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"
18 #include "validcalculator.h"
22 class SummarySharedCommand : public Command {
25 SummarySharedCommand(string);
26 SummarySharedCommand();
27 ~SummarySharedCommand();
28 vector<string> getRequiredParameters();
29 vector<string> getValidParameters();
30 vector<string> getRequiredFiles();
31 map<string, vector<string> > getOutputFiles() { return outputTypes; }
40 vector<linePair> lines;
41 GlobalData* globaldata;
43 vector<Calculator*> sumCalculators;
45 ValidCalculators* validCalculator;
47 bool abort, allLines, mult, all, createPhylip;
48 set<string> labels; //holds labels to be used
49 string label, calc, groups;
50 vector<string> Estimators, Groups, outputNames;
51 map<string, vector<string> > outputTypes;
52 vector<SharedRAbundVector*> lookup;
53 string format, outputDir;
54 int numGroups, processors;
55 int process(vector<SharedRAbundVector*>, string, string);
56 int driver(vector<SharedRAbundVector*>, int, int, string, string, vector< vector<seqDist> >&);