modifications to commands to add headers to list file.

[mothur.git] / commandfactory.hpp

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 36e8f462b146fc7846ee6cf9ead1eb42e9757a36..eb85c68513bc43ece5cf9802917ebe336bc03d5a 100644 (file)
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -27,8 +27,8 @@ public:
        bool isValidCommand(string, string);\r
        void printCommands(ostream&);\r
     void printCommandsCategories(ostream&);\r
-       void setOutputDirectory(string o)               {       outputDir = o;  m->setOutputDir(o);     }\r
-       void setInputDirectory(string i)                {       inputDir = i;           }\r
+       void setOutputDirectory(string o)               {       if(m->dirCheck(o) || (o == "")) {  outputDir = o; m->setOutputDir(o); } }\r
+       void setInputDirectory(string i)                {       if(m->dirCheck(i) || (i == "")) {  inputDir = i;        }       }\r
        void setLogfileName(string n, bool a)   {       logFileName = n;  append = a;           }\r
        string getLogfileName()                                 {       return logFileName;     }\r
        bool getAppend()                                                {       return append;                  }\r