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

[mothur.git] / reversecommand.cpp

diff --git a/reversecommand.cpp b/reversecommand.cpp
index b8ccc0747d54300f4fbc655729d9ce58b6f2d112..9e2a08b2a493fec7ed717505d7d02112a8530b49 100644 (file)
--- a/reversecommand.cpp
+++ b/reversecommand.cpp
@@ -15,7 +15,6 @@
 
 ReverseSeqsCommand::ReverseSeqsCommand(string option){
        try {
-               globaldata = GlobalData::getInstance();
                abort = false;
                
                //allow user to run help
@@ -26,23 +25,21 @@ ReverseSeqsCommand::ReverseSeqsCommand(string option){
                        string Array[] =  {"fasta"};
                        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;  }
                        }
                        
                        //check for required parameters
-                       fasta = validParameter->validFile(parameters, "fasta", true);
+                       fasta = validParameter.validFile(parameters, "fasta", true);
                        if (fasta == "not open") { abort = true; }
                        else if (fasta == "not found") { fasta = ""; cout << "fasta is a required parameter for the reverse.seqs command." << endl; abort = true;  }    
-                       else {  globaldata->setFastaFile(fasta);  globaldata->setFormat("fasta");       }
                        
-                       delete validParameter;
                }
        }
        catch(exception& e) {