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[mothur.git] / makebiomcommand.h

diff --git a/makebiomcommand.h b/makebiomcommand.h
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+#ifndef Mothur_makebiomcommand_h
+#define Mothur_makebiomcommand_h
+
+//
+//  makebiomcommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 4/16/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+
+#include "command.hpp"
+#include "sharedrabundvector.h"
+#include "inputdata.h"
+
+
+class MakeBiomCommand : public Command {
+       
+public:
+       MakeBiomCommand(string);
+       MakeBiomCommand();      
+       ~MakeBiomCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "make.biom";   }
+       string getCommandCategory()             { return "General";             }
+       string getHelpString(); 
+       string getCitation() { return "http://biom-format.org/documentation/biom_format.html, http://www.mothur.org/wiki/Make.biom"; }
+       string getDescription()         { return "creates a biom file"; }
+    
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+    
+       string sharedfile, contaxonomyfile, groups, outputDir, format, label;
+       vector<string> outputNames, Groups;
+       set<string> labels;
+    
+       bool abort, allLines;
+    
+    int getBiom(vector<SharedRAbundVector*>&);
+    vector<string> getMetaData(vector<SharedRAbundVector*>&);
+    vector<string> parseTax(string tax, vector<string>& scores);
+};
+
+
+#endif