1 #ifndef Mothur_classifytreecommand_h
2 #define Mothur_classifytreecommand_h
5 // classifytreecommand.h
8 // Created by Sarah Westcott on 2/20/12.
9 // Copyright (c) 2012 Schloss Lab. All rights reserved.
12 #include "command.hpp"
16 class ClassifyTreeCommand : public Command {
18 ClassifyTreeCommand(string);
19 ClassifyTreeCommand();
20 ~ClassifyTreeCommand(){}
22 vector<string> setParameters();
23 string getCommandName() { return "classify.tree"; }
24 string getCommandCategory() { return "Phylotype Analysis"; }
25 string getHelpString();
26 string getCitation() { return "http://www.mothur.org/wiki/Classify.tree"; }
27 string getDescription() { return "Find the consensus taxonomy for the descendant of each tree node"; }
30 void help() { m->mothurOut(getHelpString()); }
35 string treefile, taxonomyfile, groupfile, namefile, outputDir;
37 vector<string> outputNames;
38 int numUniquesInName, cutoff;
39 map<string, string> nameMap;
40 map<string, int> nameCount;
41 map<string, string> taxMap;
43 int getClassifications(Tree*&);
44 map<string, set<string> > getDescendantList(Tree*&, int, map<int, map<string, set<string> > >);
45 string getTaxonomy(set<string>, int&);
47 int readTaxonomyFile();