X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=a82962f1e0096e406e7cc21d03dba08a3039ea3a;hb=5e8fcd2454ba4bd2e11983afd682b8aa6f7bb5c2;hp=fd9998e8246792388c563f327d5610271452edb6;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index fd9998e..a82962f 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -14,13 +14,16 @@
 ValidParameters::ValidParameters() {
 	try {
 	
-		parameters["distfile"]			= "distfile"; 
-		parameters["listfile"]			= "listfile"; 
-		parameters["rabundfile"]		= "rabundfile"; 
-		parameters["sabundfile"]		= "sabundfile"; 
-		parameters["namefile"]			= "namefile"; 
-		parameters["groupfile"]			= "groupfile"; 
-		parameters["orderfile"]			= "orderfile"; 
+		parameters["phylip"]		= "phylip";
+		parameters["column"]		= "column";
+		parameters["list"]			= "list"; 
+		parameters["rabund"]		= "rabund"; 
+		parameters["sabund"]		= "sabund"; 
+		parameters["name"]			= "name"; 
+		parameters["group"]			= "group"; 
+		parameters["order"]			= "order"; 
+		parameters["fasta"]			= "fasta"; 
+		parameters["tree"]			= "tree";
 		parameters["fileroot"]			= "fileroot";
 		parameters["cutoff"]			= "cutoff"; 
 		parameters["method"]			= "method";
@@ -37,7 +40,10 @@ ValidParameters::ValidParameters() {
 		parameters["shared"]			= "shared"; 
 		parameters["summary"]			= "summary"; 
 		parameters["sharedsummary"]		= "sharedsummary";
-
+		parameters["random"]			= "random";
+		parameters["groups"]			= "groups";
+		parameters["calc"]				= "calc";
+		
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -61,7 +67,12 @@ bool ValidParameters::isValidParameter(string parameter) {
 		if ((parameters.find(parameter)) != (parameters.end())) {
 			return true;
 		}else{
-			cout << parameter << " is not a valid parameter in Mothur." << endl;
+			cout << parameter << " is not a valid parameter in Mothur. Valid parameters are " << endl;
+			for (it = parameters.begin(); it != parameters.end(); it++) {
+				cout << it->first << ", ";
+			}
+			cout << endl;
+
 			return false;
 		}
 		
@@ -76,4 +87,4 @@ bool ValidParameters::isValidParameter(string parameter) {
 	}
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/