X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=25cc5c5868e46a9659fc88e924a6f03baf48b7da;hb=e4827e0945cbda536064e5a345996b2a7dfcbb81;hp=7f83ac7107757f35f5e29fe8b4de5b99237f4f8c;hpb=9ca2caadbeac83bb84b3330d9204b1b659d62941;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 7f83ac7..25cc5c5 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -18,6 +18,10 @@ ValidCalculators::ValidCalculators() {
 		 initialSharedRarefact();
 		 initialSummary();
 		 initialSharedSummary();
+		 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";
@@ -108,7 +112,51 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 				}
 				cout << endl;
 				return false; }
-		//not a valid paramter
+		}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 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; }
 		
 	}
@@ -125,17 +173,23 @@ 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["nseqs"]		= "nseqs";
+		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["nseqs"]			= "nseqs";
+		single["coverage"]		= "coverage";
+		
+		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";
@@ -153,15 +207,24 @@ 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["jabund"]				= "jabund";
+		shared["sorensonabund"]			= "sorensonabund";
+		shared["jclass"]				= "jclass";
+		shared["sorclass"]				= "sorclass";
+		shared["jest"]					= "jest";
+		shared["sorest"]				= "sorest";
+		shared["thetayc"]				= "thetayc";
+		shared["thetan"]				= "thetan";
+		shared["kstest"]				= "kstest";
+		shared["bdiversity"]			= "bdiversity";
 		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) {
@@ -186,6 +249,7 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["simpson"]		= "simpson";
 		rarefaction["bootstrap"]	= "bootstrap";
 		rarefaction["nseqs"]		= "nseqs";
+		rarefaction["coverage"]		= "coverage";
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -209,8 +273,14 @@ void ValidCalculators::initialSummary() {
 		summary["shannon"]		= "shannon";
 		summary["npshannon"]	= "npshannon";
 		summary["simpson"]		= "simpson";
+		summary["bergerparker"] = "bergerparker";
+		summary["geometric"]    = "geometric";
 		summary["bootstrap"]	= "bootstrap";
+		summary["logsd"]        = "logsd";
+		summary["qstat"]        = "qstat";
+		summary["bstick"]       = "bstick";
 		summary["nseqs"]		= "nseqs";
+		summary["coverage"]		= "coverage";
 		summary["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -229,15 +299,24 @@ 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["jabund"]					= "jabund";
+		sharedsummary["sorensonabund"]			= "sorensonabund";
+		sharedsummary["jclass"]					= "jclass";
+		sharedsummary["sorclass"]				= "sorclass";
+		sharedsummary["jest"]					= "jest";
+		sharedsummary["sorest"]					= "sorest";
+		sharedsummary["thetayc"]				= "thetayc";
+		sharedsummary["thetan"]					= "thetan";
+		sharedsummary["kstest"]					= "kstest";
+		sharedsummary["bdiversity"]				= "bdiversity";
 		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) {
@@ -269,7 +348,150 @@ 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["sorensonabund"]			= "sorensonabund";
+		treegroup["jclass"]					= "jclass";
+		treegroup["sorclass"]				= "sorclass";
+		treegroup["jest"]					= "jest";
+		treegroup["sorest"]					= "sorest";
+		treegroup["thetayc"]				= "thetayc";
+		treegroup["thetan"]					= "thetan";
+		treegroup["morisitahorn"]			= "morisitahorn";
+	}
+	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["sorensonabund"]		= "sorensonabund";
+		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);
+	}	
 
+}
+/********************************************************************/