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mexttree.cpp
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mexttree.cpp
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/***************************************************************************
* Copyright (C) 2006 by BUI Quang Minh, Steffen Klaere, Arndt von Haeseler *
* minh.bui@univie.ac.at *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include "mexttree.h"
#include "alignment.h"
void MExtTree::generateRandomTree(TreeGenType tree_type, Params ¶ms, bool binary) {
Alignment *alignment = NULL;
if (params.aln_file) {
// generate random tree with leaf sets taken from an alignment
alignment = new Alignment(params.aln_file, params.sequence_type, params.intype);
params.sub_size = alignment->getNSeq();
}
if (params.sub_size < 3) {
outError(ERR_FEW_TAXA);
}
switch (tree_type) {
case YULE_HARDING:
generateYuleHarding(params, binary);
break;
case UNIFORM:
generateUniform(params.sub_size, binary);
break;
case CATERPILLAR:
generateCaterpillar(params.sub_size);
break;
case BALANCED:
generateBalanced(params.sub_size);
break;
case STAR_TREE:
generateStarTree(params);
break;
default:
break;
}
if (!alignment) return;
NodeVector taxa;
getTaxa(taxa);
assert(taxa.size() == params.sub_size);
for (NodeVector::iterator it = taxa.begin(); it != taxa.end(); it++)
(*it)->name = alignment->getSeqName((*it)->id);
}
void MExtTree::setZeroInternalBranches(int num_zero_len) {
NodeVector nodes, nodes2;
getInternalBranches(nodes, nodes2);
if (num_zero_len > nodes.size()) outError("The specified number of zero branches is too much");
for (int i = 0; i < num_zero_len;) {
int id = random_int(nodes.size());
if (!nodes[id]) continue;
i++;
nodes[id]->findNeighbor(nodes2[id])->length = 0.0;
nodes2[id]->findNeighbor(nodes[id])->length = 0.0;
nodes[id] = NULL;
nodes2[id] = NULL;
}
}
void MExtTree::collapseZeroBranches(Node *node, Node *dad) {
if (!node) node = root;
FOR_NEIGHBOR_DECLARE(node, dad, it) {
collapseZeroBranches((*it)->node, node);
}
NeighborVec nei_vec;
nei_vec.insert(nei_vec.begin(), node->neighbors.begin(), node->neighbors.end());
for (it = nei_vec.begin(); it != nei_vec.end(); it++)
if ((*it)->node != dad) {
if ((*it)->length == 0.0) { // delete the child node
Node *child = (*it)->node;
bool first = true;
FOR_NEIGHBOR_IT(child, node, it2) {
if (first)
node->updateNeighbor(child, (*it2)->node, (*it2)->length);
else
node->addNeighbor((*it2)->node, (*it2)->length);
(*it2)->node->updateNeighbor(child, node);
first = false;
}
delete child;
}
}
}
void MExtTree::generateCaterpillar(int size) {
if (size < 3)
outError(ERR_FEW_TAXA);
root = newNode();
int i;
NodeVector myleaves;
NodeVector innodes;
Node *node;
double len;
innodes.push_back(root);
// create initial tree with 3 leaves
for (i = 0; i < 3; i++)
{
node = newNode();
len = random_double();
root->addNeighbor(node, len);
node->addNeighbor(root, len);
myleaves.push_back(node);
}
// additionally add a leaf
for (i = 3; i < size; i++)
{
int index;
index = i-1;
node = myleaves[index];
innodes.push_back(node);
// add the first leaf
Node *newleaf = newNode();
len = random_double();
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves[index] = newleaf;
// add the second leaf
newleaf = newNode();
len = random_double();
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves.push_back(newleaf);
}
root = myleaves[0];
// indexing the leaves
setLeavesName(myleaves);
leafNum = myleaves.size();
nodeNum = leafNum;
initializeTree();
}
void MExtTree::generateBalanced(int size) {
if (size < 3)
outError(ERR_FEW_TAXA);
root = newNode();
int i;
NodeVector myleaves;
Node *node;
double len;
myleaves.push_back(root);
// create initial tree with 2 leaves
node = newNode();
len = random_double();
