added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6a1e3555f80ffd3f6f5a1565296faf4072995629..c07deff1f19c0315b29e0f488572b3feacb7114f 100644 (file)
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -30,6 +30,7 @@ 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 {
                        vector<string> myArray = setParameters();
@@ -90,8 +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;               
        }