2 // classifysharedcommand.h
5 // Created by Abu Zaher Md. Faridee on 8/13/12.
6 // Copyright (c) 2012 Schloss Lab. All rights reserved.
9 #ifndef __Mothur__classifysharedcommand__
10 #define __Mothur__classifysharedcommand__
12 #include "command.hpp"
13 #include "inputdata.h"
15 class ClassifySharedCommand : public Command {
17 ClassifySharedCommand();
18 ClassifySharedCommand(string);
19 ~ClassifySharedCommand() {};
21 vector<string> setParameters();
22 string getCommandName() { return "classify.shared"; }
23 string getCommandCategory() { return "OTU-Based Approaches"; }
24 string getHelpString();
25 string getOutputPattern(string);
26 string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; }
27 string getDescription() { return "description"; }
30 void help() { m->mothurOut(getHelpString()); }
35 vector<string> outputNames, Groups;
37 string sharedfile, designfile;
47 string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
48 bool doPruning, discardHighErrorTrees;
49 double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
51 void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
54 #endif /* defined(__Mothur__classifysharedcommand__) */