1.18.0

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index abc07d0743a0a3e8f7172c27fe4094571abb3d5c..6a1e3555f80ffd3f6f5a1565296faf4072995629 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -10,40 +10,20 @@
 #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(){      
+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", "getRequiredFiles");
+               m->errorOut(e, "SystemCommand", "setParameters");
                exit(1);
        }
 }
 //**********************************************************************************************************************
-
 SystemCommand::SystemCommand(string option)  {
        try {
                abort = false; calledHelp = false;   
@@ -52,8 +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(',');
                                
@@ -74,12 +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");