X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=edcf8c7a33269ece0758903f4d1fc425da558e97;hb=2bb51be6ba6a3fa741f2131d328cf21c395b506a;hp=8659be3d85f1956f788f13355bea8f9fa67e5052;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 8659be3..edcf8c7 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -18,6 +18,11 @@ ValidCalculators::ValidCalculators() {
 		 initialSharedRarefact();
 		 initialSummary();
 		 initialSharedSummary();
+		 initialVennSingle();
+		 initialVennShared();
+		 initialTreeGroups();
+		 initialBoot();
+		 initialDistance();
 	}
 	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";
@@ -42,38 +47,128 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			//is it valid
 			if ((single.find(calculator)) != (single.end())) {
 				return true;
-			}else { cout << calculator << " is not a valid single estimator. Valid single estimators are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << endl; return false; }
+			}else { 
+				cout << 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 << ", ";
+				}
+				cout << endl;
+				return false; }
 		//are you looking for a calculator for a shared parameter
 		}else if (parameter == "shared") {
 			//is it valid
 			if ((shared.find(calculator)) != (shared.end())) {
 				return true;
-			}else { cout << calculator << " is not a valid shared estimator.  Valid shared estimators are sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << endl; return false; }
+			}else { 
+				cout << 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 << ", ";
+				}
+				cout << endl;
+				return false; }
 		//are you looking for a calculator for a rarefaction parameter
 		}else if (parameter == "rarefaction") {
 			//is it valid
 			if ((rarefaction.find(calculator)) != (rarefaction.end())) {
 				return true;
-			}else { cout << calculator << " is not a valid rarefaction estimator. Valid rarefaction estimators are rarefaction-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson." << endl; return false; }
+			}else { 
+				cout << 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 << ", ";
+				}
+				cout << endl;
+				return false; }
 		//are you looking for a calculator for a summary parameter
 		}else if (parameter == "summary") {
 			//is it valid
 			if ((summary.find(calculator)) != (summary.end())) {
 				return true;
-			}else { cout << calculator << " is not a valid summary estimator. Valid summary estimators are collect-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << endl; return false; }
+			}else { 
+				cout << 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 << ", ";
+				}
+				cout << endl;
+				return false; }
 		//are you looking for a calculator for a sharedsummary parameter
 		}else if (parameter == "sharedsummary") {
 			//is it valid
 			if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
 				return true;
-			}else { cout << calculator << " is not a valid sharedsummary estimator. Valid sharedsummary estimators are: sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << endl; return false; }
-
+			}else { 
+				cout << 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 << ", ";
+				}
+				cout << endl;
+				return false; }
 		}else if (parameter == "sharedrarefaction") {
 			//is it valid
 			if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 				return true;
-			}else { cout << calculator << " is not a valid sharedrarefaction estimator. Valid sharedrarefaction estimator is sharedobserved." << endl; return false; }
-		//not a valid paramter
+			}else { 
+				cout << 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 << ", ";
+				}
+				cout << endl;
+				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 ";
+				for (it = vennsingle.begin(); it != vennsingle.end(); it++) {
+					cout << it->first << ", ";
+				}
+				cout << endl;
+				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 ";
+				for (it = vennshared.begin(); it != vennshared.end(); it++) {
+					cout << it->first << ", ";
+				}
+				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 == "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; }
 		
 	}
@@ -90,16 +185,27 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 /********************************************************************/
 void ValidCalculators::initialSingle() {
 	try {	
-	
-		single["sobs"]	= "sobs";
-		single["chao"]		= "chao";
-		single["ace"]		= "ace";
-		single["jack"]		= "jack";
-		single["shannon"]	= "shannon";
-		single["npshannon"]	= "npshannon";
-		single["simpson"]	= "simpson";
-		single["bootstrap"]	= "bootstrap";
-		single["default"]	= "default";
+		single["sobs"]	        = "sobs";
+		single["chao"]		    = "chao";
+		single["ace"]		    = "ace";
+		single["jack"]		    = "jack";
+		single["shannon"]	    = "shannon";
+		single["npshannon"]    	= "npshannon";
+		single["simpson"]	    = "simpson";
+		single["bergerparker"]  = "bergerparker";
+		single["bootstrap"]    	= "bootstrap";
+		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";
@@ -114,16 +220,27 @@ void ValidCalculators::initialSingle() {
 /********************************************************************/
 void ValidCalculators::initialShared() {
 	try {	
-		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["sharedsobs"]			= "sharedsobs";
+		shared["sharedchao"]			= "sharedchao";
+		shared["sharedace"]				= "sharedace";
+		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["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) {
@@ -147,6 +264,8 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["npshannon"]	= "npshannon";
 		rarefaction["simpson"]		= "simpson";
 		rarefaction["bootstrap"]	= "bootstrap";
+		rarefaction["nseqs"]		= "nseqs";
+		rarefaction["coverage"]		= "coverage";
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -170,7 +289,19 @@ void ValidCalculators::initialSummary() {
 		summary["shannon"]		= "shannon";
 		summary["npshannon"]	= "npshannon";
 		summary["simpson"]		= "simpson";
+		summary["bergerparker"] = "bergerparker";
+		summary["geometric"]    = "geometric";
 		summary["bootstrap"]	= "bootstrap";
+		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) {
@@ -186,16 +317,27 @@ void ValidCalculators::initialSummary() {
 /********************************************************************/
 void ValidCalculators::initialSharedSummary() {
 	try {	
-		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["sharedsobs"]				= "sharedsobs";
+		sharedsummary["sharedchao"]				= "sharedchao";
+		sharedsummary["sharedace"]				= "sharedace";
+		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["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) {
@@ -214,6 +356,7 @@ void ValidCalculators::initialSharedSummary() {
 void ValidCalculators::initialSharedRarefact() {
 	try {	
 		sharedrarefaction["sharedobserved"]	= "sharedobserved";
+		sharedrarefaction["sharednseqs"]	= "sharednseqs";
 		sharedrarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -226,7 +369,173 @@ void ValidCalculators::initialSharedRarefact() {
 	}	
 }
 
+
 /********************************************************************/
+void ValidCalculators::initialVennSingle() {
+	try {
+		vennsingle["sobs"]	        = "sobs";
+		vennsingle["chao"]		    = "chao";
+		vennsingle["ace"]			= "ace";
+		vennsingle["jack"]		    = "jack";
+		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";
+		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::initialVennShared() {
+	try {
+		vennshared["sharedsobs"]	= "sharedsobs";
+		vennshared["sharedchao"]	= "sharedchao";
+		vennshared["sharedace"]		= "sharedace";
+		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";
+		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["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::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);
+	}	
+
+}
+/********************************************************************/