X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=makebiomcommand.h;fp=makebiomcommand.h;h=9f80c2e70215b130a9020a83ce2daebb9e63a089;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/makebiomcommand.h b/makebiomcommand.h
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+++ 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