version 1.4

[mothur.git] / deconvolutecommand.cpp

diff --git a/deconvolutecommand.cpp b/deconvolutecommand.cpp
index 96682af26b8bcb1b62c17987c82355856cfaf919..2fe7a251ca41a5d833ad7f643970a1d9847a8361 100644 (file)
--- a/deconvolutecommand.cpp
+++ b/deconvolutecommand.cpp
@@ -12,7 +12,6 @@
 /**************************************************************************************/
 DeconvoluteCommand::DeconvoluteCommand(string option) {        
        try {
-               globaldata = GlobalData::getInstance();
                abort = false;
                
                //allow user to run help
@@ -23,23 +22,21 @@ DeconvoluteCommand::DeconvoluteCommand(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
-                       filename = validParameter->validFile(parameters, "fasta", true);
+                       filename = validParameter.validFile(parameters, "fasta", true);
                        if (filename == "not open") { abort = true; }
                        else if (filename == "not found") { filename = ""; cout << "fasta is a required parameter for the unique.seqs command." << endl; abort = true;  }       
-                       else {  globaldata->setFastaFile(filename);  globaldata->setFormat("fasta");    }
                        
-                       delete validParameter;
                }
 
        }
@@ -99,6 +96,7 @@ int DeconvoluteCommand::execute() {
                fastamap->printNamesFile(out);
                fastamap->printCondensedFasta(outFasta);
                
+               in.close();
                out.close();
                outFasta.close();