added citation function to commands

[mothur.git] / sensspeccommand.h

diff --git a/sensspeccommand.h b/sensspeccommand.h
index 687834c5b1b9098830747b79dd0e9e6135e6951b..b2833bf70fc71c24dc76c0d71910b181fc09aa3c 100644 (file)
--- a/sensspeccommand.h
+++ b/sensspeccommand.h
@@ -19,13 +19,16 @@ 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();
+       ~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();
@@ -33,11 +36,10 @@ private:
        void setUpOutput();
        void outputStatistics(string, string);
        
-       string listFile, distFile, nameFile, sensSpecFileName;
+       string listFile, distFile, nameFile, sensSpecFileName, phylipfile, columnfile;
        string outputDir;
        string format;
        vector<string> outputNames;
-       map<string, vector<string> > outputTypes;
 
        long int truePositives, falsePositives, trueNegatives, falseNegatives;
        bool abort;
@@ -47,4 +49,7 @@ private:
        int precision;
 };
 
-#endif
\ No newline at end of file
+#endif
+
+
+