X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.hpp;fp=commandfactory.hpp;h=a6dc5b72e0b403df37dd77b7ee593ca5ff19de73;hb=8bc3e5b38c2317a1715f53be22fa96455868c281;hp=44e78fd66fa290d9664d773f470249f0600a2836;hpb=f663afa231c9bc1b5e18e0ea3bdd2b2ee784f5b2;p=mothur.git

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 44e78fd..a6dc5b7 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -18,11 +18,14 @@ class Command;
 class CommandFactory {
 public:
 	static CommandFactory* getInstance();
+	Command* getCommand(string, string, string);
 	Command* getCommand(string, string);
-	Command* getCommand();
+	Command* getCommand(string);
+	//Command* getCommand();
 	bool isValidCommand(string);
+	bool isValidCommand(string, string);
 	void printCommands(ostream&);
-	void setOutputDirectory(string o)		{	outputDir = o;		}
+	void setOutputDirectory(string o)		{	outputDir = o;	m->setOutputDir(o);	}
 	void setInputDirectory(string i)		{	inputDir = i;		}
 	void setLogfileName(string n, bool a)	{	logFileName = n;  append = a;		}
 	string getLogfileName()					{	return logFileName; 	}
@@ -32,6 +35,8 @@ public:
 
 private:
 	Command* command;
+	Command* shellcommand;
+	Command* pipecommand;
 	MothurOut* m;
 	map<string, string> commands;
 	map<string, string>::iterator it;