class CommandFactory {\r
public:\r
static CommandFactory* getInstance();\r
+ Command* getCommand(string, string, string);\r
Command* getCommand(string, string);\r
- Command* getCommand();\r
+ Command* getCommand(string);\r
+ //Command* getCommand();\r
bool isValidCommand(string);\r
+ bool isValidCommand(string, string);\r
void printCommands(ostream&);\r
- void setOutputDirectory(string o) { outputDir = o; }\r
+ void setOutputDirectory(string o) { outputDir = o; m->setOutputDir(o); }\r
void setInputDirectory(string i) { inputDir = i; }\r
void setLogfileName(string n, bool a) { logFileName = n; append = a; }\r
string getLogfileName() { return logFileName; }\r
\r
private:\r
Command* command;\r
+ Command* shellcommand;\r
+ Command* pipecommand;\r
MothurOut* m;\r
map<string, string> commands;\r
map<string, string>::iterator it;\r