X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcommands.cpp;h=1ccb8fca51577674af1ecb2fa5fe895655330654;hb=39ef0543b73cb12dfc64529522b66ad3df7527d0;hp=bd9d80eb9efb960fcb8bec4218a30be7e198b04a;hpb=fd282e6b4be2560f5b1bd154a9e8d24b798eefaf;p=mothur.git

diff --git a/validcommands.cpp b/validcommands.cpp
index bd9d80e..1ccb8fc 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -15,17 +15,25 @@ ValidCommands::ValidCommands() {
 	try {
 	
 		commands["read.dist"]			= "read.dist"; 
-		commands["read.otu"]			= "read.otu"; 
+		commands["read.otu"]			= "read.otu";
+		commands["read.tree"]			= "read.tree"; 
 		commands["cluster"]				= "cluster"; 
 		commands["deconvolute"]			= "deconvolute"; 
+		commands["parsimony"]			= "parsimony";
 		commands["help"]				= "help"; 
 		commands["quit"]				= "quit"; 
 		commands["collect.single"]		= "collect.single"; 
 		commands["collect.shared"]		= "collect.shared"; 
+		commands["get.group"]           = "get.group";
+		commands["get.label"]           = "get.label";
+		commands["get.line"]            = "get.line";
 		commands["rarefaction.single"]	= "rarefaction.single"; 
 		commands["rarefaction.shared"]	= "rarefaction.shared"; 
 		commands["summary.single"]		= "summary.single"; 
 		commands["summary.shared"]		= "summary.shared"; 
+		commands["unifrac.weighted"]	= "unifrac.weighted"; 
+		commands["unifrac.unweighted"]	= "unifrac.unweighted"; 
+
 				
 	}
 	catch(exception& e) {
@@ -50,7 +58,11 @@ bool ValidCommands::isValidCommand(string command) {
 		if ((commands.find(command)) != (commands.end())) {
 			return true;
 		}else{
-			cout << command << " is not a valid command in Mothur.  Valid commands are read.dist(), read.otu(), cluster(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), quit(), help()." << endl;
+			cout << command << " is not a valid command in Mothur.  Valid commands are ";
+			for (it = commands.begin(); it != commands.end(); it++) {
+				cout << it->first << ", ";
+			}
+			cout << endl;
 			return false;
 		}
 		
@@ -65,4 +77,25 @@ bool ValidCommands::isValidCommand(string command) {
 	}
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/
+void ValidCommands::printCommands(ostream& out) {
+	try {	
+		out << "Valid commands are ";
+		for (it = commands.begin(); it != commands.end(); it++) {
+			out << it->first << ", ";
+		}
+		out << endl;
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ValidCommands class function printCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+}
+
+
+
+