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

[mothur.git] / summarysharedcommand.cpp

diff --git a/summarysharedcommand.cpp b/summarysharedcommand.cpp
index 363506c406490e999a2700974e538489616b8d5a..a32b202d827d8df18c5696c3fc9ace85f3ddbf22 100644 (file)
--- a/summarysharedcommand.cpp
+++ b/summarysharedcommand.cpp
@@ -52,14 +52,14 @@ SummarySharedCommand::SummarySharedCommand(string option){
                        string Array[] =  {"line","label","calc","groups"};
                        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;  }
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -71,14 +71,14 @@ SummarySharedCommand::SummarySharedCommand(string option){
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
-                       line = validParameter->validFile(parameters, "line", false);                            
+                       line = validParameter.validFile(parameters, "line", false);                             
                        if (line == "not found") { line = "";  }
                        else { 
                                if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                        
-                       label = validParameter->validFile(parameters, "label", false);                  
+                       label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = ""; }
                        else { 
                                if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
@@ -94,22 +94,20 @@ SummarySharedCommand::SummarySharedCommand(string option){
                                lines = globaldata->lines;
                        }
                                
-                       calc = validParameter->validFile(parameters, "calc", false);                    
+                       calc = validParameter.validFile(parameters, "calc", false);                     
                        if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
                        else { 
                                 if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
                        }
                        splitAtDash(calc, Estimators);
                        
-                       groups = validParameter->validFile(parameters, "groups", false);                        
+                       groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
                                splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                        
-                       delete validParameter;
-                       
                        if (abort == false) {
                        
                                validCalculator = new ValidCalculators();
@@ -165,7 +163,7 @@ SummarySharedCommand::SummarySharedCommand(string option){
                                
                                outputFileName = ((getRootName(globaldata->inputFileName)) + "shared.summary");
                                openOutputFile(outputFileName, outputFileHandle);
-                               format = globaldata->getFormat();
+//                             format = globaldata->getFormat();
                                mult = false;
                        }
                }