added citation function to commands

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 52ab31ea6c96c88edb1b9b360cac7f9e38979a4e..b2833bf70fc71c24dc76c0d71910b181fc09aa3c 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -18,22 +18,38 @@ class SensSpecCommand : public Command {
        
 public:
        SensSpecCommand(string);
-       ~SensSpecCommand();
-       int execute();
-       void help();
+       SensSpecCommand();
+       ~SensSpecCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "sens.spec";                           }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Sens.spec"; }
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 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, phylipfile, columnfile;
+       string outputDir;
        string format;
-//     int numSeqs, numDists;
-       int truePositives, falsePositives, trueNegatives, falseNegatives;
+       vector<string> outputNames;
+
+       long int truePositives, falsePositives, trueNegatives, falseNegatives;
        bool abort;
        bool hard;
        string lineLabel;
        double cutoff;
+       int precision;
 };
 
-#endif
\ No newline at end of file
+#endif
+
+
+