fixing minor bugs

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 1f1ad971738596854650363ef01672aa19e0748b..ba7eae42a668e7fa9bf3a9f8d33c4746b55ce810 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -24,40 +24,40 @@ ReadOtuCommand::ReadOtuCommand(string option){
                        string Array[] =  {"list","order","shared", "line", "label","group","sabund", "rabund"};
                        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;  }
                        }
                        
                        globaldata->newRead();
                        
                        //check for required parameters
-                       listfile = validParameter->validFile(parameters, "list", true);
+                       listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = ""; }    
                        else {  globaldata->setListFile(listfile);  globaldata->setFormat("list");      }
                        
-                       sabundfile = validParameter->validFile(parameters, "sabund", true);
+                       sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { abort = true; } 
                        else if (sabundfile == "not found") { sabundfile = ""; }
                        else {  globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
 
-                       rabundfile = validParameter->validFile(parameters, "rabund", true);
+                       rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { abort = true; } 
                        else if (rabundfile == "not found") { rabundfile = ""; }
                        else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
                        
-                       sharedfile = validParameter->validFile(parameters, "shared", true);
+                       sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; } 
                        else if (sharedfile == "not found") { sharedfile = ""; }
                        else {  globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile");     }
                        
-                       groupfile = validParameter->validFile(parameters, "group", true);
+                       groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
                        else {  
@@ -76,7 +76,7 @@ ReadOtuCommand::ReadOtuCommand(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;  }
@@ -84,7 +84,7 @@ ReadOtuCommand::ReadOtuCommand(string option){
                                globaldata->lines = lines;
                        }
                        
-                       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;  }
@@ -97,17 +97,16 @@ ReadOtuCommand::ReadOtuCommand(string option){
                        //make sure user did not use both the line and label parameters
                        if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
                        
-                       orderfile = validParameter->validFile(parameters, "order", true);
+                       orderfile = validParameter.validFile(parameters, "order", true);
                        if (orderfile == "not open") { abort = true; }  
                        else if (orderfile == "not found") { orderfile = ""; }
                        else {  globaldata->setOrderFile(orderfile);    }
                        
-                       delete validParameter;
                        
                        if (abort == false) {
                                //gets whichever one of the above is set
                                filename = globaldata->inputFileName;
-                               read = new ReadOTUFile(filename);
+                               //read = new ReadOTUFile(filename);
                        }
 
                }
@@ -156,7 +155,8 @@ void ReadOtuCommand::help(){
 //**********************************************************************************************************************
 
 ReadOtuCommand::~ReadOtuCommand(){
-       if (abort == false) {  delete read;  }
+       if (abort == false) {  //delete read; 
+        }
 }
 
 //**********************************************************************************************************************
@@ -166,17 +166,20 @@ int ReadOtuCommand::execute(){
        
                if (abort == true) {    return 0;       }
                
-               read->read(&*globaldata); 
+               //read->read(&*globaldata); 
                if (globaldata->getFormat() == "shared") {
                        groupMap->readMap();
                        
                        //if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
-                       globaldata->gGroupmap = groupMap;               
-                       shared = new SharedCommand();
-                       shared->execute();
-
+                       globaldata->gGroupmap = groupMap;
+                       
                        parselist = new ParseListCommand();
                        parselist->execute();
+                       delete parselist;
+                       
+                       shared = new SharedCommand();
+                       shared->execute();
+                       delete shared;
                        
                        //change format to shared  to speed up commands
                        globaldata->setFormat("sharedfile");