8 * Created by Pat Schloss on 8/15/08.
9 * Copyright 2008 Patrick D. Schloss. All rights reserved.
16 #include "commandoptionparser.hpp"
17 #include "command.hpp"
18 #include "commandfactory.hpp"
19 #include "mothurout.h"
25 virtual bool getInput() = 0;
26 virtual string getCommand();
27 virtual string getOutputDir() { return cFactory->getOutputDir(); }
28 virtual string getLogFileName() { return cFactory->getLogfileName(); }
29 virtual bool getAppend() { return cFactory->getAppend(); }
31 vector<string> getOptions() { return options; }
33 vector<string> options;
34 CommandFactory* cFactory;
36 string findMothursPath();
41 class BatchEngine : public Engine {
43 BatchEngine(string, string);
45 virtual bool getInput();
48 ifstream inputBatchFile;
49 string getNextCommand(ifstream&);
55 class InteractEngine : public Engine {
57 InteractEngine(string);
59 virtual bool getInput();
65 class ScriptEngine : public Engine {
67 ScriptEngine(string, string);
69 virtual bool getInput();
72 string listOfCommands;
73 string getNextCommand(string&);