added code to format fast files for uchime. started work on sff.multiple command

[mothur.git] / sffmultiplecommand.h

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