X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=6a1e3555f80ffd3f6f5a1565296faf4072995629;hb=9d6f36294dcaef3ac65a0e69fd8140077c3209e0;hp=6b0a6d06474809f16fae1a0c17338ef1f7458dc7;hpb=f0a594f6676ef5a52d1f122b6de70de2fda08c81;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6b0a6d0..6a1e355 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,7 +9,20 @@
 
 #include "systemcommand.h"
 
-
+//**********************************************************************************************************************
+vector<string> SystemCommand::setParameters(){	
+	try {
+		CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
+				
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SystemCommand", "setParameters");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 SystemCommand::SystemCommand(string option)  {
 	try {
@@ -19,8 +32,22 @@ SystemCommand::SystemCommand(string option)  {
 		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
-			if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
-			else { 
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters();
+			map<string, string>::iterator it;
+			
+			ValidParameters validParameter;
+			
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			string commandOption = validParameter.validFile(parameters, "command", false);			
+			if (commandOption == "not found") { commandOption = ""; }
+			else { command = commandOption; }
+			
+			if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+			else if (commandOption == "") { 
 				//check for outputdir and inputdir parameters
 				int commaPos = option.find_first_of(',');