2 // mergetaxsummarycommand.h
5 // Created by Sarah Westcott on 2/13/13.
6 // Copyright (c) 2013 Schloss Lab. All rights reserved.
9 #ifndef Mothur_mergetaxsummarycommand_h
10 #define Mothur_mergetaxsummarycommand_h
13 #include "command.hpp"
14 #include "phylosummary.h"
16 class MergeTaxSummaryCommand : public Command {
18 MergeTaxSummaryCommand(string);
19 MergeTaxSummaryCommand();
20 ~MergeTaxSummaryCommand(){}
22 vector<string> setParameters();
23 string getCommandName() { return "merge.taxsummary"; }
24 string getCommandCategory() { return "Phylotype Analysis"; }
25 string getHelpString();
26 string getOutputPattern(string){ return ""; }
27 string getCitation() { return "http://www.mothur.org/wiki/Merge.taxsummary"; }
28 string getDescription() { return "merges tax summary files creating one file"; }
32 void help() { m->mothurOut(getHelpString()); }
35 vector<string> fileNames, outputNames;
36 string outputFileName;
40 int addTaxToTree(vector<rawTaxNode>&, int, int, string, int, map<string, int>);
41 int assignRank(int index, vector<rawTaxNode>& tree);
42 int print(ofstream& out, vector<rawTaxNode>& tree, set<string> groups);
43 int print(int, ofstream& out, vector<rawTaxNode>& tree, set<string> groups);