#include "tree.h"
+/*****************************************************************/
+Tree::Tree(int num, CountTable* t) : ct(t) {
+ try {
+ 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) { //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();
+ parseTreeFile(); m->runParse = false;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree - just parse");
+ exit(1);
+ }
+}
+/*****************************************************************/
+Tree::Tree(CountTable* t) : ct(t) {
+ try {
+ m = MothurOut::getInstance();
+
+ if (m->runParse == true) { parseTreeFile(); m->runParse = false; }
+
+ numLeaves = m->Treenames.size();
+ numNodes = 2*numLeaves - 1;
+
+ tree.resize(numNodes);
+
+ //initialize groupNodeInfo
+ vector<string> namesOfGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[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(m->Treenames[i]);
+
+ //save group info
+ int maxPars = 1;
+ vector<string> group;
+ vector<int> counts = ct->getGroupCounts(m->Treenames[i]);
+ for (int j = 0; j < namesOfGroups.size(); j++) {
+ if (counts[j] != 0) { //you have seqs from this group
+ groupNodeInfo[namesOfGroups[j]].push_back(i);
+ group.push_back(namesOfGroups[j]);
+ tree[i].pGroups[namesOfGroups[j]] = counts[j];
+ tree[i].pcount[namesOfGroups[j]] = counts[j];
+ //keep highest group
+ if(counts[j] > maxPars){ maxPars = counts[j]; }
+ }
+ }
+ tree[i].setGroup(group);
+ setIndex(m->Treenames[i], i);
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//end if
+
+ //intialize non leaf nodes
+ }else if (i > (numLeaves-1)) {
+ tree[i].setName("");
+ vector<string> tempGroups;
+ tree[i].setGroup(tempGroups);
+ }
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree");
+ exit(1);
+ }
+}
+/*****************************************************************/
+Tree::Tree(CountTable* t, vector< vector<double> >& sims) : ct(t) {
+ try {
+ m = MothurOut::getInstance();
+
+ if (m->runParse == true) { parseTreeFile(); m->runParse = false; }
+ numLeaves = m->Treenames.size();
+ numNodes = 2*numLeaves - 1;
+
+ tree.resize(numNodes);
+
+ //initialize groupNodeInfo
+ vector<string> namesOfGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[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(m->Treenames[i]);
+
+ //save group info
+ int maxPars = 1;
+ vector<string> group;
+ vector<int> counts = ct->getGroupCounts(m->Treenames[i]);
+ for (int j = 0; j < namesOfGroups.size(); j++) {
+ if (counts[j] != 0) { //you have seqs from this group
+ groupNodeInfo[namesOfGroups[j]].push_back(i);
+ group.push_back(namesOfGroups[j]);
+ tree[i].pGroups[namesOfGroups[j]] = counts[j];
+ tree[i].pcount[namesOfGroups[j]] = counts[j];
+ //keep highest group
+ if(counts[j] > maxPars){ maxPars = counts[j]; }
+ }
+ }
+ tree[i].setGroup(group);
+ setIndex(m->Treenames[i], i);
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//end if
+
+ //intialize non leaf nodes
+ }else if (i > (numLeaves-1)) {
+ tree[i].setName("");
+ vector<string> tempGroups;
+ tree[i].setGroup(tempGroups);
+ }
+ }
+
+
+ //build tree from matrix
+ //initialize indexes
+ map<int, int> thisIndexes; //maps row in simMatrix to vector index in the tree
+ for (int g = 0; g < numLeaves; g++) { thisIndexes[g] = g; }
+
+ //do merges and create tree structure by setting parents and children
+ //there are numGroups - 1 merges to do
+ for (int i = 0; i < (numLeaves - 1); i++) {
+ float largest = -1000.0;
+
+ if (m->control_pressed) { break; }
+
+ int row, column;
+ //find largest value in sims matrix by searching lower triangle
+ for (int j = 1; j < sims.size(); j++) {
+ for (int k = 0; k < j; k++) {
+ if (sims[j][k] > largest) { largest = sims[j][k]; row = j; column = k; }
+ }
+ }
+
+ //set non-leaf node info and update leaves to know their parents
+ //non-leaf
+ tree[numLeaves + i].setChildren(thisIndexes[row], thisIndexes[column]);
+
+ //parents
+ tree[thisIndexes[row]].setParent(numLeaves + i);
+ tree[thisIndexes[column]].setParent(numLeaves + i);
+
+ //blength = distance / 2;
+ float blength = ((1.0 - largest) / 2);
+
+ //branchlengths
+ tree[thisIndexes[row]].setBranchLength(blength - tree[thisIndexes[row]].getLengthToLeaves());
+ tree[thisIndexes[column]].setBranchLength(blength - tree[thisIndexes[column]].getLengthToLeaves());
+
+ //set your length to leaves to your childs length plus branchlength
+ tree[numLeaves + i].setLengthToLeaves(tree[thisIndexes[row]].getLengthToLeaves() + tree[thisIndexes[row]].getBranchLength());
+
+
+ //update index
+ thisIndexes[row] = numLeaves+i;
+ thisIndexes[column] = numLeaves+i;
+
+ //remove highest value that caused the merge.
