fixed bug in unifrac commands with nexus translation if files don't match

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 06f92cf46e22cbb28f4ff28596977d5b62fb7e02..02f400407cfaa5f8c9283fa4f96d8bbc2fb0c3d8 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -330,7 +330,9 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                                
                                                copy->tree[i].setParent(grandparent);
                                                copy->tree[i].setBranchLength((copy->tree[i].getBranchLength()+copy->tree[parent].getBranchLength()));
-                                               copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
+                                               if (grandparent != -1) {
+                                                       copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
+                                               }
                                                removedLeaves.insert(sibIndex);
                                        }
                                }else{
@@ -357,7 +359,9 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                                
                                                copy->tree[sibIndex].setParent(grandparent);
                                                copy->tree[sibIndex].setBranchLength((copy->tree[sibIndex].getBranchLength()+copy->tree[parent].getBranchLength()));
-                                               copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
+                                               if (grandparent != -1) {
+                                                       copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
+                                               }
                                                removedLeaves.insert(i);
                                        }else{
                                                //neither of us are, so we want to eliminate ourselves and our parent
@@ -367,8 +371,11 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                                int parentsSibIndex;
                                                if (grandparent != -1) {
                                                        int greatgrandparent = copy->tree[grandparent].getParent();
-                                                       int greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
-                                                       int greatgrandparentRC = copy->tree[greatgrandparent].getRChild();
+                                                       int greatgrandparentLC, greatgrandparentRC;
+                                                       if (greatgrandparent != -1) {
+                                                               greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
+                                                               greatgrandparentRC = copy->tree[greatgrandparent].getRChild();
+                                                       }
                                                        
                                                        int grandparentLC = copy->tree[grandparent].getLChild();
                                                        int grandparentRC = copy->tree[grandparent].getRChild();
@@ -382,10 +389,12 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                                        
                                                        copy->tree[parentsSibIndex].setParent(greatgrandparent);
                                                        copy->tree[parentsSibIndex].setBranchLength((copy->tree[parentsSibIndex].getBranchLength()+copy->tree[grandparent].getBranchLength()));
-                                                       copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
+                                                       if (greatgrandparent != -1) {
+                                                               copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
+                                                       }
                                                }else{
-                                                       copy->tree[parent].setChildren(-1, -1);
-                                                       cout << "issues with making subtree" << endl;
+                                                       copy->tree[parent].setParent(-1);
+                                                       //cout << "issues with making subtree" << endl;
                                                }
                                                removedLeaves.insert(sibIndex);
                                                removedLeaves.insert(i);
@@ -403,7 +412,6 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                
                int nextSpot = numLeaves;
                populateNewTree(copy->tree, root, nextSpot);
-                               
        }
        catch(exception& e) {
                m->errorOut(e, "Tree", "getCopy");