X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sffmultiplecommand.h;fp=sffmultiplecommand.h;h=ae881aa7fcacb2aab09224d204f301db0531fa35;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=0000000000000000000000000000000000000000;hpb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;p=mothur.git

diff --git a/sffmultiplecommand.h b/sffmultiplecommand.h
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+#ifndef Mothur_sffmultiplecommand_h
+#define Mothur_sffmultiplecommand_h
+
+//
+//  sffmultiplecommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 8/14/12.
+//  Copyright (c) 2012 Schloss Lab. All rights reserved.
+//
+
+#include "command.hpp"
+
+class SffMultipleCommand : public Command {
+	
+public:
+	SffMultipleCommand(string);
+	SffMultipleCommand();
+	~SffMultipleCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "sff.multiple";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	string getOutputFileNameTag(string, string);
+	string getHelpString();	
+	string getCitation() { return "http://www.mothur.org/wiki/Sff.multiple"; }
+	string getDescription()		{ return "run multiple sff files through, sffinfo, trim.flow, shhh.flows and trim.seqs combining the results"; }
+    
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+private:
+	string filename, outputDir, flowOrder;
+	vector<string> outputNames;
+	bool abort, trim;
+	int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
+	int numFlows, numFPrimers, numRPrimers, processors;
+	float signal, noise;
+    
+    int readFile(vector<string>& sffFiles, vector<string>& oligosFiles);
+    
+};
+
+
+#endif