fixed indicator command bug

[mothur.git] / tree.cpp

diff --git a/tree.cpp b/tree.cpp
index 2a22cf3b952ff217c9e57c5ce98bbb01c5cbacb0..114b4de0d6e2c408479ae8c03b65d2b1300bb9b8 100644 (file)
--- a/tree.cpp
+++ b/tree.cpp
@@ -270,7 +270,7 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                        //initialize leaf nodes
                        if (i <= (numLeaves-1)) {
                                tree[i].setName(Groups[i]);
-                                       
+                               
                                //save group info
                                string group = globaldata->gTreemap->getGroup(Groups[i]);
                                vector<string> tempGroups; tempGroups.push_back(group);
@@ -301,6 +301,7 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                        int parent = copy->tree[i].getParent();
                        
                        if (parent != -1) {
+                               
                                if (m->inUsersGroups(copy->tree[i].getName(), Groups)) {
                                        //find my siblings name
                                        int parentRC = copy->tree[parent].getRChild();
@@ -361,7 +362,7 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                                //so set our parents sib to our great-grandparent
                                                int parent = copy->tree[i].getParent();
                                                int grandparent = copy->tree[parent].getParent();
-                                               
+                                               int parentsSibIndex;
                                                if (grandparent != -1) {
                                                        int greatgrandparent = copy->tree[grandparent].getParent();
                                                        int greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
@@ -370,8 +371,8 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                                                        int grandparentLC = copy->tree[grandparent].getLChild();
                                                        int grandparentRC = copy->tree[grandparent].getRChild();
                                                        
-                                                       int parentsSibIndex = grandparentLC;
-                                                       if (grandparentRC == parent) { parentsSibIndex = grandparentLC; }
+                                                       parentsSibIndex = grandparentLC;
+                                                       if (grandparentLC == parent) { parentsSibIndex = grandparentRC; }
 
                                                        //whichever of my greatgrandparents children was my grandparent
                                                        if (greatgrandparentLC == grandparent) { greatgrandparentLC = parentsSibIndex; }
@@ -401,7 +402,6 @@ void Tree::getSubTree(Tree* copy, vector<string> Groups) {
                int nextSpot = numLeaves;
                populateNewTree(copy->tree, root, nextSpot);
                
-               
        }
        catch(exception& e) {
                m->errorOut(e, "Tree", "getCopy");
@@ -415,17 +415,15 @@ int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
                if (oldtree[node].getLChild() != -1) {
                        int rc = populateNewTree(oldtree, oldtree[node].getLChild(), index);
                        int lc = populateNewTree(oldtree, oldtree[node].getRChild(), index);
-                       
+
                        tree[index].setChildren(lc, rc);
-                       index++;
+                       tree[rc].setParent(index);
+                       tree[lc].setParent(index);
                        
-                       return (index-1);
+                       return (index++);
                }else { //you are a leaf
                        int indexInNewTree = globaldata->gTreemap->getIndex(oldtree[node].getName());
-                       
-                       tree[indexInNewTree].setParent(index);
                        return indexInNewTree;
-                       
                }
        }
        catch(exception& e) {
@@ -895,7 +893,69 @@ try {
                exit(1);
        }
 }
-                                                                         
+/*****************************************************************/
+void Tree::printBranch(int node, ostream& out, string mode, vector<Node>& theseNodes) {
+       try {
+               
+               // you are not a leaf
+               if (theseNodes[node].getLChild() != -1) {
+                       out << "(";
+                       printBranch(theseNodes[node].getLChild(), out, mode);
+                       out << ",";
+                       printBranch(theseNodes[node].getRChild(), out, mode);
+                       out << ")";
+                       if (mode == "branch") {
+                               //if there is a branch length then print it
+                               if (theseNodes[node].getBranchLength() != -1) {
+                                       out << ":" << theseNodes[node].getBranchLength();
+                               }
+                       }else if (mode == "boot") {
+                               //if there is a label then print it
+                               if (theseNodes[node].getLabel() != -1) {
+                                       out << theseNodes[node].getLabel();
+                               }
+                       }else if (mode == "both") {
+                               if (theseNodes[node].getLabel() != -1) {
+                                       out << theseNodes[node].getLabel();
+                               }
+                               //if there is a branch length then print it
+                               if (theseNodes[node].getBranchLength() != -1) {
+                                       out << ":" << theseNodes[node].getBranchLength();
+                               }
+                       }
+               }else { //you are a leaf
+                       string leafGroup = globaldata->gTreemap->getGroup(theseNodes[node].getName());
+                       
+                       if (mode == "branch") {
+                               out << leafGroup; 
+                               //if there is a branch length then print it
+                               if (theseNodes[node].getBranchLength() != -1) {
+                                       out << ":" << theseNodes[node].getBranchLength();
+                               }
+                       }else if (mode == "boot") {
+                               out << leafGroup; 
+                               //if there is a label then print it
+                               if (theseNodes[node].getLabel() != -1) {
+                                       out << theseNodes[node].getLabel();
+                               }
+                       }else if (mode == "both") {
+                               out << theseNodes[node].getName();
+                               if (theseNodes[node].getLabel() != -1) {
+                                       out << theseNodes[node].getLabel();
+                               }
+                               //if there is a branch length then print it
+                               if (theseNodes[node].getBranchLength() != -1) {
+                                       out << ":" << theseNodes[node].getBranchLength();
+                               }
+                       }
+               }
+               
+       }
+       catch(exception& e) {
+               m->errorOut(e, "Tree", "printBranch");
+               exit(1);
+       }
+}
 /*****************************************************************/
 
 void Tree::printTree() {