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"
17 #include "validcalculator.h"
21 class SummaryCommand : public Command {
24 SummaryCommand(string);
27 vector<string> getRequiredParameters();
28 vector<string> getValidParameters();
29 vector<string> getRequiredFiles();
30 map<string, vector<string> > getOutputFiles() { return outputTypes; }
35 GlobalData* globaldata;
37 vector<Calculator*> sumCalculators;
39 ValidCalculators* validCalculator;
43 bool abort, allLines, groupMode;
44 set<string> labels; //holds labels to be used
45 string label, calc, outputDir;
46 vector<string> Estimators;
47 vector<string> inputFileNames, outputNames;
48 map<string, vector<string> > outputTypes;
49 vector<string> groups;
51 vector<string> parseSharedFile(string);
52 string createGroupSummaryFile(int, int, vector<string>&);