X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.hpp;h=eb85c68513bc43ece5cf9802917ebe336bc03d5a;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=d84be62a074dde5dc29b8006a636bd7b67b9607d;hpb=315e38cf393c82be238da5b32574f225a020d25c;p=mothur.git

diff --git a/commandfactory.hpp b/commandfactory.hpp
index d84be62..eb85c68 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -1,42 +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:
-	static CommandFactory* getInstance();
-	Command* getCommand(string, string);
-	Command* getCommand();
-	bool isValidCommand(string);
-	void printCommands(ostream&);
-	void setOutputDirectory(string o)	{	outputDir = o;		}
-	void setInputDirectory(string i)	{	inputDir = i;		}
-	string getOutputDir()				{	return outputDir;	}
-
-private:
-	Command* command;
-	map<string, string> commands;
-	map<string, string>::iterator it;
-	string outputDir, inputDir;
-	
-	static CommandFactory* _uniqueInstance;
-	CommandFactory( const CommandFactory& ); // Disable copy constructor
-	void operator=( const CommandFactory& ); // Disable assignment operator
-	CommandFactory();
-	~CommandFactory();
-
-};
-
-#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)		{	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;
+	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