X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=commandfactory.hpp;h=b1db1921a3a074ae059f8341570aa28477ef0cc0;hp=44e78fd66fa290d9664d773f470249f0600a2836;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=84f93a9e670eb7f7e69e0468b9be4c53890c07f2

diff --git a/commandfactory.hpp b/commandfactory.hpp
index 44e78fd..b1db192 100644
--- a/commandfactory.hpp
+++ b/commandfactory.hpp
@@ -12,32 +12,46 @@
 
 #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;		}
+    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;		}
+    string getInputDir()					{	return inputDir;		}
 	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