X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.hpp;h=eb85c68513bc43ece5cf9802917ebe336bc03d5a;hb=6b32d112bb60e9f7eb6d4407a4eed4c49b67bced;hp=8b08c006312240676e1e1466a0470c7f3aa11eae;hpb=48335c6b6ecee614c30d22751c2880953c20e2f4;p=mothur.git

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 8b08c00..eb85c68 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -26,14 +26,16 @@ 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;		}
 	bool MPIEnabled(string);
-
+	map<string, string> getListCommands()	{	return commands;		}
+	
 private:
 	Command* command;
 	Command* shellcommand;
@@ -47,6 +49,8 @@ private:
 	string outputDir, inputDir, logFileName;
 	bool append;
 	
+    int checkForRedirects(string);
+    
 	static CommandFactory* _uniqueInstance;
 	CommandFactory( const CommandFactory& ); // Disable copy constructor
 	void operator=( const CommandFactory& ); // Disable assignment operator