* 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.
public:
ValidParameters();
~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
+
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> 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> > parameterRanges;
+ MothurOut* m;
};