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

[mothur.git] / readtreecommand.cpp

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 6e5742ddbbc35cdc6d01b9d57b3d58a8c7856816..b030542ef8f7e5933f2bf32c4c6bf6ba9e051ee0 100644 (file)
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -23,25 +23,25 @@ ReadTreeCommand::ReadTreeCommand(string option){
                        string Array[] =  {"tree","group"};
                        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;  }
                        }
                        
                        globaldata->newRead();
                        
                        //check for required parameters
-                       treefile = validParameter->validFile(parameters, "tree", true);
+                       treefile = validParameter.validFile(parameters, "tree", true);
                        if (treefile == "not open") { abort = true; }
                        else if (treefile == "not found") { treefile = ""; cout << "tree is a required parameter for the read.tree command." << endl; abort = true;  }  
-                       else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
+//                     else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree");      }
                        
-                       groupfile = validParameter->validFile(parameters, "group", true);
+                       groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; cout << "group is a required parameter for the read.tree command." << endl; abort = true;  }
                        else {  
@@ -57,7 +57,6 @@ ReadTreeCommand::ReadTreeCommand(string option){
                                read = new ReadNewickTree(filename);
                        }
                                                
-                       delete validParameter;
                }
        }
        catch(exception& e) {