added the Calculators Thomas made in the fall. Added parameter and command error...

[mothur.git] / validparameter.h

diff --git a/validparameter.h b/validparameter.h
index b3d56e5c7eb0a69c0e4e0e4fdc9b3b224a2e225b..61b1c5b2d90ee0e805bc205c5fe8b19b5a4a5c97 100644 (file)
--- a/validparameter.h
+++ b/validparameter.h
@@ -12,6 +12,7 @@
 using namespace std;
 
 #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.
@@ -23,8 +24,12 @@ class ValidParameters {
        public:
                ValidParameters();
                ~ValidParameters();
-               bool isValidParameter(string, string);
-               
+               bool isValidParameter(string);
+               bool isValidParameter(string, string, string);
+               vector <string> addParameters(string[], int);
+               void initCommandParameters();
+               void initParameterRanges();
+
        private:
                map<string, string> readdist;
                map<string, string> readotu;
@@ -44,23 +49,8 @@ class ValidParameters {
                map<string, string> heatmap;
                
                map<string, string>::iterator it;
-               
-               void initialReaddist();
-               void initialReadotu();
-               void initialReadtree();
-               void initialCluster();
-               void initialDeconvolute();
-               void initialParsimony();
-               void initialCollectsingle();
-               void initialCollectshared();
-               void initialRarefactsingle();
-               void initialRarefactshared();
-               void initialSummarysingle();
-               void initialSummaryshared();
-               void initialUnifracweighted();
-               void initialUnifracunweighted();
-               void initialLibshuff();
-               void initialHeatmap();
+               map<string, vector<string> > commandParameters;
+               map<string, vector<string> > parameterRanges;
 
 };