X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=99cd47a13bbc78b86b9332c24337d4dd2b726a42;hb=b22853b5cfbf5c47949ad2a084f2fad88b2e4be4;hp=a875900411bd5b5b3678927e07acbd4e9cd9b9e6;hpb=f20505bcd9f07e0b5f967be0e8d414076d9a5678;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index a875900..99cd47a 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -20,6 +20,10 @@ ValidCalculators::ValidCalculators() {
 		 initialSharedSummary();
 		 initialVennSingle();
 		 initialVennShared();
+		 initialTreeGroups();
+		 initialBoot();
+		 initialDistance();
+		 initialMatrix();
 	}
 	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";
@@ -132,6 +136,50 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 				}
 				cout << endl;
 				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 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 == "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 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; }
 		
@@ -158,11 +206,17 @@ 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["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) {
@@ -181,24 +235,24 @@ 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["sharedkstest"]          = "sharedkstest";
-		shared["sharedbdiversity"]      = "sharedbdiversity";
+		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["default"]	            = "default";
 	}
 	catch(exception& e) {
@@ -223,6 +277,7 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["simpson"]		= "simpson";
 		rarefaction["bootstrap"]	= "bootstrap";
 		rarefaction["nseqs"]		= "nseqs";
+		rarefaction["coverage"]		= "coverage";
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -247,12 +302,18 @@ 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["goodscoverage"]= "goodscoverage";
+		summary["coverage"]		= "coverage";
+		summary["efron"]        = "efron";
+		summary["boneh"]        = "boneh";
+		summary["solow"]        = "solow";
+		summary["shen"]         = "shen";
 		summary["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -271,24 +332,24 @@ 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["sharedkstest"]           = "sharedkstest";
-		sharedsummary["sharedbdiversity"]       = "sharedbdiversity";
+		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["default"]				= "default";
 	}
 	catch(exception& e) {
@@ -326,9 +387,9 @@ void ValidCalculators::initialVennSingle() {
 	try {
 		vennsingle["sobs"]	        = "sobs";
 		vennsingle["chao"]		    = "chao";
-		vennsingle["ace"]				= "ace";
+		vennsingle["ace"]			= "ace";
 		vennsingle["jack"]		    = "jack";
-		vennsingle["default"]			= "default";
+		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";
@@ -359,6 +420,158 @@ void ValidCalculators::initialVennShared() {
 }
 
 /********************************************************************/
+void ValidCalculators::initialTreeGroups() {
+	try {	
+		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["morisitahorn"]			= "morisitahorn";
+		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";
+		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";
+		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["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) {
+		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::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) {
+	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 << ", ";
+			}
+		}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";
+		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);
+	}	
 
+}
+/********************************************************************/