added tree reader class to handle reading trees. Reworked the tree map to tree class...

[mothur.git] / indicatorcommand.cpp

diff --git a/indicatorcommand.cpp b/indicatorcommand.cpp
index fe99c46847ff08fa8359f6899a4ddf9a095126ea..94d5c84344f86eb4676f0e71111e898c5c28596d 100644 (file)
--- a/indicatorcommand.cpp
+++ b/indicatorcommand.cpp
@@ -99,7 +99,6 @@ IndicatorCommand::IndicatorCommand(string option)  {
                        m->clearGroups();
                        m->clearAllGroups();
                        m->Treenames.clear();
-                       m->names.clear();
                        
                        vector<string> tempOutNames;
                        outputTypes["tree"] = tempOutNames;
@@ -236,11 +235,10 @@ int IndicatorCommand::execute(){
                        designMap->readDesignMap();
                        
                        //fill Groups - checks for "all" and for any typo groups
-                       SharedUtil* util = new SharedUtil();
+                       SharedUtil util;
                        vector<string> nameGroups = designMap->getNamesOfGroups();
-                       util->setGroups(Groups, nameGroups);
+                       util.setGroups(Groups, nameGroups);
                        designMap->setNamesOfGroups(nameGroups);
-                       delete util;
                        
                        //loop through the Groups and fill Globaldata's Groups with the design file info
                        vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
@@ -320,8 +318,9 @@ int IndicatorCommand::execute(){
                                else { for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } }
                                for (int i = 0; i < T.size(); i++) {  delete T[i];  }  delete treeMap; return 0; 
                        }
-                               
-                       T[0]->assembleTree();
+            
+                       map<string, string> nameMap;    
+                       T[0]->assembleTree(nameMap);
                                        
                        /***************************************************/
                        //    create ouptut tree - respecting pickedGroups //
@@ -329,7 +328,7 @@ int IndicatorCommand::execute(){
                        Tree* outputTree = new Tree(m->getNumGroups(), treeMap); 
                        
                        outputTree->getSubTree(T[0], m->getGroups());
-                       outputTree->assembleTree();
+                       outputTree->assembleTree(nameMap);
                                
                        //no longer need original tree, we have output tree to use and label
                        for (int i = 0; i < T.size(); i++) {  delete T[i];  }