X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcalculator.cpp;h=90257c77eefbc1218698ebcc808e66d4c7bd34e9;hb=c5c7502f435e1413c19e373dab1dfebcaa67588d;hp=8659be3d85f1956f788f13355bea8f9fa67e5052;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/validcalculator.cpp b/validcalculator.cpp
index 8659be3..90257c7 100644
--- a/validcalculator.cpp
+++ b/validcalculator.cpp
@@ -18,6 +18,9 @@ ValidCalculators::ValidCalculators() {
 		 initialSharedRarefact();
 		 initialSummary();
 		 initialSharedSummary();
+		 initialVennSingle();
+		 initialVennShared();
+		 initialTreeGroups();
 	}
 	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 +45,107 @@ 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.groups 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; }
+
+		//not a valid parameter
 		}else { return false; }
 		
 	}
@@ -90,16 +162,21 @@ 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["geom"]          = "geom";
+		single["logsd"]         = "logsd";
+		single["qstat"]         = "qstat";
+		single["bstick"]        = "bstick";
+		single["nseqs"]		= "nseqs";
+		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 +191,27 @@ 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["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["sharednseqs"]			= "sharednseqs";
+		shared["sharedochiai"]			= "sharedochiai";
+		shared["sharedanderberg"]		= "sharedanderberg";
+		shared["sharedkulczynski"]		= "sharedkulczynski";
+		shared["sharedkulczynskicody"]	= "sharedkulczynskicody";
+		shared["sharedlennon"]			= "sharedlennon";
+		shared["sharedmorisitahorn"]	= "sharedmorisitahorn";
+		shared["sharedbraycurtis"]		= "sharedbraycurtis";
 		shared["default"]	            = "default";
 	}
 	catch(exception& e) {
@@ -147,6 +235,7 @@ void ValidCalculators::initialRarefaction() {
 		rarefaction["npshannon"]	= "npshannon";
 		rarefaction["simpson"]		= "simpson";
 		rarefaction["bootstrap"]	= "bootstrap";
+		rarefaction["nseqs"]		= "nseqs";
 		rarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -170,7 +259,13 @@ void ValidCalculators::initialSummary() {
 		summary["shannon"]		= "shannon";
 		summary["npshannon"]	= "npshannon";
 		summary["simpson"]		= "simpson";
+		summary["bergerparker"] = "bergerparker";
+		summary["geom"]         = "geom";
 		summary["bootstrap"]	= "bootstrap";
+		summary["logsd"]        = "logsd";
+		summary["qstat"]        = "qstat";
+		summary["bstick"]       = "bstick";
+		summary["nseqs"]		= "nseqs";
 		summary["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -186,16 +281,27 @@ 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["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["sharednseqs"]			= "sharednseqs";
+		sharedsummary["sharedochiai"]			= "sharedochiai";
+		sharedsummary["sharedanderberg"]		= "sharedanderberg";
+		sharedsummary["sharedkulczynski"]		= "sharedkulczynski";
+		sharedsummary["sharedkulczynskicody"]	= "sharedkulczynskicody";
+		sharedsummary["sharedlennon"]			= "sharedlennon";
+		sharedsummary["sharedmorisitahorn"]		= "sharedmorisitahorn";
+		sharedsummary["sharedbraycurtis"]		= "sharedbraycurtis";
 		sharedsummary["default"]				= "default";
 	}
 	catch(exception& e) {
@@ -214,6 +320,7 @@ void ValidCalculators::initialSharedSummary() {
 void ValidCalculators::initialSharedRarefact() {
 	try {	
 		sharedrarefaction["sharedobserved"]	= "sharedobserved";
+		sharedrarefaction["sharednseqs"]	= "sharednseqs";
 		sharedrarefaction["default"]	    = "default";
 	}
 	catch(exception& e) {
@@ -226,7 +333,70 @@ 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["sharedjabund"]			= "sharedjabund";
+		treegroup["sharedsorensonabund"]	= "sharedsorensonabund";
+		treegroup["sharedjclass"]			= "sharedjclass";
+		treegroup["sharedsorclass"]			= "sharedsorclass";
+		treegroup["sharedjest"]				= "sharedjest";
+		treegroup["sharedsorest"]			= "sharedsorest";
+		treegroup["sharedthetayc"]			= "sharedthetayc";
+		treegroup["sharedthetan"]			= "sharedthetan";
+		treegroup["sharedmorisitahorn"]		= "sharedmorisitahorn";
+	}
+	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);
+	}	
+}
+
+
 /********************************************************************/
 
 
 
+