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"
17 class NormalizeSharedCommand : public Command {
20 NormalizeSharedCommand(string);
21 NormalizeSharedCommand();
22 ~NormalizeSharedCommand() {}
24 vector<string> setParameters();
25 string getCommandName() { return "normalize.shared"; }
26 string getCommandCategory() { return "OTU-Based Approaches"; }
28 string getHelpString();
29 string getOutputPattern(string);
30 string getCitation() { return "http://www.mothur.org/wiki/Normalize.shared"; }
31 string getDescription() { return "normalize samples in a shared or relabund file"; }
35 void help() { m->mothurOut(getHelpString()); }
40 vector<SharedRAbundVector*> lookup;
41 vector<SharedRAbundFloatVector*> lookupFloat;
43 bool abort, allLines, pickedGroups, makeRelabund;
44 set<string> labels; //holds labels to be used
45 string groups, label, outputDir, method, sharedfile, relabundfile, format, inputfile;
47 vector<string> Groups, outputNames;
49 int normalize(vector<SharedRAbundVector*>&);
50 int normalize(vector<SharedRAbundFloatVector*>&);
51 int eliminateZeroOTUS(vector<SharedRAbundVector*>&);
52 int eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&);