\r
#include "mothur.h"\r
#include "mothurout.h"\r
+#include "currentfile.h"\r
\r
class Command;\r
\r
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 setInputDirectory(string i) { inputDir = i; }\r
- string getOutputDir() { return outputDir; }\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
+ bool getAppend() { return append; }\r
+ string getOutputDir() { return outputDir; }\r
bool MPIEnabled(string);\r
-\r
+ map<string, string> getListCommands() { return commands; }\r
+ \r
private:\r
Command* command;\r
+ Command* shellcommand;\r
+ Command* pipecommand;\r
+ \r
MothurOut* m;\r
+ CurrentFile* currentFile;\r
+ \r
map<string, string> commands;\r
map<string, string>::iterator it;\r
- string outputDir, inputDir;\r
+ string outputDir, inputDir, logFileName;\r
+ bool append;\r
\r
static CommandFactory* _uniqueInstance;\r
CommandFactory( const CommandFactory& ); // Disable copy constructor\r