root->addNeighbor(node, len);
node->addNeighbor(root, len);
myleaves.push_back(node);
while (myleaves.size() < size) {
int cur_size = myleaves.size();
// additionally add a leaf
for (i = 0; i < cur_size && myleaves.size() < size; i++)
{
int index = i;
node = myleaves[index];
// add the first leaf
Node *newleaf = newNode();
len = random_double();
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves[index] = newleaf;
// add the second leaf
newleaf = newNode();
len = random_double();
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves.push_back(newleaf);
}
}
root = myleaves[0];
// indexing the leaves
setLeavesName(myleaves);
leafNum = myleaves.size();
nodeNum = leafNum;
initializeTree();
}
/**
generate a random tree following uniform model
*/
void MExtTree::generateUniform(int size, bool binary)
{
if (size < 3)
outError(ERR_FEW_TAXA);
int i;
// list of left- and right-end of branches
NodeVector leftend, rightend, myleaves;
Node *node;
double len;
root = newNode(0, "0");
// create initial tree with 2 leaves
node = newNode(1, "1");
len = random_double();
root->addNeighbor(node, len);
node->addNeighbor(root, len);
leftend.push_back(root);
rightend.push_back(node);
myleaves.push_back(root);
myleaves.push_back(node);
// additionally add a leaf
for (i = 2; i < size; i++)
{
int index;
index = random_int(2*i-3);
//cout << "step " << i << " left = " << leftend[index]->id << " right = " << rightend[index]->id << endl;
// add an internal node
Node *newnode = newNode(size+i-2);
// reconnect the left end
node = leftend[index];
for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
if ((*it)->node == rightend[index]) {
len = random_double();
(*it)->node = newnode;
(*it)->length = len;
newnode->addNeighbor(node, len);
//cout << " left " << leftend[index]->id << " " << newnode->id << endl;
break;
}
// reconnect the right end
node = rightend[index];
for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
if ((*it)->node == leftend[index]) {
len = random_double();
(*it)->node = newnode;
(*it)->length = len;
newnode->addNeighbor(node, len);
//cout << " right " << rightend[index]->id << " " << newnode->id << endl;
break;
}
// add a new leaf
Node *newleaf = newNode(i, i);
len = random_double();
newnode->addNeighbor(newleaf, len);
newleaf->addNeighbor(newnode, len);
// update the leftend and rightend list
leftend.push_back(newnode);
rightend.push_back(rightend[index]);
leftend.push_back(newnode);
rightend.push_back(newleaf);
rightend[index] = newnode;
myleaves.push_back(newleaf);
}
// indexing the leaves
setLeavesName(myleaves);
leafNum = size;
nodeNum = leafNum;
initializeTree();
}
/**
generate a random tree following Yule Harding model
*/
void MExtTree::generateYuleHarding(Params ¶ms, bool binary) {
int size = params.sub_size;
if (size < 3)
outError(ERR_FEW_TAXA);
root = newNode();
int i;
NodeVector myleaves;
NodeVector innodes;
Node *node;
double len;
innodes.push_back(root);
// create initial tree with 3 leaves
for (i = 0; i < 3; i++) {
node = newNode();
len = randomLen(params);
root->addNeighbor(node, len);
node->addNeighbor(root, len);
myleaves.push_back(node);
}
// additionally add a leaf
for (i = 3; i < size; i++)
{
int index;
if (binary) {
index = random_int(i);
} else {
index = random_int(i + innodes.size());
}
if (index < i) {
node = myleaves[index];
innodes.push_back(node);
// add the first leaf
Node *newleaf = newNode();
len = randomLen(params);
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves[index] = newleaf;
// add the second leaf
newleaf = newNode();
len = randomLen(params);
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves.push_back(newleaf);
}
else {
node = innodes[index-i];
// add only 1 new leaf
Node *newleaf = newNode();
len = randomLen(params);
