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"; }
29 string getHelpString();
30 string getOutputPattern(string);
31 string getCitation() { return "http://www.mothur.org/wiki/Summary.single"; }
32 string getDescription() { return "generate summary file that has the calculator value for each line in the OTU data"; }
36 void help() { m->mothurOut(getHelpString()); }
39 vector<Calculator*> sumCalculators;
42 int abund, size, iters, subsampleSize;
44 bool abort, allLines, groupMode, subsample;
45 set<string> labels; //holds labels to be used
46 string label, calc, outputDir, sharedfile, listfile, rabundfile, sabundfile, format, inputfile;
47 vector<string> Estimators;
48 vector<string> inputFileNames, outputNames;
49 vector<string> groups;
51 vector<string> parseSharedFile(string);
52 vector<string> createGroupSummaryFile(int, int, vector<string>&, map<string, string>);
53 int process(SAbundVector*&, ofstream&, ofstream&);