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"; }
35 string getHelpString();
36 string getOutputPattern(string);
37 string getCitation() { return "Bunge J, Woodard L, Bohning D, Foster JA, Connolly S, Allen HK (2012). Estimating population diversity with CatchAll. Bioinformatics 28:1045.\nhttp://www.northeastern.edu/catchall/index.html\nhttp://www.mothur.org/wiki/Catchall"; }
38 string getDescription() { return "estimate number of species"; }
41 void help() { m->mothurOut(getHelpString()); }
44 string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
47 vector<string> outputNames;
48 vector<string> groups;
50 string process(SAbundVector*, string);
51 int createSummaryFile(string, string, ofstream&);
52 vector<string> parseSharedFile(string);
53 string combineSummmary(vector<string>&);
56 /****************************************************************************/