merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 36fff2242ee65d3cdb1e72868d173c69ed5bc3ff..706ff6735b32d2f93c723a5f4af2d7a402b4bb75 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -24,14 +24,14 @@ ClusterCommand::ClusterCommand(string option){
                        string Array[] =  {"cutoff","precision","method"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
-                       parser = new OptionParser();
-                       parser->parse(option, parameters);  delete parser;
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
                        
-                       ValidParameters* validParameter = new ValidParameters();
+                       ValidParameters validParameter;
                
                        //check to make sure all parameters are valid for command
-                       for (it = parameters.begin(); it != parameters.end(); it++) { 
-                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
                        //error checking to make sure they read a distance file
@@ -43,18 +43,17 @@ ClusterCommand::ClusterCommand(string option){
                        // ...at some point should added some additional type checking...
                        //get user cutoff and precision or use defaults
                        string temp;
-                       temp = validParameter->validFile(parameters, "precision", false);               if (temp == "not found") { temp = "100"; }
+                       temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
                        //saves precision legnth for formatting below
                        length = temp.length();
                        convert(temp, precision); 
                        
-                       temp = validParameter->validFile(parameters, "cutoff", false);                  if (temp == "not found") { temp = "10"; }
+                       temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
                        
-                       method = validParameter->validFile(parameters, "method", false);                        if (method == "not found") { method = "furthest"; }
+                       method = validParameter.validFile(parameters, "method", false);                 if (method == "not found") { method = "furthest"; }
 
-                       delete validParameter;
                        
                        if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
                        else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; abort = true; }