X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=abc07d0743a0a3e8f7172c27fe4094571abb3d5c;hb=4169642e8a8d45f71a4a7241ee02f1b1aae29520;hp=0820b0521961224c04f3b7c6207f4fd3d490c5fd;hpb=5ff964d3871ce86f59fec3052f9c25e872f22c42;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 0820b05..abc07d0 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,23 +9,66 @@
 
 #include "systemcommand.h"
 
+//**********************************************************************************************************************
+vector<string> SystemCommand::getValidParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SystemCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SystemCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SystemCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> SystemCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SystemCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
-SystemCommand::SystemCommand(string option){
+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 = "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
-			else { command = option; }
+			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);
+				}
+			
+				command = option;
+			}
 		}	
 
 	}
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "SystemCommand");
+		m->errorOut(e, "SystemCommand", "SystemCommand");
 		exit(1);
 	}
 }
@@ -33,13 +76,13 @@ 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 has no parameters.\n");
-		mothurOut("The system command should be in the following format: system(yourCommand).\n");
-		mothurOut("Example system(clear).\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);
 	}
 }
@@ -49,7 +92,7 @@ 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());
 		
@@ -57,7 +100,7 @@ int SystemCommand::execute(){
 	}
 
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "execute");
+		m->errorOut(e, "SystemCommand", "execute");
 		exit(1);
 	}
 }