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

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index c8582b9ae35ed3edce04052f85f53f611235ab88..24ef1d12e08262a335f7c29104120f7cddc81e1b 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -14,7 +14,6 @@
 
 SeqSummaryCommand::SeqSummaryCommand(string option){
        try {
-               globaldata = GlobalData::getInstance();
                abort = false;
                
                //allow user to run help
@@ -25,23 +24,21 @@ SeqSummaryCommand::SeqSummaryCommand(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;
                        
-                       ValidParameters* validParameter = new ValidParameters();
-               
                        //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
-                       fastafile = validParameter->validFile(parameters, "fasta", true);
+                       fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
                        else if (fastafile == "not found") { fastafile = ""; cout << "fasta is a required parameter for the summary.seqs command." << endl; abort = true;  }    
-                       else {  globaldata->setFastaFile(fastafile);  globaldata->setFormat("fasta");   }
                        
-                       delete validParameter;
                }
        }
        catch(exception& e) {