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -21,6 +21,7 @@ ValidCalculators::ValidCalculators() {
 		 initialVennSingle();
 		 initialVennShared();
 		 initialTreeGroups();
+		 initialBoot();
 	}
 	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";
@@ -138,13 +139,23 @@ 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.groups command in shared mode and will be disregarded. Valid estimators are ";
+				cout << calculator << " is not a valid estimator for the tree.shared command in shared mode 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 == "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 ";
+				for (it = boot.begin(); it != boot.end(); it++) {
+					cout << it->first << ", ";
+				}
+				cout << endl;
+				return false; }
 		//not a valid parameter
 		}else { return false; }
 		
@@ -171,11 +182,13 @@ void ValidCalculators::initialSingle() {
 		single["simpson"]	    = "simpson";
 		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["nseqs"]			= "nseqs";
+		single["coverage"]		= "coverage";
+		
 		single["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -195,7 +208,7 @@ 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";
@@ -203,7 +216,7 @@ 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";
@@ -236,6 +249,7 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["simpson"]		= "simpson";
 		rarefaction["bootstrap"]	= "bootstrap";
 		rarefaction["nseqs"]		= "nseqs";
+		rarefaction["coverage"]		= "coverage";
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -260,12 +274,13 @@ void ValidCalculators::initialSummary() {
 		summary["npshannon"]	= "npshannon";
 		summary["simpson"]		= "simpson";
 		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["coverage"]		= "coverage";
 		summary["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -285,7 +300,7 @@ 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";
@@ -293,7 +308,7 @@ 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";
@@ -375,7 +390,7 @@ void ValidCalculators::initialVennShared() {
 void ValidCalculators::initialTreeGroups() {
 	try {	
 		treegroup["jabund"]					= "jabund";
-		treegroup["sorensonabund"]			= "sorensonabund";
+		treegroup["sorabund"]			= "sorabund";
 		treegroup["jclass"]					= "jclass";
 		treegroup["sorclass"]				= "sorclass";
 		treegroup["jest"]					= "jest";
@@ -393,10 +408,90 @@ void ValidCalculators::initialTreeGroups() {
 		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";
+	}
+	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";
+		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";
+		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 == "boot") {
+			for (it = boot.begin(); it != boot.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";
+		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);
+	}	
 
-
+}
+/********************************************************************/