1 #ifndef CATCHALLCOMMAND_H
2 #define CATCHALLCOMMAND_H
8 * Created by westcott on 5/11/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
16 #include "sabundvector.hpp"
22 /****************************************************************************/
24 class CatchAllCommand : public Command {
28 CatchAllCommand(string);
31 vector<string> getRequiredParameters();
32 vector<string> getValidParameters();
33 vector<string> getRequiredFiles();
34 map< string, vector<string> > getOutputFiles() { return outputTypes; }
40 GlobalData* globaldata;
42 string outputDir, sharedfile, sabundfile, rabundfile, listfile, format, path;
45 vector<string> outputNames;
46 map< string, vector<string> > outputTypes;
47 vector<string> groups;
49 string process(SAbundVector*, string);
50 int createSummaryFile(string, string, ofstream&);
51 vector<string> parseSharedFile(string);
52 string combineSummmary(vector<string>&);
55 /****************************************************************************/