fixed some bugs and added scriptengine

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 7c78a348902e1145af1cd4395fd0e839bf3cb564..0f106c493d1d55f7e742ed1195e1557f435d6e49 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -40,28 +40,28 @@ TreeGroupCommand::TreeGroupCommand(string option){
                        string Array[] =  {"line","label","calc","groups", "phylip", "column", "name", "precision","cutoff"};
                        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;  }
                        }
                        
                        //required parameters
-                       phylipfile = validParameter->validFile(parameters, "phylip", true);
+                       phylipfile = validParameter.validFile(parameters, "phylip", true);
                        if (phylipfile == "not open") { abort = true; }
                        else if (phylipfile == "not found") { phylipfile = ""; }        
-                       else {  globaldata->setPhylipFile(phylipfile);  globaldata->setFormat("phylip");        }
+                       else {  format = "phylip";      }
                        
-                       columnfile = validParameter->validFile(parameters, "column", true);
+                       columnfile = validParameter.validFile(parameters, "column", true);
                        if (columnfile == "not open") { abort = true; } 
                        else if (columnfile == "not found") { columnfile = ""; }
-                       else {  globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
+                       else {  format = "column";      }
                        
-                       namefile = validParameter->validFile(parameters, "name", true);
+                       namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
                        else {  globaldata->setNameFile(namefile);      }
@@ -78,14 +78,14 @@ TreeGroupCommand::TreeGroupCommand(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;  }
@@ -101,14 +101,14 @@ TreeGroupCommand::TreeGroupCommand(string option){
                                lines = globaldata->lines;
                        }
                                
-                       groups = validParameter->validFile(parameters, "groups", false);                        
+                       groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = ""; }
                        else { 
                                splitAtDash(groups, Groups);
                                globaldata->Groups = Groups;
                        }
                                
-                       calc = validParameter->validFile(parameters, "calc", false);                    
+                       calc = validParameter.validFile(parameters, "calc", false);                     
                        if (calc == "not found") { calc = "jclass-thetayc";  }
                        else { 
                                 if (calc == "default")  {  calc = "jclass-thetayc";  }
@@ -116,16 +116,14 @@ TreeGroupCommand::TreeGroupCommand(string option){
                        splitAtDash(calc, Estimators);
 
                        string temp;
-                       temp = validParameter->validFile(parameters, "precision", false);                       if (temp == "not found") { temp = "100"; }
+                       temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
                        convert(temp, precision); 
                        
-                       temp = validParameter->validFile(parameters, "cutoff", false);                  if (temp == "not found") { temp = "10"; }
+                       temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
                        convert(temp, cutoff); 
                        cutoff += (5 / (precision * 10.0));
 
-       
-                       delete validParameter;
-                       
+                               
                        if (abort == false) {
                        
                                validCalculator = new ValidCalculators();
@@ -236,6 +234,8 @@ int TreeGroupCommand::execute(){
                        
                        if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0; }
                
+                       globaldata->runParse = false;
+                       
                        //create tree file
                        makeSimsShared();
                }else{
@@ -271,7 +271,9 @@ int TreeGroupCommand::execute(){
                
                        //fills globaldatas tree names
                        globaldata->Treenames = globaldata->Groups;
-
+                       
+                       globaldata->runParse = false;
+                       
                        makeSimsDist();
 
                        //create a new filename
@@ -564,7 +566,7 @@ void TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
                                                        }
                                                }
                                        }
-                                       
+                               
                                        //creates tree from similarity matrix and write out file
                                        createTree();
                                }