+ sims[row][column] = -1000.0;
+ sims[column][row] = -1000.0;
+
+ //merge values in simsMatrix
+ for (int n = 0; n < sims.size(); n++) {
+ //row becomes merge of 2 groups
+ sims[row][n] = (sims[row][n] + sims[column][n]) / 2;
+ sims[n][row] = sims[row][n];
+ //delete column
+ sims[column][n] = -1000.0;
+ sims[n][column] = -1000.0;
+ }
+ }
+
+ //adjust tree to make sure root to tip length is .5
+ int root = findRoot();
+ tree[root].setBranchLength((0.5 - tree[root].getLengthToLeaves()));
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "Tree");
+ exit(1);
+ }
+}
+/*****************************************************************/
+Tree::~Tree() {}
+/*****************************************************************
+void Tree::addNamesToCounts(map<string, string> nameMap) {
+ try {
+ //ex. seq1 seq2,seq3,se4
+ // seq1 = pasture
+ // seq2 = forest
+ // seq4 = pasture
+ // seq3 = ocean
+
+ //before this function seq1.pcount = pasture -> 1
+ //after seq1.pcount = pasture -> 2, forest -> 1, ocean -> 1
+
+ //before this function seq1.pgroups = pasture -> 1
+ //after seq1.pgroups = pasture -> 1 since that is the dominant group
+
+
+ //go through each leaf and update its pcounts and pgroups
+
+ //float A = clock();
+
+ for (int i = 0; i < numLeaves; i++) {
+
+ string name = tree[i].getName();
+
+ map<string, string>::iterator itNames = nameMap.find(name);
+
+ if (itNames == nameMap.end()) { m->mothurOut(name + " is not in your name file, please correct."); m->mothurOutEndLine(); exit(1); }
+ else {
+ vector<string> dupNames;
+ m->splitAtComma(nameMap[name], dupNames);
+
+ map<string, int>::iterator itCounts;
+ int maxPars = 1;
+ set<string> groupsAddedForThisNode;
+ for (int j = 0; j < dupNames.size(); j++) {
+
+ string group = tmap->getGroup(dupNames[j]);
+
+ if (dupNames[j] != name) {//you already added yourself in the constructor
+
+ if (groupsAddedForThisNode.count(group) == 0) { groupNodeInfo[group].push_back(i); groupsAddedForThisNode.insert(group); } //if you have not already added this node for this group, then add it
+
+ //update pcounts
+ itCounts = tree[i].pcount.find(group);
+ if (itCounts == tree[i].pcount.end()) { //new group, add it
+ tree[i].pcount[group] = 1;
+ }else {
+ tree[i].pcount[group]++;
+ }
+
+ //update pgroups
+ itCounts = tree[i].pGroups.find(group);
+ if (itCounts == tree[i].pGroups.end()) { //new group, add it
+ tree[i].pGroups[group] = 1;
+ }else{
+ tree[i].pGroups[group]++;
+ }
+
+ //keep highest group
+ if(tree[i].pGroups[group] > maxPars){
+ maxPars = tree[i].pGroups[group];
+ }
+ }else { groupsAddedForThisNode.insert(group); } //add it so you don't add it to groupNodeInfo again
+ }//end for
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//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
+
+ //float B = clock();
+ //cout << "addNamesToCounts\t" << (B - A) / CLOCKS_PER_SEC << endl;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "addNamesToCounts");
+ exit(1);
+ }
+}*/
+/*****************************************************************/
+int Tree::getIndex(string searchName) {
+ try {
+ map<string, int>::iterator itIndex = indexes.find(searchName);
+ if (itIndex != indexes.end()) {
+ return itIndex->second;
+ }
+ return -1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getIndex");
+ exit(1);
+ }
+}
+/*****************************************************************/
+
+void Tree::setIndex(string searchName, int index) {
+ try {
+ map<string, int>::iterator itIndex = indexes.find(searchName);
+ if (itIndex == indexes.end()) {
+ indexes[searchName] = index;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "setIndex");
