X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcommands.cpp;h=ec60b3b974ad832be1b71092bf3cfbdf9bf28e71;hb=74c78f9abd9e733f0c2f812efec97a76632fcbf8;hp=734e0ce697a5dff86261ef2451d2fbcdd323b0a0;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/validcommands.cpp b/validcommands.cpp
index 734e0ce..ec60b3b 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -16,17 +16,40 @@ ValidCommands::ValidCommands() {
 	
 		commands["read.dist"]			= "read.dist"; 
 		commands["read.otu"]			= "read.otu";
-	//	commands["read.tree"]			= "read.tree"; 
+		commands["read.tree"]			= "read.tree"; 
+		commands["bin.seqs"]			= "bin.seqs"; 
+		commands["get.oturep"]			= "get.oturep";
 		commands["cluster"]				= "cluster"; 
-		commands["deconvolute"]			= "deconvolute"; 
-		commands["help"]				= "help"; 
-		commands["quit"]				= "quit"; 
+		commands["unique.seqs"]			= "unique.seqs"; 
+		commands["dist.seqs"]			= "dist.seqs";
+		commands["dist.shared"]			= "dist.shared";
 		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["get.sabund"]          = "get.sabund";
+		commands["get.rabund"]          = "get.rabund";
+		commands["bootstrap.shared"]	= "bootstrap.shared";
+		commands["concensus"]			= "concensus";
+		commands["help"]				= "help"; 
+		commands["filter.seqs"]			= "filter.seqs";
+		commands["align.seqs"]			= "align.seqs";
+		commands["summary.seqs"]		= "summary.seqs";
+		commands["screen.seqs"]			= "screen.seqs";
+		commands["quit"]				= "quit"; 
+
 				
 	}
 	catch(exception& e) {
@@ -51,7 +74,11 @@ 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;
 		}
 		
@@ -67,3 +94,24 @@ 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);
+	}
+}
+
+
+
+