1.18.0

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6b0a6d06474809f16fae1a0c17338ef1f7458dc7..6a1e3555f80ffd3f6f5a1565296faf4072995629 100644 (file)
--- 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(',');