+ exit(1);
+ }
+}
+/*****************************************************************/
+int Tree::assembleTree() {
+ try {
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { return 1; }
+
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "assembleTree");
+ exit(1);
+ }
+}
+/*****************************************************************/
+//assumes leaf node names are in groups and no names file - used by indicator command
+void Tree::getSubTree(Tree* Ctree, vector<string> Groups) {
+ try {
+
+ //copy Tree since we are going to destroy it
+ Tree* copy = new Tree(ct);
+ copy->getCopy(Ctree);
+ copy->assembleTree();
+
+ //we want to select some of the leaf nodes to create the output tree
+ //go through the input Tree starting at parents of leaves
+ //initialize groupNodeInfo
+ vector<string> namesOfGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < namesOfGroups.size(); i++) { groupNodeInfo[namesOfGroups[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(Groups[i]);
+
+ //save group info
+ int maxPars = 1;
+ vector<string> group;
+ vector<int> counts = ct->getGroupCounts(Groups[i]);
+ for (int j = 0; j < namesOfGroups.size(); j++) {
+ if (counts[j] != 0) { //you have seqs from this group
+ groupNodeInfo[namesOfGroups[j]].push_back(i);
+ group.push_back(namesOfGroups[j]);
+ tree[i].pGroups[namesOfGroups[j]] = counts[j];
+ tree[i].pcount[namesOfGroups[j]] = counts[j];
+ //keep highest group
+ if(counts[j] > maxPars){ maxPars = counts[j]; }
+ }
+ }
+ tree[i].setGroup(group);
+ setIndex(Groups[i], i);
+
+ if (maxPars > 1) { //then we have some more dominant groups
+ //erase all the groups that are less than maxPars because you found a more dominant group.
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();){
+ if(it->second < maxPars){
+ tree[i].pGroups.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ for(it=tree[i].pGroups.begin();it!=tree[i].pGroups.end();it++){
+ tree[i].pGroups[it->first] = 1;
+ }
+ }//end if
+
+ //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);
+
+ delete copy;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getSubTree");
+ exit(1);
+ }
+}
+/*****************************************************************
+//assumes nameMap contains unique names as key or is empty.
+//assumes numLeaves defined in tree constructor equals size of seqsToInclude and seqsToInclude only contains unique seqs.
+int Tree::getSubTree(Tree* copy, vector<string> seqsToInclude, map<string, string> nameMap) {
+ try {
+
+ if (numLeaves != seqsToInclude.size()) { m->mothurOut("[ERROR]: numLeaves does not equal numUniques, cannot create subtree.\n"); m->control_pressed = true; return 0; }
+
+ getSubTree(copy, seqsToInclude);
+ if (nameMap.size() != 0) { addNamesToCounts(nameMap); }
+
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { return 1; }
+
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getSubTree");
+ 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 = getIndex(oldtree[node].getName());
+ return indexInNewTree;
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "populateNewTree");
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::getCopy(Tree* copy, bool subsample) {
+ try {
+
+ //for each node in the tree copy its info
+ for (int i = 0; i < numNodes; i++) {
+ //copy branch length
+ tree[i].setBranchLength(copy->tree[i].getBranchLength());
+
+ //copy parent
+ tree[i].setParent(copy->tree[i].getParent());
+
+ //copy children
+ tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+ }
+
+ //build the pGroups in non leaf nodes to be used in the parsimony calcs.
