made sorting optional but sort by default, in case the user wants to see the heatmap...

[mothur.git] / validparameter.h

diff --git a/validparameter.h b/validparameter.h
index e0477aab0e9c1f39ffa19c836ef960de2c0e2bfa..61b1c5b2d90ee0e805bc205c5fe8b19b5a4a5c97 100644 (file)
--- a/validparameter.h
+++ b/validparameter.h
@@ -11,9 +11,8 @@
  */
 using namespace std;
 
-#include <iostream>
-#include <string>
-#include <map>
+#include "mothur.h"
+#include "utilities.hpp"
 
 //This class contains a list of all valid parameters in Mothur.  
 //It has a function which will tell you if your parameter is valid.
@@ -26,8 +25,32 @@ class ValidParameters {
                ValidParameters();
                ~ValidParameters();
                bool isValidParameter(string);
+               bool isValidParameter(string, string, string);
+               vector <string> addParameters(string[], int);
+               void initCommandParameters();
+               void initParameterRanges();
+
        private:
-               map<string, string> parameters;
+               map<string, string> readdist;
+               map<string, string> readotu;
+               map<string, string> readtree;
+               map<string, string> cluster;
+               map<string, string> deconvolute;
+               map<string, string> parsimony;
+               map<string, string> collectsingle;
+               map<string, string> collectshared;
+               map<string, string> rarefactsingle;
+               map<string, string> rarefactshared;
+               map<string, string> summarysingle;
+               map<string, string> summaryshared;
+               map<string, string> unifracweighted;
+               map<string, string> unifracunweighted;
+               map<string, string> libshuff;
+               map<string, string> heatmap;
+               
+               map<string, string>::iterator it;
+               map<string, vector<string> > commandParameters;
+               map<string, vector<string> > parameterRanges;
 
 };