fixed valid parameters to include shared parameter for read.shared command.

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 70287c907b0d92e92c43780299603b3a05b09f02..3a96cc64893e4d0b5b8b755202dda24316ba1a08 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -18,28 +18,27 @@ ValidParameters::ValidParameters() {
                parameters["column"]            = "column";
                parameters["list"]                      = "list"; 
                parameters["rabund"]            = "rabund"; 
-               parameters["sabund"]            = "sabund"; 
+               parameters["sabund"]            = "sabund";
+               parameters["shared"]            = "shared";
                parameters["name"]                      = "name"; 
                parameters["group"]                     = "group"; 
                parameters["order"]                     = "order"; 
                parameters["fasta"]                     = "fasta"; 
-               parameters["treefile"]                  = "treefile";
+               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["line"]                              = "line";
                parameters["iters"]                             = "iters"; 
                parameters["jumble"]                    = "jumble"; 
                parameters["freq"]                              = "freq"; 
-               parameters["single"]                    = "single"; 
-               parameters["rarefaction"]               = "rarefaction"; 
-               parameters["sharedrarefaction"] = "sharedrarefaction";
-               parameters["shared"]                    = "shared"; 
-               parameters["summary"]                   = "summary"; 
-               parameters["sharedsummary"]             = "sharedsummary";
+               parameters["abund"]             = "abund";
+               parameters["random"]                    = "random";
+               parameters["groups"]                    = "groups";
+               parameters["calc"]                              = "calc";
 
        }
        catch(exception& e) {
@@ -64,7 +63,12 @@ bool ValidParameters::isValidParameter(string parameter) {
                if ((parameters.find(parameter)) != (parameters.end())) {
                        return true;
                }else{
-                       cout << parameter << " is not a valid parameter in Mothur." << endl;
+                       cout << parameter << " is not a valid parameter in Mothur. Valid parameters are " << endl;
+                       for (it = parameters.begin(); it != parameters.end(); it++) {
+                               cout << it->first << ", ";
+                       }
+                       cout << endl;
+
                        return false;
                }
                
@@ -79,4 +83,4 @@ bool ValidParameters::isValidParameter(string parameter) {
        }
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/