+ for (int i = numLeaves; i < numNodes; i++) {
+ if (m->control_pressed) { break; }
+
+ tree[i].pGroups = (mergeGroups(i));
+ tree[i].pcount = (mergeGcounts(i));
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getCopy");
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::getCopy(Tree* copy) {
+ try {
+
+ //for each node in the tree copy its info
+ for (int i = 0; i < numNodes; i++) {
+ //copy name
+ tree[i].setName(copy->tree[i].getName());
+
+ //copy group
+ tree[i].setGroup(copy->tree[i].getGroup());
+
+ //copy branch length
+ tree[i].setBranchLength(copy->tree[i].getBranchLength());
+
+ //copy parent
+ tree[i].setParent(copy->tree[i].getParent());
+
+ //copy children
+ tree[i].setChildren(copy->tree[i].getLChild(), copy->tree[i].getRChild());
+
+ //copy index in node and tmap
+ setIndex(copy->tree[i].getName(), getIndex(copy->tree[i].getName()));
+ tree[i].setIndex(copy->tree[i].getIndex());
+
+ //copy pGroups
+ tree[i].pGroups = copy->tree[i].pGroups;
+
+ //copy pcount
+ tree[i].pcount = copy->tree[i].pcount;
+ }
+
+ groupNodeInfo = copy->groupNodeInfo;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "getCopy");
+ exit(1);
+ }
+}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeGroups(int i) {
+ try {
+ int lc = tree[i].getLChild();
+ int rc = tree[i].getRChild();
+
+ //set parsimony groups to left child
+ map<string,int> parsimony = tree[lc].pGroups;
+
+ int maxPars = 1;
+
+ //look at right child groups and update maxPars if right child has something higher for that group.
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+ it2 = parsimony.find(it->first);
+ if (it2 != parsimony.end()) {
+ parsimony[it->first]++;
+ }else {
+ parsimony[it->first] = 1;
+ }
+
+ if(parsimony[it->first] > maxPars){
+ maxPars = parsimony[it->first];
+ }
+ }
+
+ // this is true if right child had a greater parsimony for a certain group
+ if(maxPars > 1){
+ //erase all the groups that are only 1 because you found something with 2.
+ for(it=parsimony.begin();it!=parsimony.end();){
+ if(it->second == 1){
+ parsimony.erase(it++);
+ }else { it++; }
+ }
+ //set one remaining groups to 1
+ //so with our above example p[white] = 2 would be left and it would become p[white] = 1
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ parsimony[it->first] = 1;
+ }
+
+ }
+
+ return parsimony;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "mergeGroups");
+ exit(1);
+ }
+}
+/*****************************************************************/
+//returns a map with a groupname and the number of times that group was seen in the children
+//for instance if your children are white and black then it would return a map with 2 entries
+// p[white] = 1 and p[black] = 1. Now go up a level and merge that with a node who has p[white] = 1
+//and you get p[white] = 2, p[black] = 1, but you erase the p[black] because you have a p value higher than 1.
+
+map<string, int> Tree::mergeUserGroups(int i, vector<string> g) {
+ try {
+
+ int lc = tree[i].getLChild();
+ int rc = tree[i].getRChild();
+
+ //loop through nodes groups removing the ones the user doesn't want
+ for(it=tree[lc].pGroups.begin();it!=tree[lc].pGroups.end();){
+ if (m->inUsersGroups(it->first, g) != true) {
+ tree[lc].pGroups.erase(it++);
+ }else { it++; }
+ }
+
+ //loop through nodes groups removing the ones the user doesn't want
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();){
+ if (m->inUsersGroups(it->first, g) != true) {
+ tree[rc].pGroups.erase(it++);
+ }else { it++; }
+ }
+
+ //set parsimony groups to left child
+ map<string,int> parsimony = tree[lc].pGroups;
+
+ int maxPars = 1;
+
+ //look at right child groups and update maxPars if right child has something higher for that group.
