X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.hpp;h=b1db1921a3a074ae059f8341570aa28477ef0cc0;hb=7a1e4b563011b1fe4d466d64915a3cb960747125;hp=e95db8016a4149c9c2defdbb9e7933ff6ee3905a;hpb=eb4bb52af987ff4df7354d95d60cd763aec537e1;p=mothur.git

diff --git a/commandfactory.hpp b/commandfactory.hpp
index e95db80..b1db192 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -26,12 +26,14 @@ public:
 	bool isValidCommand(string);
 	bool isValidCommand(string, string);
 	void printCommands(ostream&);
-	void setOutputDirectory(string o)		{	outputDir = o;	m->setOutputDir(o);	}
-	void setInputDirectory(string i)		{	inputDir = i;		}
+    void printCommandsCategories(ostream&);
+	void setOutputDirectory(string o)		{	if(m->dirCheck(o) || (o == "")) {  outputDir = o; m->setOutputDir(o); }	}
+	void setInputDirectory(string i)		{	if(m->dirCheck(i) || (i == "")) {  inputDir = i;	}	}
 	void setLogfileName(string n, bool a)	{	logFileName = n;  append = a;		}
 	string getLogfileName()					{	return logFileName; 	}
 	bool getAppend()						{	return append;			}
 	string getOutputDir()					{	return outputDir;		}
+    string getInputDir()					{	return inputDir;		}
 	bool MPIEnabled(string);
 	map<string, string> getListCommands()	{	return commands;		}