X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=0ade87338bb9c2b264f99200a3c7e09fac3fdd12;hb=c5f38b0c83719306fd2e5a7a83e04988b1853f62;hp=f6fe280a86474ea35e78a18245ac24a0ba5e5349;hpb=c196b6b4768ccb84955d773ff0f22e4994d1ba7b;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index f6fe280..0ade873 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -12,6 +12,8 @@
 /********************************************************************/
 ValidCalculators::ValidCalculators() {
 	try {
+		 m = MothurOut::getInstance();
+		
 		 initialSingle();
 		 initialShared();
 		 initialRarefaction();
@@ -22,15 +24,14 @@ ValidCalculators::ValidCalculators() {
 		 initialVennShared();
 		 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";
+		m->errorOut(e, "ValidCalculator", "ValidCalculator");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function ValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}		 
 }
 
 /********************************************************************/
@@ -47,11 +48,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((single.find(calculator)) != (single.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the collect.single command and will be disregarded. Valid estimators are ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a shared parameter
 		}else if (parameter == "shared") {
@@ -59,11 +60,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((shared.find(calculator)) != (shared.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the collect.shared command and will be disregarded.  Valid estimators are ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a rarefaction parameter
 		}else if (parameter == "rarefaction") {
@@ -71,11 +72,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((rarefaction.find(calculator)) != (rarefaction.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the rarefaction.single command and will be disregarded. Valid estimators are ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a summary parameter
 		}else if (parameter == "summary") {
@@ -83,11 +84,11 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((summary.find(calculator)) != (summary.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//are you looking for a calculator for a sharedsummary parameter
 		}else if (parameter == "sharedsummary") {
@@ -95,79 +96,108 @@ bool ValidCalculators::isValidCalculator(string parameter, string calculator) {
 			if ((sharedsummary.find(calculator)) != (sharedsummary.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the summary.shared command and will be disregarded. Valid estimators are ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		}else if (parameter == "sharedrarefaction") {
 			//is it valid
 			if ((sharedrarefaction.find(calculator)) != (sharedrarefaction.end())) {
 				return true;
 			}else { 
-				cout << calculator << " is not a valid estimator for the rarefaction.shared command and will be disregarded. Valid estimator is ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				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 ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				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 ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				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 ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "matrix") {
+			//is it valid
+			if ((matrix.find(calculator)) != (matrix.end())) {
+				return true;
+			}else { 
+				m->mothurOut(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++) {
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "heat") {
+			//is it valid
+			if ((heat.find(calculator)) != (heat.end())) {
+				return true;
+			}else { 
+				m->mothurOut(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++) {
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
 				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 ";
+				m->mothurOut(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 << ", ";
+					m->mothurOut(it->first + ", ");
+				}
+				m->mothurOutEndLine();
+				return false; }
+		}else if (parameter == "distance") {
+			//is it valid
+			if ((distance.find(calculator)) != (distance.end())) {
+				return true;
+			}else { 
+				m->mothurOut(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++) {
+					m->mothurOut(it->first + ", ");
 				}
-				cout << endl;
+				m->mothurOutEndLine();
 				return false; }
 		//not a valid parameter
 		}else { return false; }
 		
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "isValidCalculator");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function isValidCalculator. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -189,16 +219,16 @@ 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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSingle. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSingle");
 		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);
-	}	
 }
 
 /********************************************************************/
@@ -208,7 +238,7 @@ void ValidCalculators::initialShared() {
 		shared["sharedchao"]			= "sharedchao";
 		shared["sharedace"]				= "sharedace";
 		shared["jabund"]				= "jabund";
-		shared["sorabund"]			= "sorabund";
+		shared["sorabund"]				= "sorabund";
 		shared["jclass"]				= "jclass";
 		shared["sorclass"]				= "sorclass";
 		shared["jest"]					= "jest";
@@ -228,13 +258,9 @@ void ValidCalculators::initialShared() {
 		shared["default"]	            = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialShared");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -253,13 +279,9 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialRarefaction");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialRarefaction. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -282,16 +304,16 @@ 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) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSummary");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 /********************************************************************/
@@ -321,13 +343,9 @@ void ValidCalculators::initialSharedSummary() {
 		sharedsummary["default"]				= "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSharedSummary");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSharedSummary. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 
@@ -340,13 +358,9 @@ void ValidCalculators::initialSharedRarefact() {
 		sharedrarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
-		cout << "Standard Error: " << e.what() << " has occurred in the ValidCalculator class Function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialSharedRarefact");
 		exit(1);
 	}
-	catch(...) {
-		cout << "An unknown error has occurred in the ValidCalculator class function initialSharedRarefact. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-		exit(1);
-	}	
 }
 
 
@@ -360,13 +374,9 @@ void ValidCalculators::initialVennSingle() {
 		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";
+		m->errorOut(e, "ValidCalculator", "initialVennSingle");
 		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);
-	}	
 }
 
 /********************************************************************/
@@ -378,20 +388,16 @@ void ValidCalculators::initialVennShared() {
 		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";
+		m->errorOut(e, "ValidCalculator", "initialVennShared");
 		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["sorabund"]				= "sorabund";
 		treegroup["jclass"]					= "jclass";
 		treegroup["sorclass"]				= "sorclass";
 		treegroup["jest"]					= "jest";
@@ -399,22 +405,58 @@ void ValidCalculators::initialTreeGroups() {
 		treegroup["thetayc"]				= "thetayc";
 		treegroup["thetan"]					= "thetan";
 		treegroup["morisitahorn"]			= "morisitahorn";
-		treegroup["braycurtis"]			= "braycurtis";
+		treegroup["braycurtis"]				= "braycurtis";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "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 initialTreeGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		m->errorOut(e, "ValidCalculator", "initialHeat");
 		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";
+}
+
+/********************************************************************/
+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) {
+		m->errorOut(e, "ValidCalculator", "initialMatrix");
 		exit(1);
-	}	
+	}
 }
+
 /********************************************************************/
 void ValidCalculators::initialBoot() {
 	try {	
 		boot["jabund"]				= "jabund";
-		boot["sorabund"]		= "sorabund";
+		boot["sorabund"]			= "sorabund";
 		boot["jclass"]				= "jclass";
 		boot["sorclass"]			= "orclass";
 		boot["jest"]				= "jest";
@@ -425,13 +467,21 @@ void ValidCalculators::initialBoot() {
 		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";
+		m->errorOut(e, "ValidCalculator", "initialBoot");
 		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";
+}
+/********************************************************************/
+void ValidCalculators::initialDistance() {
+	try {	
+		distance["nogaps"]		= "nogaps";
+		distance["eachgap"]		= "eachgap";
+		distance["onegap"]		= "onegap";
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ValidCalculator", "initialDistance");
 		exit(1);
-	}	
+	}
 }
 
 /********************************************************************/
@@ -479,22 +529,30 @@ 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 << ", ";
 			}
+		}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";
+		m->errorOut(e, "ValidCalculator", "printCalc");
 		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);
-	}	
-
 }
 /********************************************************************/