X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.hpp;h=36e8f462b146fc7846ee6cf9ead1eb42e9757a36;hp=e3eea41cd73e3583e57f5f2ce503233b54a02d55;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=0470f6d037aacb3563c3f7010708120a4a67d4e6

diff --git a/commandfactory.hpp b/commandfactory.hpp
index e3eea41..36e8f46 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -1,27 +1,62 @@
-#ifndef COMMANDFACTORY_HPP
-#define COMMANDFACTORY_HPP
-
-/*
- *  commandfactory.h
- *  
- *
- *  Created by Pat Schloss on 10/25/08.
- *  Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "mothur.h"
-
-class Command;
-
-class CommandFactory {
-public:
-	CommandFactory();
-	~CommandFactory();
-	Command* getCommand(string, string);
-private:
-	Command* command;
-
-};
-
-#endif
+#ifndef COMMANDFACTORY_HPP
+#define COMMANDFACTORY_HPP
+
+/*
+ *  commandfactory.h
+ *  
+ *
+ *  Created by Pat Schloss on 10/25/08.
+ *  Copyright 2008 Patrick D. Schloss. All rights reserved.
+ *
+ */
+
+#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(string);
+	//Command* getCommand();
+	bool isValidCommand(string);
+	bool isValidCommand(string, string);
+	void printCommands(ostream&);
+    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, logFileName;
+	bool append;
+	
+    int checkForRedirects(string);
+    
+	static CommandFactory* _uniqueInstance;
+	CommandFactory( const CommandFactory& ); // Disable copy constructor
+	void operator=( const CommandFactory& ); // Disable assignment operator
+	CommandFactory();
+	~CommandFactory();
+
+};
+
+#endif