#include "tree.h"
/*****************************************************************/
-Tree::Tree(string g) {
+Tree::Tree(int num, TreeMap* t) : tmap(t) {
try {
- globaldata = GlobalData::getInstance();
m = MothurOut::getInstance();
- parseTreeFile(); globaldata->runParse = false;
+ numLeaves = num;
+ numNodes = 2*numLeaves - 1;
+
+ tree.resize(numNodes);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree - numNodes");
+ exit(1);
+ }
+}
+/*****************************************************************/
+Tree::Tree(string g) { //do not use tree generated by this its just to extract the treenames, its a chicken before the egg thing that needs to be revisited.
+ try {
+ m = MothurOut::getInstance();
+
+ tmap = NULL;
+
+ parseTreeFile(); m->runParse = false;
}
catch(exception& e) {
m->errorOut(e, "Tree", "Tree - just parse");
}
}
/*****************************************************************/
-Tree::Tree() {
+Tree::Tree(TreeMap* t) : tmap(t) {
try {
- globaldata = GlobalData::getInstance();
m = MothurOut::getInstance();
- if (globaldata->runParse == true) { parseTreeFile(); globaldata->runParse = false; }
+ if (m->runParse == true) { parseTreeFile(); m->runParse = false; }
//for(int i = 0; i < globaldata->Treenames.size(); i++) { cout << i << '\t' << globaldata->Treenames[i] << endl; }
- numLeaves = globaldata->Treenames.size();
+ numLeaves = m->Treenames.size();
numNodes = 2*numLeaves - 1;
tree.resize(numNodes);
-
+
//initialize groupNodeInfo
- for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
- groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+ for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
+ groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
}
-
+
//initialize tree with correct number of nodes, name and group info.
for (int i = 0; i < numNodes; i++) {
//initialize leaf nodes
if (i <= (numLeaves-1)) {
- tree[i].setName(globaldata->Treenames[i]);
+ tree[i].setName(m->Treenames[i]);
//save group info
- string group = globaldata->gTreemap->getGroup(globaldata->Treenames[i]);
+ string group = tmap->getGroup(m->Treenames[i]);
+
vector<string> tempGroups; tempGroups.push_back(group);
tree[i].setGroup(tempGroups);
groupNodeInfo[group].push_back(i);
tree[i].pGroups[group] = 1;
//Treemap knows name, group and index to speed up search
- globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
+ tmap->setIndex(m->Treenames[i], i);
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
tree[i].setGroup(tempGroups);
}
}
+
}
catch(exception& e) {
m->errorOut(e, "Tree", "Tree");
string name = tree[i].getName();
- map<string, string>::iterator itNames = globaldata->names.find(name);
+ map<string, string>::iterator itNames = m->names.find(name);
- if (itNames == globaldata->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
+ if (itNames == m->names.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
else {
vector<string> dupNames;
- m->splitAtComma(globaldata->names[name], dupNames);
+ m->splitAtComma(m->names[name], dupNames);
map<string, int>::iterator itCounts;
int maxPars = 1;
set<string> groupsAddedForThisNode;
for (int j = 0; j < dupNames.size(); j++) {
- string group = globaldata->gTreemap->getGroup(dupNames[j]);
+ string group = tmap->getGroup(dupNames[j]);
if (dupNames[j] != name) {//you already added yourself in the constructor
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]++;
}
try {
//Treemap knows name, group and index to speed up search
// getIndex function will return the vector index or -1 if seq is not found.
- int index = globaldata->gTreemap->getIndex(searchName);
+ int index = tmap->getIndex(searchName);
return index;
}
void Tree::setIndex(string searchName, int index) {
try {
//set index in treemap
- globaldata->gTreemap->setIndex(searchName, index);
+ tmap->setIndex(searchName, index);
}
catch(exception& e) {
m->errorOut(e, "Tree", "setIndex");
//float A = clock();
//if user has given a names file we want to include that info in the pgroups and pcount info.
