X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=3a96cc64893e4d0b5b8b755202dda24316ba1a08;hb=9651e8e7172d86707b34af15e95ec60ad4c3c3f9;hp=dc4ec6276a5b23d38358096373c802830c8e3756;hpb=d5c8caf2d08b7ac6de30e33b1d19cfd246d08f03;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index dc4ec62..3a96cc6 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -14,30 +14,31 @@
 ValidParameters::ValidParameters() {
 	try {
 	
-		parameters["phylipfile"]		= "phylipfile";
-		parameters["columnfile"]		= "columnfile";
-		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["shared"]		= "shared";
+		parameters["name"]			= "name"; 
+		parameters["group"]			= "group"; 
+		parameters["order"]			= "order"; 
+		parameters["fasta"]			= "fasta"; 
+		parameters["tree"]			= "tree";
 		parameters["fileroot"]			= "fileroot";
 		parameters["cutoff"]			= "cutoff"; 
 		parameters["method"]			= "method";
 		parameters["format"]			= "format"; 
 		parameters["precision"]			= "precision"; 
 		parameters["label"]				= "label"; 
-		parameters["line"]				= "line"; 
+		parameters["line"]				= "line";
 		parameters["iters"]				= "iters"; 
 		parameters["jumble"]			= "jumble"; 
 		parameters["freq"]				= "freq"; 
-		parameters["single"]			= "single"; 
-		parameters["rarefaction"]		= "rarefaction"; 
-		parameters["sharedrarefaction"]	= "sharedrarefaction";
-		parameters["shared"]			= "shared"; 
-		parameters["summary"]			= "summary"; 
-		parameters["sharedsummary"]		= "sharedsummary";
+		parameters["abund"]             = "abund";
+		parameters["random"]			= "random";
+		parameters["groups"]			= "groups";
+		parameters["calc"]				= "calc";
 
 	}
 	catch(exception& e) {
@@ -62,7 +63,12 @@ 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;
 		}
 		
@@ -77,4 +83,4 @@ bool ValidParameters::isValidParameter(string parameter) {
 	}
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/