fixed bug in read tree

diff --git a/readtree.cpp b/readtree.cpp
index 4d3bd6daa435e303f236b8ca9dd31385a2df21dd..59239c8af0d24e089bfc7eade92ed055ffaa6e64 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -273,7 +273,6 @@ void ReadNewickTree::readTreeString() {
                        T->tree[n].setParent(-1);
                        if(lc!=-1){             T->tree[lc].setParent(n);               }
                        if(rc!=-1){             T->tree[rc].setParent(n);               }
-                       cout << "new loop "<< endl;
                }
        
        }
@@ -335,7 +334,7 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                        
                        //adds sequence names that are not in group file to the "xxx" group
                        if(n1 == -1) {
-                               cerr << "Name: " << name << " not found in your groupfile and it will be ignored. \n";
+                               cerr << "Name: " << name << " not found in your groupfile.. \n"; exit(1);
                                
                                globaldata->gTreemap->namesOfSeqs.push_back(name);
                                globaldata->gTreemap->treemap[name].groupname = "xxx";
@@ -355,11 +354,10 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                group = "xxx";
                                numLeaves++;
                                numNodes = 2*numLeaves - 1;
-                               T->resetTree();
+                               //T->resetTree();
                        }
                        
                        T->tree[n1].setGroup(group);
-                       T->printTree();
                        T->tree[n1].setChildren(-1,-1);
                
                        if(blen == 1){