+ for(it=tree[rc].pGroups.begin();it!=tree[rc].pGroups.end();it++){
+ it2 = parsimony.find(it->first);
+ if (it2 != parsimony.end()) {
+ parsimony[it->first]++;
+ }else {
+ parsimony[it->first] = 1;
+ }
+
+ if(parsimony[it->first] > maxPars){
+ maxPars = parsimony[it->first];
+ }
+ }
+
+ // this is true if right child had a greater parsimony for a certain group
+ if(maxPars > 1){
+ //erase all the groups that are only 1 because you found something with 2.
+ for(it=parsimony.begin();it!=parsimony.end();){
+ if(it->second == 1){
+ parsimony.erase(it++);
+ }else { it++; }
+ }
+
+ for(it=parsimony.begin();it!=parsimony.end();it++){
+ parsimony[it->first] = 1;
+ }
+ }
+
+ return parsimony;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "mergeUserGroups");
+ exit(1);
+ }
+}
+
+
+/**************************************************************************************************/
+
+map<string,int> Tree::mergeGcounts(int position) {
+ try{
+ map<string,int>::iterator pos;
+
+ int lc = tree[position].getLChild();
+ int rc = tree[position].getRChild();
+
+ map<string,int> sum = tree[lc].pcount;
+
+ for(it=tree[rc].pcount.begin();it!=tree[rc].pcount.end();it++){
+ sum[it->first] += it->second;
+ }
+ return sum;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "mergeGcounts");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Tree::randomLabels(vector<string> g) {
+ try {
+
+ //initialize groupNodeInfo
+ for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
+ groupNodeInfo[(ct->getNamesOfGroups())[i]].resize(0);
+ }
+
+ for(int i = 0; i < numLeaves; i++){
+ int z;
+ //get random index to switch with
+ z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ //you only want to randomize the nodes that are from a group the user wants analyzed, so
+ //if either of the leaf nodes you are about to switch are not in the users groups then you don't want to switch them.
+ bool treez, treei;
+
+ treez = m->inUsersGroups(tree[z].getGroup(), g);
+ treei = m->inUsersGroups(tree[i].getGroup(), g);
+
+ if ((treez == true) && (treei == true)) {
+ //switches node i and node z's info.
+ map<string,int> lib_hold = tree[z].pGroups;
+ tree[z].pGroups = (tree[i].pGroups);
+ tree[i].pGroups = (lib_hold);
+
+ vector<string> zgroup = tree[z].getGroup();
+ tree[z].setGroup(tree[i].getGroup());
+ tree[i].setGroup(zgroup);
+
+ string zname = tree[z].getName();
+ tree[z].setName(tree[i].getName());
+ tree[i].setName(zname);
+
+ map<string,int> gcount_hold = tree[z].pcount;
+ tree[z].pcount = (tree[i].pcount);
+ tree[i].pcount = (gcount_hold);
+ }
+
+ for (int k = 0; k < (tree[i].getGroup()).size(); k++) { groupNodeInfo[(tree[i].getGroup())[k]].push_back(i); }
+ for (int k = 0; k < (tree[z].getGroup()).size(); k++) { groupNodeInfo[(tree[z].getGroup())[k]].push_back(z); }
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "randomLabels");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+void Tree::randomBlengths() {
+ try {
+ for(int i=numNodes-1;i>=0;i--){
+ int z = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
+
+ float bl_hold = tree[z].getBranchLength();
+ tree[z].setBranchLength(tree[i].getBranchLength());
+ tree[i].setBranchLength(bl_hold);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "randomBlengths");
+ exit(1);
+ }
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(vector<string> g) {
+ randomLabels(g);
+ assembleTree();
+}
+/*************************************************************************************************/
+void Tree::assembleRandomUnifracTree(string groupA, string groupB) {
+ vector<string> temp; temp.push_back(groupA); temp.push_back(groupB);
+ randomLabels(temp);
+ assembleTree();
+}
+
+/*************************************************************************************************/
+//for now it's just random topology but may become random labels as well later that why this is such a simple function now...
