X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcommands.cpp;h=5549e6396527c198a5131ba85c42ee356c07774f;hb=ec453945974b5c72af0bea042e3517312566d592;hp=53ee7431b49fecc06002e5b9330259371bd35729;hpb=b2dca66a02f8f82aa5528e531eace60fbbd2967b;p=mothur.git

diff --git a/validcommands.cpp b/validcommands.cpp
index 53ee743..5549e63 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -17,19 +17,33 @@ ValidCommands::ValidCommands() {
 		commands["read.dist"]			= "read.dist"; 
 		commands["read.otu"]			= "read.otu";
 		commands["read.tree"]			= "read.tree"; 
+		commands["read.seqs"]           = "read.seqs";
+		commands["bin.seqs"]			= "bin.seqs"; 
+		commands["get.oturep"]			= "get.oturep";
 		commands["cluster"]				= "cluster"; 
 		commands["deconvolute"]			= "deconvolute"; 
-		commands["parsimony"]			= "parsimony";
-		commands["help"]				= "help"; 
-		commands["quit"]				= "quit"; 
+		commands["dist.seqs"]			= "dist.seqs"; 
 		commands["collect.single"]		= "collect.single"; 
 		commands["collect.shared"]		= "collect.shared"; 
 		commands["rarefaction.single"]	= "rarefaction.single"; 
 		commands["rarefaction.shared"]	= "rarefaction.shared"; 
 		commands["summary.single"]		= "summary.single"; 
 		commands["summary.shared"]		= "summary.shared"; 
+		commands["parsimony"]			= "parsimony";
 		commands["unifrac.weighted"]	= "unifrac.weighted"; 
 		commands["unifrac.unweighted"]	= "unifrac.unweighted"; 
+		commands["libshuff"]			= "libshuff";
+		commands["tree.shared"]			= "tree.shared";
+		commands["heatmap"]				= "heatmap";
+		commands["venn"]				= "venn";
+		commands["get.group"]           = "get.group";
+		commands["get.label"]           = "get.label";
+		commands["get.line"]            = "get.line";
+		commands["bootstrap.shared"]	= "bootstrap.shared";
+		commands["concensus"]			= "concensus";
+		commands["help"]				= "help"; 
+		commands["filter.seqs"]			= "filter.seqs";
+		commands["quit"]				= "quit"; 
 
 				
 	}
@@ -55,7 +69,11 @@ 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(), read.tree(), cluster(), deconvolute(), collect.single(), collect.shared(), rarefaction.single(), rarefaction.shared(), summary.single(), summary.shared(), parsimony(), unifrac.weighted(), unifrac.unweighted(), 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;
 		}
 		
@@ -71,3 +89,24 @@ bool ValidCommands::isValidCommand(string command) {
 }
 
 /***********************************************************************/
+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);
+	}
+}
+
+
+
+