node->addNeighbor(newleaf, len);
newleaf->addNeighbor(node, len);
myleaves.push_back(newleaf);
}
}
root = myleaves[0];
// indexing the leaves
setLeavesName(myleaves);
leafNum = myleaves.size();
nodeNum = leafNum;
initializeTree();
}
void MExtTree::generateStarTree(Params ¶ms) {
generateYuleHarding(params);
NodeVector nodes, nodes2;
getInternalBranches(nodes, nodes2);
for (int i = 0; i < nodes.size(); i++) {
nodes[i]->findNeighbor(nodes2[i])->length = 0.0;
nodes2[i]->findNeighbor(nodes[i])->length = 0.0;
}
}
void MExtTree::generateRandomBranchLengths(Params ¶ms, Node *node, Node *dad) {
if (!node) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
double len = randomLen(params);
(*it)->length = len;
(*it)->node->findNeighbor(node)->length = len;
generateRandomBranchLengths(params, (*it)->node, node);
}
}
void MExtTree::setLeavesName(NodeVector &myleaves) {
for (int i = 0; i < myleaves.size(); i++)
{
myleaves[i]->id = i;
stringstream str;
str << 'T' << myleaves[i]->id;
myleaves[i]->name = str.str();
}
}
void MExtTree::reportDisagreedTrees(vector<string> &taxname, MTreeSet &trees, Split &mysplit) {
for (MTreeSet::iterator it = trees.begin(); it != trees.end(); it++) {
MTree *tree = (*it);
SplitGraph sg;
tree->convertSplits(taxname, sg);
if (!sg.containSplit(mysplit)) {
tree->printTree(cout, 0); // don't print branch lengths
cout << endl;
}
}
}
void MExtTree::createBootstrapSupport(vector<string> &taxname, MTreeSet &trees, SplitGraph &sg, SplitIntMap &hash_ss, Node *node, Node *dad) {
if (!node) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
if (!node->isLeaf() && !(*it)->node->isLeaf()) {
vector<int> taxa;
getTaxaID(taxa, (*it)->node, node);
Split mysplit(leafNum, 0.0, taxa);
if (mysplit.shouldInvert())
mysplit.invert();
//mysplit.report(cout);
//SplitIntMap::iterator ass_it = hash_ss.find(&mysplit);
Split *sp = hash_ss.findSplit(&mysplit);
// if found smt
if (sp != NULL) {
//Split *sp = ass_it->first;
/*char tmp[100];
if ((*it)->node->name.empty()) {
sprintf(tmp, "%d", round(sp->getWeight()));
} else
sprintf(tmp, "/%d", round(sp->getWeight()));*/
stringstream tmp;
if ((*it)->node->name.empty())
tmp << sp->getWeight();
else
tmp << "/" << sp->getWeight();
(*it)->node->name.append(tmp.str());
} else {
if (!(*it)->node->name.empty()) (*it)->node->name.append("/");
(*it)->node->name.append("0");
if (verbose_mode >= VB_MED) {
cout << "split not found:" << endl;
mysplit.report(cout);
}
}
/* new stuff: report trees that do not contain the split */
if (strncmp((*it)->node->name.c_str(), "INFO", 4) == 0) {
cout << "Reporting trees not containing the split " << (*it)->node->name << endl;
reportDisagreedTrees(taxname, trees, mysplit);
}
}
createBootstrapSupport(taxname, trees, sg, hash_ss, (*it)->node, node);
}
}
void MExtTree::createCluster(NodeVector &taxa, matrix(int) &clusters, Node *node, Node *dad) {
if (node == NULL) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
// if both end-nodes are bifurcating
Node *child = (*it)->node;
if (!child->isLeaf()) child->name = "";
if (node->degree() == 3 && child->degree() == 3) {
int count = 0;
FOR_NEIGHBOR_DECLARE(child, node, it2)
createCluster(count++, (*it2)->node, child);
if (!rooted) {
FOR_NEIGHBOR(node, child, it2)
createCluster(count++, (*it2)->node, node);
} else createCluster(count++, node, child);
clusters.resize(clusters.size()+1);
for (NodeVector::iterator nit = taxa.begin(); nit != taxa.end(); nit++) {
clusters.back().push_back((int)((*nit)->height));
}
child->name = "";
child->name += clusters.size();
}
createCluster(taxa, clusters, child, node);
}
}
void MExtTree::createCluster(int clu_num, Node *node, Node *dad) {
if (node->isLeaf()) node->height = clu_num;
FOR_NEIGHBOR_IT(node, dad, it) {
createCluster(clu_num, (*it)->node, node);
}
}