working on readtree

[mothur.git] / readtree.cpp

diff --git a/readtree.cpp b/readtree.cpp
index 81a7729ffb474294502407eec1c44620bfff3378..4d3bd6daa435e303f236b8ca9dd31385a2df21dd 100644 (file)
--- a/readtree.cpp
+++ b/readtree.cpp
@@ -124,7 +124,8 @@ void ReadNewickTree::read() {
                                numNodes = T->getNumNodes();
                                numLeaves = T->getNumLeaves();
                                
-                               readTreeString();  
+                               readTreeString(); 
+                               
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
                                gobble(filehandle);
@@ -157,12 +158,12 @@ void ReadNewickTree::read() {
                                numLeaves = T->getNumLeaves();
                                
                                //read tree info
-                               readTreeString();  
+                               readTreeString(); 
+                                
                                //save trees for later commands
                                globaldata->gTree.push_back(T); 
                        }
                }
-               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ReadNewickTree class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -272,6 +273,7 @@ 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;
                }
        
        }
@@ -334,6 +336,7 @@ 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";
+                               
                                globaldata->gTreemap->namesOfSeqs.push_back(name);
                                globaldata->gTreemap->treemap[name].groupname = "xxx";
                                globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
@@ -350,10 +353,13 @@ int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
                                //find index in tree of name
                                n1 = T->getIndex(name);
                                group = "xxx";
+                               numLeaves++;
+                               numNodes = 2*numLeaves - 1;
+                               T->resetTree();
                        }
                        
                        T->tree[n1].setGroup(group);
-               
+                       T->printTree();
                        T->tree[n1].setChildren(-1,-1);
                
                        if(blen == 1){