1 #ifndef SUMMARYCOMMAND_H
2 #define SUMMARYCOMMAND_H
7 * Created by Sarah Westcott on 1/2/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
12 #include "command.hpp"
13 #include "sabundvector.hpp"
14 #include "inputdata.h"
15 #include "calculator.h"
16 #include "validcalculator.h"
18 class SummaryCommand : public Command {
21 SummaryCommand(string);
25 vector<string> setParameters();
26 string getCommandName() { return "summary.single"; }
27 string getCommandCategory() { return "OTU-Based Approaches"; }
28 string getHelpString();
29 string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
30 string getDescription() { return "generate summary file that has the calculator value for each line in the OTU data"; }
34 void help() { m->mothurOut(getHelpString()); }
37 vector<Calculator*> sumCalculators;
42 bool abort, allLines, groupMode;
43 set<string> labels; //holds labels to be used
44 string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
45 vector<string> Estimators;
46 vector<string> inputFileNames, outputNames;
47 vector<string> groups;
49 vector<string> parseSharedFile(string);
50 string createGroupSummaryFile(int, int, vector<string>&);