added heatmap command

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 50610f0bbc43d0903e60d6def31fe46b0401ad65..9c8ce2e89136a671d775cb6b41484b3bc6cc869a 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -13,38 +13,9 @@
 
 ValidParameters::ValidParameters() {
        try {
-               parameters["phylip"]            = "phylip";
-               parameters["column"]                = "column";
-               parameters["list"]                      = "list"; 
-               parameters["rabund"]            = "rabund"; 
-               parameters["sabund"]            = "sabund"; 
-               parameters["name"]                      = "name"; 
-               parameters["group"]                     = "group"; 
-               parameters["order"]             = "order"; 
-               parameters["fasta"]                         = "fasta"; 
-               parameters["tree"]                      = "tree";
-               parameters["fileroot"]                  = "fileroot";
-               parameters["cutoff"]                    = "cutoff"; 
-               parameters["method"]                    = "method";
-               parameters["format"]                    = "format"; 
-               parameters["precision"]                 = "precision"; 
-               parameters["label"]                             = "label"; 
-               parameters["line"]                              = "line";
-               parameters["iters"]                             = "iters"; 
-               parameters["jumble"]                    = "jumble"; 
-               parameters["freq"]                              = "freq"; 
-               parameters["abund"]             = "abund";
-               parameters["random"]                    = "random";
-               parameters["groups"]                    = "groups";
-               parameters["calc"]                              = "calc";
-               parameters["sharedrarefaction"] = "sharedrarefaction";
-               parameters["sharedsummary"]     = "sharedsummary";
-               parameters["shared"]            = "shared";
-               parameters["single"]            = "single";
-               parameters["rarefaction"]       = "rarefaction";
-               
                initCommandParameters();                
                initParameterRanges();
+
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function ValidParameters. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -284,7 +255,10 @@ void ValidParameters::initCommandParameters() {
 
                string rarefactionsharedArray[] =  {"iters","jumble","line","label","sharedrarefaction"};
                commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
-
+               
+               string libshuffArray[] =  {"iters","groups","step","form","cutoff"};
+               commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
+               
                string summarysingleArray[] =  {"line","label","summary","abund"};
                commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
 
@@ -369,5 +343,4 @@ vector<string> ValidParameters::addParameters(string parameters[], int size) {
        }
 }
 
-/***********************************************************************/