1 #ifndef SUMMARYSHAREDCOMMAND_H
2 #define SUMMARYSHAREDCOMMAND_H
4 * summarysharedcommand.h
7 * Created by Sarah Westcott on 1/2/09.
8 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
13 #include "command.hpp"
14 #include "sharedrabundvector.h"
15 #include "inputdata.h"
16 #include "calculator.h"
17 #include "validcalculator.h"
19 class SummarySharedCommand : public Command {
22 SummarySharedCommand(string);
23 SummarySharedCommand();
24 ~SummarySharedCommand() {}
26 vector<string> setParameters();
27 string getCommandName() { return "summary.shared"; }
28 string getCommandCategory() { return "OTU-Based Approaches"; }
29 string getHelpString();
30 string getCitation() { return "http://www.mothur.org/wiki/Summary.shared"; }
31 string getDescription() { return "generate a summary file containing calculator values for each line in the OTU data and for all possible comparisons between groups"; }
34 void help() { m->mothurOut(getHelpString()); }
42 vector<linePair> lines;
43 vector<Calculator*> sumCalculators;
46 bool abort, allLines, mult, all, createPhylip;
47 set<string> labels; //holds labels to be used
48 string label, calc, groups, sharedfile;
49 vector<string> Estimators, Groups, outputNames;
50 vector<SharedRAbundVector*> lookup;
51 string format, outputDir;
52 int numGroups, processors;
53 int process(vector<SharedRAbundVector*>, string, string);
54 int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);