1 #ifndef METASTATSCOMMAND_H
2 #define METASTATSCOMMAND_H
8 * Created by westcott on 9/16/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
16 #include "sharedrabundvector.h"
20 class MetaStatsCommand : public Command {
23 MetaStatsCommand(string);
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 map<string, vector<string> > getOutputFiles() { return outputTypes; }
37 linePair(int i, int j) : start(i), num(j) {}
39 vector<linePair> lines;
41 GlobalData* globaldata;
45 vector<SharedRAbundVector*> lookup;
46 map<string, vector<string> > outputTypes;
48 bool abort, allLines, pickedGroups;
49 set<string> labels; //holds labels to be used
50 string groups, label, outputDir, inputDir, designfile, sets;
51 vector<string> Groups, outputNames, Sets;
52 vector< vector<string> > namesOfGroupCombos;
53 int iters, processors;
56 int process(vector<SharedRAbundVector*>&);
57 int driver(int, int, vector<SharedRAbundVector*>&);