X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=708724a4e5cd46643e7ec29464b61c1f34c7cd41;hb=bd93b1a6f9fe9a6a4a7ac2e9f106e5c83a438856;hp=5bc9b46e47522d38fe4a89f0119df8785a4d8d4d;hpb=55dad85695dba70b4447d1430733ecd85754783c;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 5bc9b46..708724a 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-SystemCommand::SystemCommand(string option){
+SystemCommand::SystemCommand(string option)  {
 	try {
 		abort = false;
 		
@@ -19,28 +19,23 @@ SystemCommand::SystemCommand(string option){
 		if(option == "help") { help(); abort = true; }
 		
 		else {
-			//valid paramters for this command
-			string Array[] =  {"command"};
-			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			if (option == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+			else { 
+				//check for outputdir and inputdir parameters
+				int commaPos = option.find_first_of(',');
+				
+				//if there is a comma then grab string up to that pos
+				if (commaPos != option.npos) {
+					option = option.substr(0, commaPos);
+				}
 			
-			OptionParser parser(option);
-			map<string,string> parameters = parser.getParameters();
-			
-			ValidParameters validParameter;
-			
-			//check to make sure all parameters are valid for command
-			for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
-				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+				command = option;
 			}
-			
-			//check for required parameters
-			command = validParameter.validFile(parameters, "command", false);
-			if (command == "not found") { mothurOut("command is a required parameter."); mothurOutEndLine(); abort = true; }
 		}	
 
 	}
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "SystemCommand");
+		m->errorOut(e, "SystemCommand", "SystemCommand");
 		exit(1);
 	}
 }
@@ -48,14 +43,13 @@ SystemCommand::SystemCommand(string option){
 
 void SystemCommand::help(){
 	try {
-		mothurOut("The system command allows you to execute a system command from within mothur.\n");
-		mothurOut("The system command parameter is command and it is required.\n");
-		mothurOut("The system command should be in the following format: system(command=yourCommand).\n");
-		mothurOut("Example system(command=clear).\n");
-		mothurOut("Note: No spaces between parameter labels (i.e. command), '=' and parameters (i.e.yourCommand).\n\n");
+		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");
 	}
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "help");
+		m->errorOut(e, "SystemCommand", "help");
 		exit(1);
 	}
 }
@@ -73,7 +67,7 @@ int SystemCommand::execute(){
 	}
 
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "execute");
+		m->errorOut(e, "SystemCommand", "execute");
 		exit(1);
 	}
 }