+void Tree::assembleRandomTree() {
+ randomTopology();
+ assembleTree();
+}
+/**************************************************************************************************/
+
+void Tree::randomTopology() {
+ try {
+ for(int i=0;i<numNodes;i++){
+ tree[i].setParent(-1);
+ }
+ for(int i=numLeaves;i<numNodes;i++){
+ tree[i].setChildren(-1, -1);
+ }
+
+ for(int i=numLeaves;i<numNodes;i++){
+ int escape =0;
+ int rnd_index1, rnd_index2;
+ while(escape == 0){
+ rnd_index1 = (int)(((double)rand() / (double) RAND_MAX)*i);
+ if(tree[rnd_index1].getParent() == -1){escape = 1;}
+ }
+
+ escape = 0;
+ while(escape == 0){
+ rnd_index2 = (int)(((double)rand() / (double) RAND_MAX)*i);
+ if(rnd_index2 != rnd_index1 && tree[rnd_index2].getParent() == -1){
+ escape = 1;
+ }
+ }
+
+ tree[i].setChildren(rnd_index1,rnd_index2);
+ tree[i].setParent(-1);
+ tree[rnd_index1].setParent(i);
+ tree[rnd_index2].setParent(i);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "randomTopology");
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::print(ostream& out) {
+ try {
+ int root = findRoot();
+ printBranch(root, out, "branch");
+ out << ";" << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "print");
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::print(ostream& out, map<string, string> nameMap) {
+ try {
+ int root = findRoot();
+ printBranch(root, out, nameMap);
+ out << ";" << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "print");
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::print(ostream& out, string mode) {
+ try {
+ int root = findRoot();
+ printBranch(root, out, mode);
+ out << ";" << endl;
+ }
+ catch(exception& e) {
+ 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 = f;
+
+ m->openOutputFile(filename, out);
+
+ printBranch(root, out, "branch");
+
+ // you are at the end of the tree
+ out << ";" << endl;
+ out.close();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "createNewickFile");
+ exit(1);
+ }
+}
+
+/*****************************************************************/
+//This function finds the index of the root node.
+
+int Tree::findRoot() {
+ try {
+ for (int i = 0; i < numNodes; i++) {
+ //you found the root
+ if (tree[i].getParent() == -1) { return i; }
+ //cout << "i = " << i << endl;
+ //cout << "i's parent = " << tree[i].getParent() << endl;
+ }
+ return -1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "findRoot");
+ exit(1);
+ }
+}
+/*****************************************************************/
+void Tree::printBranch(int node, ostream& out, map<string, string> names) {
+try {
+
+// you are not a leaf
+ if (tree[node].getLChild() != -1) {
+ out << "(";
+ printBranch(tree[node].getLChild(), out, names);
+ out << ",";
+ printBranch(tree[node].getRChild(), out, names);
+ out << ")";
+
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
+
+ }else { //you are a leaf
+ map<string, string>::iterator itNames = names.find(tree[node].getName());
+
+ string outputString = "";
+ if (itNames != 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) {
+ try {
+
+ // you are not a leaf
+ if (tree[node].getLChild() != -1) {
+ out << "(";
+ printBranch(tree[node].getLChild(), out, mode);
+ out << ",";
+ printBranch(tree[node].getRChild(), out, mode);
+ out << ")";
+ if (mode == "branch") {
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ //if there is a label then print it
+ 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
+ vector<string> leafGroup = ct->getGroups(tree[node].getName());
+
+ if (mode == "branch") {
+ out << leafGroup[0];
+ //if there is a branch length then print it
+ if (tree[node].getBranchLength() != -1) {
+ out << ":" << tree[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ out << leafGroup[0];
+ //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();
+ }
+ }
+ }
+
+ }
+ 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
+ vector<string> leafGroup = ct->getGroups(theseNodes[node].getName());
+
+ if (mode == "branch") {
+ out << leafGroup[0];
+ //if there is a branch length then print it
+ if (theseNodes[node].getBranchLength() != -1) {
+ out << ":" << theseNodes[node].getBranchLength();
+ }
+ }else if (mode == "boot") {
+ out << leafGroup[0];
+ //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() {
+
+ for(int i=0;i<numNodes;i++){
+ cout << i << '\t';
+ tree[i].printNode();
+ }
+
+}
+
+/*****************************************************************/
+//this code is a mess and should be rethought...-slw
+int Tree::parseTreeFile() {
+
+ //only takes names from the first tree and assumes that all trees use the same names.
