#include "tree.h"
+/*****************************************************************/
+Tree::Tree(int num) {
+ try {
+ globaldata = GlobalData::getInstance();
+ m = MothurOut::getInstance();
+
+ numLeaves = num;
+ numNodes = 2*numLeaves - 1;
+
+ tree.resize(numNodes);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree - numNodes");
+ exit(1);
+ }
+}
/*****************************************************************/
Tree::Tree(string g) {
try {
itCounts = tree[i].pGroups.find(group);
if (itCounts == tree[i].pGroups.end()) { //new group, add it
tree[i].pGroups[group] = 1;
- }else {
+ }else{
tree[i].pGroups[group]++;
}
exit(1);
}
}
+/*****************************************************************/
+void Tree::getSubTree(Tree* copy, vector<string> Groups) {
+ try {
+
+ //we want to select some of the leaf nodes to create the output tree
+ //go through the input Tree starting at parents of leaves
+ for (int i = 0; i < numNodes; i++) {
+
+ //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);
+ tree[i].setGroup(tempGroups);
+ groupNodeInfo[group].push_back(i);
+
+ //set pcount and pGroup for groupname to 1.
+ tree[i].pcount[group] = 1;
+ tree[i].pGroups[group] = 1;
+
+ //Treemap knows name, group and index to speed up search
+ globaldata->gTreemap->setIndex(Groups[i], i);
+
+ //intialize non leaf nodes
+ }else if (i > (numLeaves-1)) {
+ tree[i].setName("");
+ vector<string> tempGroups;
+ tree[i].setGroup(tempGroups);
+ }
+ }
+
+ set<int> removedLeaves;
+ for (int i = 0; i < copy->getNumLeaves(); i++) {
+
+ if (removedLeaves.count(i) == 0) {
+
+ //am I in the group
+ 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();
+ int parentLC = copy->tree[parent].getLChild();
+
+ //if I am the right child, then my sib is the left child
+ int sibIndex = parentRC;
+ if (parentRC == i) { sibIndex = parentLC; }
+
+ string sibsName = copy->tree[sibIndex].getName();
+
+ //if yes, is my sibling
+ if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
+ //we both are okay no trimming required
+ }else{
+ //i am, my sib is not, so remove sib by setting my parent to my grandparent
+ int grandparent = copy->tree[parent].getParent();
+ int grandparentLC = copy->tree[grandparent].getLChild();
+ int grandparentRC = copy->tree[grandparent].getRChild();
+
+ //whichever of my granparents children was my parent now equals me
+ if (grandparentLC == parent) { grandparentLC = i; }
+ else { grandparentRC = i; }
+
+ copy->tree[i].setParent(grandparent);
+ copy->tree[i].setBranchLength((copy->tree[i].getBranchLength()+copy->tree[parent].getBranchLength()));
+ copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
+ removedLeaves.insert(sibIndex);
+ }
+ }else{
+ //find my siblings name
+ int parentRC = copy->tree[parent].getRChild();
+ int parentLC = copy->tree[parent].getLChild();
+
+ //if I am the right child, then my sib is the left child
+ int sibIndex = parentRC;
+ if (parentRC == i) { sibIndex = parentLC; }
+
+ string sibsName = copy->tree[sibIndex].getName();
+
+ //if no is my sibling
+ if ((m->inUsersGroups(sibsName, Groups)) || (sibsName == "")) {
+ //i am not, but my sib is
+ int grandparent = copy->tree[parent].getParent();
+ int grandparentLC = copy->tree[grandparent].getLChild();
+ int grandparentRC = copy->tree[grandparent].getRChild();
+
+ //whichever of my granparents children was my parent now equals my sib
+ if (grandparentLC == parent) { grandparentLC = sibIndex; }
+ else { grandparentRC = sibIndex; }
+
+ copy->tree[sibIndex].setParent(grandparent);
+ copy->tree[sibIndex].setBranchLength((copy->tree[sibIndex].getBranchLength()+copy->tree[parent].getBranchLength()));
+ copy->tree[grandparent].setChildren(grandparentLC, grandparentRC);
+ removedLeaves.insert(i);
+ }else{
+ //neither of us are, so we want to eliminate ourselves and our parent
+ //so set our parents sib to our great-grandparent
+ int parent = copy->tree[i].getParent();
