major change to the tree class to use the count table class instead of tree map....

[mothur.git] / treegroupscommand.cpp

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 6633e5160559297c23a542c373ed1b1cc9a3ccdc..fb4887c73da88c0c631895e82f05090e97645761 100644 (file)
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -287,7 +287,7 @@ TreeGroupCommand::~TreeGroupCommand(){
        if (abort == false) {
                if (format == "sharedfile") {  delete input; }
                else { delete list; }
-               delete tmap;  
+               delete ct;  
        }
        
 }
@@ -400,8 +400,16 @@ int TreeGroupCommand::execute(){
                        m->runParse = false;
                        
                        //create treemap class from groupmap for tree class to use
-                       tmap = new TreeMap();
-                       tmap->makeSim(m->getAllGroups());
+                       ct = new CountTable();
+            set<string> nameMap;
+            map<string, string> groupMap;
+            set<string> gps;
+            for (int i = 0; i < m->getAllGroups().size(); i++) { 
+                nameMap.insert(m->getAllGroups()[i]); 
+                gps.insert(m->getAllGroups()[i]); 
+                groupMap[m->getAllGroups()[i]] = m->getAllGroups()[i];
+            }
+            ct->createTable(nameMap, groupMap, gps);
                        
                        //clear globaldatas old tree names if any
                        m->Treenames.clear();
@@ -429,22 +437,26 @@ int TreeGroupCommand::execute(){
                                nameMap = new NameAssignment(namefile);
                                nameMap->readMap();
                        }
-                       else{
-                               nameMap = NULL;
-                       }
+                       else{ nameMap = NULL; }
        
                        readMatrix->read(nameMap);
                        list = readMatrix->getListVector();
                        SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
 
                        //make treemap
-                       tmap = new TreeMap();
-                       
-                       if (m->control_pressed) { return 0; }
-                       
-                       tmap->makeSim(list);
+                       ct = new CountTable();
+            set<string> nameMap;
+            map<string, string> groupMap;
+            set<string> gps;
+            for (int i = 0; i < list->getNumBins(); i++) {
+                string bin = list->get(i);
+                nameMap.insert(bin); 
+                gps.insert(bin); 
+                groupMap[bin] = bin;
+            }
+            ct->createTable(nameMap, groupMap, gps);
                        
-                       vector<string> namesGroups = tmap->getNamesOfGroups();
+                       vector<string> namesGroups = ct->getNamesOfGroups();
                        m->setGroups(namesGroups);
                
                        //clear globaldatas old tree names if any
@@ -505,13 +517,12 @@ int TreeGroupCommand::execute(){
 Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
        try {
                //create tree
-               t = new Tree(tmap, simMatrix);
+               t = new Tree(ct, simMatrix);
         
         if (m->control_pressed) { delete t; t = NULL; return t; }
                
         //assemble tree
-        map<string, string> empty;
-               t->assembleTree(empty);
+               t->assembleTree();
 
                return t;
        }