1 #ifndef NORMALIZESHAREDCOMMAND_H
2 #define NORMALIZESHAREDCOMMAND_H
5 * normalizesharedcommand.h
8 * Created by westcott on 9/15/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
13 #include "command.hpp"
14 #include "inputdata.h"
16 #include "sharedrabundvector.h"
20 class NormalizeSharedCommand : public Command {
23 NormalizeSharedCommand(string);
24 NormalizeSharedCommand();
25 ~NormalizeSharedCommand();
26 vector<string> getRequiredParameters();
27 vector<string> getValidParameters();
28 vector<string> getRequiredFiles();
29 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 GlobalData* globaldata;
37 vector<SharedRAbundVector*> lookup;
39 bool abort, allLines, pickedGroups;
40 set<string> labels; //holds labels to be used
41 string groups, label, outputDir, method;
43 vector<string> Groups, outputNames;
44 map<string, vector<string> > outputTypes;
46 int normalize(vector<SharedRAbundVector*>&, ofstream&);
47 int eliminateZeroOTUS(vector<SharedRAbundVector*>& thislookup);