minor bugs fixes and added line and label options to read.otu's parselist and shared...

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index b58a8ff8878b76da789a0f2a1ebc1784a11781bf..a82962f1e0096e406e7cc21d03dba08a3039ea3a 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -14,15 +14,16 @@
 ValidParameters::ValidParameters() {
        try {
        
-               parameters["phylipfile"]                = "phylipfile";
-               parameters["columnfile"]                = "columnfile";
-               parameters["listfile"]                  = "listfile"; 
-               parameters["rabundfile"]                = "rabundfile"; 
-               parameters["sabundfile"]                = "sabundfile"; 
-               parameters["namefile"]                  = "namefile"; 
-               parameters["groupfile"]                 = "groupfile"; 
-               parameters["orderfile"]                 = "orderfile"; 
-               parameters["fastafile"]                 = "fastafile"; 
+               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";
@@ -39,7 +40,10 @@ ValidParameters::ValidParameters() {
                parameters["shared"]                    = "shared"; 
                parameters["summary"]                   = "summary"; 
                parameters["sharedsummary"]             = "sharedsummary";
-
+               parameters["random"]                    = "random";
+               parameters["groups"]                    = "groups";
+               parameters["calc"]                              = "calc";
+               
        }
        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";
@@ -63,7 +67,12 @@ 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;
                }
                
@@ -78,4 +87,4 @@ bool ValidParameters::isValidParameter(string parameter) {
        }
 }
 
-/***********************************************************************/
\ No newline at end of file
+/***********************************************************************/