- if(globaldata->names.size() != 0) { addNamesToCounts(); }
+ if(m->names.size() != 0) { addNamesToCounts(); }
//build the pGroups in non leaf nodes to be used in the parsimony calcs.
for (int i = numLeaves; i < numNodes; i++) {
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 = tmap->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
+ tmap->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()));
+ if (grandparent != -1) {
+ 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()));
+ 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
+ //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, 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();
+
+ parentsSibIndex = grandparentLC;
+ if (grandparentLC == parent) { parentsSibIndex = grandparentRC; }
+
+ //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()));
+ if (greatgrandparent != -1) {
+ copy->tree[greatgrandparent].setChildren(greatgrandparentLC, greatgrandparentRC);
+ }
+ }else{
+ copy->tree[parent].setParent(-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);
+ tree[rc].setParent(index);
+ tree[lc].setParent(index);
+
+ tree[index].setBranchLength(oldtree[node].getBranchLength());
+ tree[rc].setBranchLength(oldtree[oldtree[node].getLChild()].getBranchLength());
+ tree[lc].setBranchLength(oldtree[oldtree[node].getRChild()].getBranchLength());
+
+ return (index++);
+ }else { //you are a leaf
+ int indexInNewTree = tmap->getIndex(oldtree[node].getName());
+ return indexInNewTree;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "populateNewTree");
+ exit(1);
+ }
+}
/*****************************************************************/
void Tree::getCopy(Tree* copy) {
try {
try {
//initialize groupNodeInfo
- for (int i = 0; i < globaldata->gTreemap->namesOfGroups.size(); i++) {
- groupNodeInfo[globaldata->gTreemap->namesOfGroups[i]].resize(0);
+ for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
+ groupNodeInfo[(tmap->getNamesOfGroups())[i]].resize(0);
}
for(int i = 0; i < numLeaves; i++){
exit(1);
}
}
-/**************************************************************************************************/
+**************************************************************************************************/
void Tree::randomBlengths() {
try {
for(int i=numNodes-1;i>=0;i--){
}
}
/*****************************************************************/
-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) {
try {
int root = findRoot();
- //filename = m->getRootName(globaldata->getTreeFile()) + "newick";
+
filename = f;
m->openOutputFile(filename, out);
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 if (mode == "deunique") {
+ //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());
+ string leafGroup = tmap->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();
+ }
+ }else if (mode == "deunique") {
+ map<string, string>::iterator itNames = m->names.find(tree[node].getName());
+
+ string outputString = "";
+ if (itNames != m->names.end()) {
+
+ vector<string> dupNames;
+ m->splitAtComma((itNames->second), dupNames);
+
+ if (dupNames.size() == 1) {
+ outputString += tree[node].getName();
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(tree[node].getBranchLength());
+ }
+ }else {
+ outputString += "(";
+
+ for (int u = 0; u < dupNames.size()-1; u++) {
+ outputString += dupNames[u];
+
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(0.0);
+ }
+ outputString += ",";
+ }
+
+ outputString += dupNames[dupNames.size()-1];
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(0.0);
+ }
+
+ outputString += ")";
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(tree[node].getBranchLength());
+ }
+ }
+ }else {
+ outputString = tree[node].getName();
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ outputString += ":" + toString(tree[node].getBranchLength());
+ }
+
+ m->mothurOut("[ERROR]: " + tree[node].getName() + " is not in your namefile, please correct."); m->mothurOutEndLine();
+ }
+
+ out << outputString;
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "printBranch");
+ 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 = tmap->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();
+ }
}
}
exit(1);
}
}
-
/*****************************************************************/
void Tree::printTree() {
//only takes names from the first tree and assumes that all trees use the same names.
try {
- string filename = globaldata->getTreeFile();
+ string filename = m->getTreeFile();
ifstream filehandle;
m->openInputFile(filename, filehandle);
int c, comment;
//c = , until done with translation then c = ;
h = name.substr(name.length()-1, name.length());
name.erase(name.end()-1); //erase the comma
- globaldata->Treenames.push_back(number);
+ m->Treenames.push_back(number);
}
- if(number == ";") { globaldata->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
+ if(number == ";") { m->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
}
}
filehandle.close();
}
//cout << "name = " << name << endl;
- globaldata->Treenames.push_back(name);
+ m->Treenames.push_back(name);
filehandle.putback(c);
//k = c;
//cout << " after putback" << k << endl;
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