+ try {
+ string filename = m->getTreeFile();
+ ifstream filehandle;
+ m->openInputFile(filename, filehandle);
+ int c, comment;
+ comment = 0;
+ int done = 1;
+
+ //ifyou are not a nexus file
+ if((c = filehandle.peek()) != '#') {
+ while((c = filehandle.peek()) != ';') {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ while ((c = filehandle.peek()) != ';') {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
+ done = readTreeString(filehandle);
+ if (done == 0) { break; }
+ }
+ //ifyou are a nexus file
+ }else if((c = filehandle.peek()) == '#') {
+ string holder = "";
+
+ // get past comments
+ while(holder != "translate" && holder != "Translate"){
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ if(holder == "[" || holder == "[!"){
+ comment = 1;
+ }
+ if(holder == "]"){
+ comment = 0;
+ }
+ filehandle >> holder;
+
+ //if there is no translate then you must read tree string otherwise use translate to get names
+ if((holder == "tree") && (comment != 1)){
+ //pass over the "tree rep.6878900 = "
+ while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
+
+ if(c == EOF) { break; }
+ filehandle.putback(c); //put back first ( of tree.
+ done = readTreeString(filehandle);
+
+ break;
+ }
+
+ if (done == 0) { break; }
+ }
+
+ //use nexus translation rather than parsing tree to save time
+ if((holder == "translate") || (holder == "Translate")) {
+
+ string number, name, h;
+ h = ""; // so it enters the loop the first time
+ while((h != ";") && (number != ";")) {
+ if (m->control_pressed) { filehandle.close(); return 0; }
+ filehandle >> number;
+ filehandle >> name;
+
+ //c = , until done with translation then c = ;
+ h = name.substr(name.length()-1, name.length());
+ name.erase(name.end()-1); //erase the comma
+ m->Treenames.push_back(number);
+ }
+ if(number == ";") { m->Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
+ }
+ }
+ filehandle.close();
+ return 0;
+ //for (int i = 0; i < globaldata->Treenames.size(); i++) {
+//cout << globaldata->Treenames[i] << endl; }
+//cout << globaldata->Treenames.size() << endl;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "parseTreeFile");
+ exit(1);
+ }
+}
+/*******************************************************/
+
+/*******************************************************/
+int Tree::readTreeString(ifstream& filehandle) {
+ try {
+ int c;
+ string name; //, k
+
+ while((c = filehandle.peek()) != ';') {
+ if (m->control_pressed) { return 0; }
+//k = c;
+//cout << " at beginning of while " << k << endl;
+ if(c == ')') {
+ //to pass over labels in trees
+ c=filehandle.get();
+ while((c!=',') && (c != -1) && (c!= ':') && (c!=';')){ c=filehandle.get(); }
+ filehandle.putback(c);
+ }
+ if(c == ';') { return 0; }
+ if(c == -1) { return 0; }
+ //if you are a name
+ if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
+ name = "";
+ c = filehandle.get();
+ //k = c;
+//cout << k << endl;
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
+ name += c;
+ c = filehandle.get();
+ //k = c;
+//cout << " in name while " << k << endl;
+ }
+
+//cout << "name = " << name << endl;
+ if (name != "\r" ) {
+ m->Treenames.push_back(name); } //cout << m->Treenames.size() << '\t' << name << endl;
+
+ filehandle.putback(c);
+//k = c;
+//cout << " after putback" << k << endl;
+ }
+
+ if(c == ':') { //read until you reach the end of the branch length
+ while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
+ c = filehandle.get();
+ //k = c;
+ //cout << " in branch while " << k << endl;
+ }
+ filehandle.putback(c);
+ }
+
+ c = filehandle.get();
+//k = c;
+ //cout << " here after get " << k << endl;
+ if(c == ';') { return 0; }
+ if(c == ')') { filehandle.putback(c); }
+ //k = c;
+//cout << k << endl;
+
+ }
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Tree", "readTreeString");
+ exit(1);
+ }
+}
+
+/*******************************************************/
+
+/*******************************************************/
+