added merge.taxsummary command. added column format to dist.shared.

[mothur.git] / mergetaxsummarycommand.h

diff --git a/mergetaxsummarycommand.h b/mergetaxsummarycommand.h
new file mode 100644 (file)
index 0000000..d39617a
--- /dev/null
+++ b/mergetaxsummarycommand.h
@@ -0,0 +1,47 @@
+//
+//  mergetaxsummarycommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 2/13/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_mergetaxsummarycommand_h
+#define Mothur_mergetaxsummarycommand_h
+
+#include "mothur.h"
+#include "command.hpp"
+#include "phylosummary.h"
+
+class MergeTaxSummaryCommand : public Command {
+public:
+       MergeTaxSummaryCommand(string);
+       MergeTaxSummaryCommand();
+       ~MergeTaxSummaryCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "merge.taxsummary";    }
+       string getCommandCategory()             { return "Phylotype Analysis";          }
+       string getHelpString(); 
+    string getOutputPattern(string){ return "";  }     
+       string getCitation() { return "http://www.mothur.org/wiki/Merge.taxsummary"; }
+       string getDescription()         { return "merges tax summary files creating one file"; }
+    
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       vector<string> fileNames, outputNames;
+       string outputFileName;
+       int numInputFiles;
+       bool abort;
+       
+    int addTaxToTree(vector<rawTaxNode>&, int, int, string, int, map<string, int>);
+    int assignRank(int index, vector<rawTaxNode>& tree);
+    int print(ofstream& out, vector<rawTaxNode>& tree, set<string> groups);
+    int print(int, ofstream& out, vector<rawTaxNode>& tree, set<string> groups);
+};
+
+
+#endif