shhh.seqs and trim.flows modifications.

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 52ab31ea6c96c88edb1b9b360cac7f9e38979a4e..5e25afd2098e2fed0385178eecfcfd60a65fb461 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -18,22 +18,36 @@ class SensSpecCommand : public Command {
        
 public:
        SensSpecCommand(string);
+       SensSpecCommand();
        ~SensSpecCommand();
+       vector<string> getRequiredParameters();
+       vector<string> getValidParameters();
+       vector<string> getRequiredFiles();
+       map<string, vector<string> > getOutputFiles() { return outputTypes; }
        int execute();
        void help();
        
 private:
        void processPhylip();
-///    void processColumn(map<string, int>);
+       void processColumn();
+       void setUpOutput();
+       void outputStatistics(string, string);
        
-       string listFile, distFile, nameFile, outputDir;
+       string listFile, distFile, nameFile, sensSpecFileName;
+       string outputDir;
        string format;
-//     int numSeqs, numDists;
-       int truePositives, falsePositives, trueNegatives, falseNegatives;
+       vector<string> outputNames;
+       map<string, vector<string> > outputTypes;
+
+       long int truePositives, falsePositives, trueNegatives, falseNegatives;
        bool abort;
        bool hard;
        string lineLabel;
        double cutoff;
+       int precision;
 };
 
-#endif
\ No newline at end of file
+#endif
+
+
+