X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.hpp;h=36e8f462b146fc7846ee6cf9ead1eb42e9757a36;hp=3b6a17e38b2abb74b152da573a9bf2f1666e62e6;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=2bbb7273d4bf5209f098c764551c6e072d60df36

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 3b6a17e..36e8f46 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -12,28 +12,45 @@
 
 #include "mothur.h"
 #include "mothurout.h"
+#include "currentfile.h"
 
 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 setInputDirectory(string i)	{	inputDir = i;		}
-	string getOutputDir()			{	return outputDir;		}
+    void printCommandsCategories(ostream&);
+	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; 	}
+	bool getAppend()						{	return append;			}
+	string getOutputDir()					{	return outputDir;		}
 	bool MPIEnabled(string);
-
+	map<string, string> getListCommands()	{	return commands;		}
+	
 private:
 	Command* command;
+	Command* shellcommand;
+	Command* pipecommand;
+	
 	MothurOut* m;
+	CurrentFile* currentFile;
+	
 	map<string, string> commands;
 	map<string, string>::iterator it;
-	string outputDir, inputDir;
+	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