working on pam

[mothur.git] / validparameter.h

diff --git a/validparameter.h b/validparameter.h
index c59c1571e38d5b4ffba3004dd19957752d4339bb..04d201d2c62152ec9f50cd5fce17d35b30d7b41e 100644 (file)
--- a/validparameter.h
+++ b/validparameter.h
@@ -9,9 +9,9 @@
  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  *
  */
-using namespace std;
 
 #include "mothur.h"
+#include "mothurout.h"
 
 //This class contains a list of all valid parameters in Mothur.  
 //It has a function which will tell you if your parameter is valid.
@@ -22,43 +22,19 @@ class ValidParameters {
 
        public:
                ValidParameters();
+               ValidParameters(string);
                ~ValidParameters();
-               bool isValidParameter(string, string);
-               
+               //bool isValidParameter(string, string, string) {return true;}
+               bool isValidParameter(string, vector<string>, string);
+               vector <string> addParameters(string[], int);
+               void initParameterRanges();
+               string validFile(map<string, string>&, string, bool); //container, parameter, isFile, commandName
+
        private:
-               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>::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();
+               map<string, vector<string> > parameterRanges;
+               MothurOut* m;
+               string commandName;
 
 };