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

[mothur.git] / rarefactsharedcommand.cpp

diff --git a/rarefactsharedcommand.cpp b/rarefactsharedcommand.cpp
index 66ef6ddf24d6132bd355663c3dbdd24d5662c18c..d0179be91a5b2eac505632797a8ebb3f74232282 100644 (file)
--- a/rarefactsharedcommand.cpp
+++ b/rarefactsharedcommand.cpp
@@ -30,14 +30,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
                        string Array[] =  {"iters","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;
                        
-                       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;  }
                        }
                        
                        //make sure the user has already run the read.otu command
@@ -49,14 +49,14 @@ RareFactSharedCommand::RareFactSharedCommand(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;  }
@@ -72,14 +72,14 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
                                lines = globaldata->lines;
                        }
                                
-                       calc = validParameter->validFile(parameters, "calc", false);                    
+                       calc = validParameter.validFile(parameters, "calc", false);                     
                        if (calc == "not found") { calc = "sharedobserved";  }
                        else { 
                                 if (calc == "default")  {  calc = "sharedobserved";  }
                        }
                        splitAtDash(calc, Estimators);
                        
-                       groups = validParameter->validFile(parameters, "groups", false);                        
+                       groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
                                splitAtDash(groups, Groups);
@@ -87,20 +87,18 @@ RareFactSharedCommand::RareFactSharedCommand(string option){
                        }
                        
                        string temp;
-                       temp = validParameter->validFile(parameters, "iters", false);                   if (temp == "not found") { temp = "1000"; }
+                       temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
                        convert(temp, nIters); 
                        
-                       delete validParameter;
-                       
                        if (abort == false) {
                        
                                string fileNameRoot = getRootName(globaldata->inputFileName);
-                               format = globaldata->getFormat();
-                               int i;
+//                             format = globaldata->getFormat();
+
                                
                                validCalculator = new ValidCalculators();
                                
-                               for (i=0; i<Estimators.size(); i++) {
+                               for (int i=0; i<Estimators.size(); i++) {
                                        if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) { 
                                                if (Estimators[i] == "sharedobserved") { 
                                                        rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));