+ int grandparent = copy->tree[parent].getParent();
+
+ if (grandparent != -1) {
+ int greatgrandparent = copy->tree[grandparent].getParent();
+ int greatgrandparentLC = copy->tree[greatgrandparent].getLChild();
+ int greatgrandparentRC = copy->tree[greatgrandparent].getRChild();
+
+ int grandparentLC = copy->tree[grandparent].getLChild();
+ int grandparentRC = copy->tree[grandparent].getRChild();
+
+ int parentsSibIndex = grandparentLC;
+ if (grandparentRC == parent) { parentsSibIndex = grandparentLC; }
+ //whichever of my greatgrandparents children was my grandparent
+ if (greatgrandparentLC == grandparent) { greatgrandparentLC = parentsSibIndex; }
+ else { greatgrandparentRC = parentsSibIndex; }
+
+ copy->tree[parentsSibIndex].setParent(greatgrandparent);
+ copy->tree[parentsSibIndex].setBranchLength((copy->tree[parentsSibIndex].getBranchLength()+copy->tree[grandparent].getBranchLength()));
+ copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
+ }else{
+ copy->tree[parent].setChildren(-1, -1);
+ cout << "issues with making subtree" << endl;
+ }
+ removedLeaves.insert(sibIndex);
+ removedLeaves.insert(i);
+ }
+ }
+ }
+ }
+ }
+
+ int root = 0;
+ for (int i = 0; i < copy->getNumNodes(); i++) {
+ //you found the root
+ if (copy->tree[i].getParent() == -1) { root = i; break; }
+ }
+
+ int nextSpot = numLeaves;
+ populateNewTree(copy->tree, root, nextSpot);
+
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getCopy");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int Tree::populateNewTree(vector<Node>& oldtree, int node, int& index) {
+ try {
+
+ 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++;
+
+ return (index-1);
+ }else { //you are a leaf
+ int indexInNewTree = globaldata->gTreemap->getIndex(oldtree[node].getName());
+
+ tree[indexInNewTree].setParent(index);
+ return indexInNewTree;
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "populateNewTree");
+ exit(1);
+ }
+}
/*****************************************************************/
void Tree::getCopy(Tree* copy) {
try {
}
}
/*****************************************************************/
-void Tree::printForBoot(ostream& out) {
+void Tree::print(ostream& out, string mode) {
try {
int root = findRoot();
- printBranch(root, out, "boot");
+ printBranch(root, out, mode);
out << ";" << endl;
}
catch(exception& e) {
- m->errorOut(e, "Tree", "printForBoot");
+ m->errorOut(e, "Tree", "print");
exit(1);
}
}
-
/*****************************************************************/
// This prints out the tree in Newick form.
void Tree::createNewickFile(string f) {
exit(1);
}
}
-
/*****************************************************************/
void Tree::printBranch(int node, ostream& out, string mode) {
- try {
-
- // you are not a leaf
+try {
+
+// you are not a leaf
if (tree[node].getLChild() != -1) {
out << "(";
printBranch(tree[node].getLChild(), out, mode);
if (tree[node].getLabel() != -1) {
out << tree[node].getLabel();
}
+ }else if (mode == "both") {
+ if (tree[node].getLabel() != -1) {
+ out << tree[node].getLabel();
+ }
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
}
}else { //you are a leaf
string leafGroup = globaldata->gTreemap->getGroup(tree[node].getName());
- out << leafGroup;
if (mode == "branch") {
+ out << leafGroup;
//if there is a branch length then print it
if (tree[node].getBranchLength() != -1) {
out << ":" << tree[node].getBranchLength();
}
}else if (mode == "boot") {
+ out << leafGroup;
//if there is a label then print it
if (tree[node].getLabel() != -1) {
out << tree[node].getLabel();
}
+ }else if (mode == "both") {
+ out << tree[node].getName();
+ if (tree[node].getLabel() != -1) {
+ out << tree[node].getLabel();
+ }
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
}
}
exit(1);
}
}
-
+
/*****************************************************************/
void Tree::printTree() {
projects / mothur.git / blobdiff