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"
15 #include "sharedrabundvector.h"
19 class NormalizeSharedCommand : public Command {
22 NormalizeSharedCommand(string);
23 NormalizeSharedCommand();
24 ~NormalizeSharedCommand();
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
33 GlobalData* globaldata;
35 vector<SharedRAbundVector*> lookup;
36 vector<SharedRAbundFloatVector*> lookupFloat;
38 bool abort, allLines, pickedGroups, makeRelabund;
39 set<string> labels; //holds labels to be used
40 string groups, label, outputDir, method;
42 vector<string> Groups, outputNames;
43 map<string, vector<string> > outputTypes;
45 int normalize(vector<SharedRAbundVector*>&, ofstream&);
46 int normalize(vector<SharedRAbundFloatVector*>&, ofstream&);
47 int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
48 int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);