sens.spec changes

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
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+#ifndef SENSSPECCOMMAND_H
+#define SENSSPECCOMMAND_H
+
+
+/*
+ *  sensspeccommand.h
+ *  Mothur
+ *
+ *  Created by Pat Schloss on 7/6/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "command.hpp"
+
+class SensSpecCommand : public Command {
+       
+public:
+       SensSpecCommand(string);
+       ~SensSpecCommand();
+       int execute();
+       void help();
+       
+private:
+       void processPhylip();
+///    void processColumn(map<string, int>);
+       
+       string listFile, distFile, nameFile, outputDir;
+       string format;
+//     int numSeqs, numDists;
+       int truePositives, falsePositives, trueNegatives, falseNegatives;
+       bool abort;
+       bool hard;
+       string lineLabel;
+       double cutoff;
+};
+
+#endif
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