X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=6a1e3555f80ffd3f6f5a1565296faf4072995629;hb=9d6f36294dcaef3ac65a0e69fd8140077c3209e0;hp=708724a4e5cd46643e7ec29464b61c1f34c7cd41;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 708724a..6a1e355 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -10,17 +10,44 @@
 #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 {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		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(',');
 				
@@ -41,12 +68,14 @@ SystemCommand::SystemCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void SystemCommand::help(){
+string SystemCommand::getHelpString(){
 	try {
-		m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
-		m->mothurOut("The system has no parameters.\n");
-		m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
-		m->mothurOut("Example system(clear).\n");
+		string helpString = "";
+		helpString += "The system command allows you to execute a system command from within mothur.\n";
+		helpString += "The system has no parameters.\n";
+		helpString += "The system command should be in the following format: system(yourCommand).\n";
+		helpString += "Example system(clear).\n";
+		return helpString;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "SystemCommand", "help");
@@ -59,7 +88,7 @@ void SystemCommand::help(){
 int SystemCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		system(command.c_str());