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"; }
25 string getHelpString();
26 string getOutputPattern(string);
27 string getCitation() { return "http://www.mothur.org/wiki/Classify.shared\n"; }
28 string getDescription() { return "description"; }
31 void help() { m->mothurOut(getHelpString()); }
36 vector<string> outputNames, Groups;
38 string sharedfile, designfile, otupersplit, splitcriteria;
48 string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
49 bool doPruning, discardHighErrorTrees;
50 double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
52 void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
55 #endif /* defined(__Mothur__classifysharedcommand__) */