sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6b0a6d06474809f16fae1a0c17338ef1f7458dc7..b5b4945b92b6d664e6d81aa2dc6911a2d30414c3 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 {
@@ -17,10 +30,25 @@ SystemCommand::SystemCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); 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(',');
                                
@@ -63,8 +91,31 @@ int SystemCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
+               //if command contains a redirect don't add the redirect
+               bool usedRedirect = false;
+               if ((command.find('>')) == string::npos) {
+                       command += " > ./commandScreen.output 2>&1";
+                       usedRedirect = true;
+               }
+               
                system(command.c_str());
                
+               if (usedRedirect) {
+                       ifstream in;
+                       string filename = "./commandScreen.output";
+                       m->openInputFile(filename, in, "no error");
+                       
+                       string output = "";
+                       while(char c = in.get()){
+                               if(in.eof())            {       break;                  }
+                               else                            {       output += c;    }
+                       }
+                       in.close();
+                       
+                       m->mothurOut(output); m->mothurOutEndLine();
+                       m->mothurRemove(filename);
+               }
+               
                return 0;               
        }