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"
15 #include "sabundvector.hpp"
21 /****************************************************************************/
23 class CatchAllCommand : public Command {
27 CatchAllCommand(string);
31 vector<string> setParameters();
32 string getCommandName() { return "catchall"; }
33 string getCommandCategory() { return "OTU-Based Approaches"; }
34 string getHelpString();
35 string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
36 string getDescription() { return "estimate number of species"; }
39 void help() { m->mothurOut(getHelpString()); }
42 string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
45 vector<string> outputNames;
46 vector<string> groups;
48 string process(SAbundVector*, string);
49 int createSummaryFile(string, string, ofstream&);
50 vector<string> parseSharedFile(string);
51 string combineSummmary(vector<string>&);
54 /****************************************************************************/