chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector...

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 52b7322cb1064546fd0f446f63fd61ef61d868fe..731eb64d93f95b485f8607308e3e88345138813c 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -27,7 +27,8 @@ Tree::Tree() {
                        //initialize leaf nodes
                        if (i <= (numLeaves-1)) {
                                tree[i].setName(globaldata->Treenames[i]);
-                               tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+                               vector<string> tempGroups; tempGroups.push_back(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
+                               tree[i].setGroup(tempGroups);
                                //set pcount and pGroup for groupname to 1.
                                tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
                                tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
@@ -37,7 +38,8 @@ Tree::Tree() {
                        //intialize non leaf nodes
                        }else if (i > (numLeaves-1)) {
                                tree[i].setName("");
-                               tree[i].setGroup("");
+                               vector<string> tempGroups;
+                               tree[i].setGroup(tempGroups);
                        }
                }
        }
@@ -119,6 +121,14 @@ void Tree::addNamesToCounts() {
                                        }
                                }//end if
                                
+                               //update groups to reflect all the groups this node represents
+                               vector<string> nodeGroups;
+                               map<string, int>::iterator itGroups;
+                               for (itGroups = tree[i].pcount.begin(); itGroups != tree[i].pcount.end(); itGroups++) {
+                                       nodeGroups.push_back(itGroups->first);
+                               }
+                               tree[i].setGroup(nodeGroups);
+                               
                        }//end else
                }//end for
                                
@@ -375,7 +385,7 @@ void Tree::randomLabels(vector<string> g) {
                                tree[z].pGroups = (tree[i].pGroups);
                                tree[i].pGroups = (lib_hold);
                                
-                               string zgroup = tree[z].getGroup();
+                               vector<string> zgroup = tree[z].getGroup();
                                tree[z].setGroup(tree[i].getGroup());
                                tree[i].setGroup(zgroup);
                                
@@ -394,7 +404,7 @@ void Tree::randomLabels(vector<string> g) {
                exit(1);
        }
 }
-/**************************************************************************************************/
+/**************************************************************************************************
 
 void Tree::randomLabels(string groupA, string groupB) {
        try {
@@ -447,7 +457,9 @@ void Tree::assembleRandomUnifracTree(vector<string> g) {
 }
 /*************************************************************************************************/
 void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
-       randomLabels(groupA, groupB);
+
+       vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
+       randomLabels(temp);
        assembleTree();
 }
 
@@ -584,7 +596,9 @@ void Tree::printBranch(int node, ostream& out, string mode) {
                                }
                        }
                }else { //you are a leaf
-                       out << tree[node].getGroup(); 
+                       string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
+                       
+                       out << leafGroup; 
                        if (mode == "branch") {
                                //if there is a branch length then print it
                                if (tree[node].getBranchLength() != -1) {