X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validcommands.cpp;h=787cc8025a6c62d01be190a63c33e42429fe21a4;hb=0e14094b51dd81c07c6a56b7b51533eff2332339;hp=9b6aeed326a4a27aa9c687bf3817985a9fcb4d61;hpb=20a2d0350a737a434c89f303662d64a8eeea7b05;p=mothur.git

diff --git a/validcommands.cpp b/validcommands.cpp
index 9b6aeed..787cc80 100644
--- a/validcommands.cpp
+++ b/validcommands.cpp
@@ -14,24 +14,41 @@
 ValidCommands::ValidCommands() {
 	try {
 	
-		commands["read.phylip"]			= "read.phylip"; 
-		commands["read.column"]			= "read.column"; 
-		commands["read.list"]			= "read.list"; 
-		commands["read.rabund"]			= "read.rabund"; 
-		commands["read.sabund"]			= "read.sabund"; 
-		commands["read.shared"]			= "read.shared"; 
+		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.repseqs"]			= "get.repseqs"; 
+		commands["get.oturep"]			= "get.oturep";
 		commands["cluster"]				= "cluster"; 
-		commands["help"]				= "help"; 
-		commands["quit"]				= "quit"; 
+		commands["deconvolute"]			= "deconvolute"; 
+		commands["dist.seqs"]			= "dist.seqs";
+		commands["dist.shared"]			= "dist.shared";  //matrix output
 		commands["collect.single"]		= "collect.single"; 
-		commands["shared"]				= "shared"; 
 		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["parselist"]			= "parselist"; 
-		
+		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["align.seqs"]			= "align.seqs";
+		commands["quit"]				= "quit"; 
+
+				
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ValidCommands class Function ValidCommands. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -55,7 +72,11 @@ 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.phylip(), read.column(), read.list(), read.rabund(), read.sabund(), read.shared(), cluster(), collect.single(), collect.shared(), parselist(), 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;
 		}
 		
@@ -70,4 +91,25 @@ 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);
+	}
+}
+
+
+
+