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mtree.cpp
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mtree.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 "mtree.h"
#include <iostream>
//#include <fstream>
#include <iterator>
#include "splitgraph.h"
/*********************************************
class MTree
*********************************************/
MTree::MTree() {
root = NULL;
leafNum = 0;
nodeNum = 0;
rooted = false;
num_precision = 6;
len_scale = 1.0;
fig_char = "|-+++";
}
MTree::MTree(const char *userTreeFile, bool &is_rooted)
{
init(userTreeFile, is_rooted);
}
void MTree::init(const char *userTreeFile, bool &is_rooted) {
num_precision = 6;
len_scale = 1.0;
readTree(userTreeFile, is_rooted);
//printInfo();
fig_char = "|-+++";
}
/**
constructor, get from another tree
*/
MTree::MTree(MTree &tree) {
init(tree);
}
void MTree::init(MTree &tree) {
root = tree.root;
leafNum = tree.leafNum;
nodeNum = tree.nodeNum;
rooted = tree.rooted;
//userFile = tree.userFile;
// have to delete the root when exchange to another object
tree.root = NULL;
num_precision = tree.num_precision;
len_scale = tree.len_scale;
fig_char = tree.fig_char;
}
void MTree::copyTree(MTree *tree) {
if (root) freeNode();
stringstream ss;
tree->printTree(ss);
readTree(ss, tree->rooted);
}
void MTree::copyTree(MTree *tree, string &taxa_set) {
if (tree->leafNum != taxa_set.length()) outError("#leaves and taxa_set do not match!");
leafNum = nodeNum = branchNum = 0;
for (string::iterator it = taxa_set.begin(); it != taxa_set.end(); it++)
nodeNum += (*it);
double new_len;
if (root) freeNode();
root = NULL;
root = copyTree(tree, taxa_set, new_len);
}
Node* MTree::copyTree(MTree *tree, string &taxa_set, double &len, Node *node, Node *dad) {
if (!node) {
if (taxa_set[tree->root->id]) {
node = tree->root;
} else {
for (int i = 0; i < tree->leafNum; i++)
if (taxa_set[i]) {
node = tree->findNodeID(i);
break;
}
}
}
Node *new_node = NULL;
NodeVector new_nodes;
DoubleVector new_lens;
if (node->isLeaf()) {
len = 0.0;
if (taxa_set[node->id]) {
new_node = newNode(leafNum++, node->name.c_str());
}
if (dad) return new_node;
}
if (new_node) {
new_nodes.push_back(new_node);
new_lens.push_back(len);
}
FOR_NEIGHBOR_IT(node, dad, it) {
double new_len;
new_node = copyTree(tree, taxa_set, new_len, (*it)->node, node);
if (new_node) {
new_nodes.push_back(new_node);
new_lens.push_back((*it)->length + new_len);
}
}
if (new_nodes.empty()) return NULL;
if (new_nodes.size() == 1) {
len = new_lens[0];
return new_nodes[0];
}
if (!dad && new_nodes.size() == 2) {
double sum_len = new_lens[0] + new_lens[1];
new_nodes[0]->addNeighbor(new_nodes[1], sum_len, branchNum);
new_nodes[1]->addNeighbor(new_nodes[0], sum_len, branchNum);
branchNum++;
return new_nodes[0];
}
Node* int_node = newNode(nodeNum++, node->name.c_str());
len = 0.0;
for (int i = 0; i < new_nodes.size(); i++) {
int_node->addNeighbor(new_nodes[i], new_lens[i], branchNum);
new_nodes[i]->addNeighbor(int_node, new_lens[i], branchNum);
branchNum++;
}
return int_node;
}
Node* MTree::newNode(int node_id, const char* node_name) {
return new Node(node_id, node_name);
}
Node* MTree::newNode(int node_id, int node_name) {
return new Node(node_id, node_name);
}
void MTree::printInfo(Node *node, Node *dad)
{
if (node == NULL) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
cout << node->name << " " << (*it)->node->name << " " << (*it)->length << endl;
printInfo((*it)->node, node);
}
}
int MTree::countZeroBranches(Node *node, Node *dad, double epsilon) {
int count = 0;
if (node == NULL) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
if ((*it)->length <= epsilon) count++;
count += countZeroBranches((*it)->node, node, epsilon);
}
return count;
}
int MTree::countZeroInternalBranches(Node *node, Node *dad, double epsilon) {
int count = 0;
if (node == NULL) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
if ((*it)->length <= epsilon && !(*it)->node->isLeaf() && !node->isLeaf()) count++;
count += countZeroInternalBranches((*it)->node, node, epsilon);
}
return count;
}
int MTree::countLongBranches(Node *node, Node *dad, double upper_limit) {
int count = 0;
if (node == NULL) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
if ((*it)->length >= upper_limit) count++;
count += countLongBranches((*it)->node, node, upper_limit);
}
return count;
}
void MTree::printTree(const char *ofile, int brtype)
{
try {
ofstream out;
out.exceptions(ios::failbit | ios::badbit);
if (brtype & WT_APPEND)
out.open(ofile, ios_base::out | ios_base::app);
else
out.open(ofile);
printTree(out, brtype);
out.close();
if (verbose_mode >= VB_MED)
cout << "Tree was printed to " << ofile << endl;
} catch (ios::failure) {
outError(ERR_WRITE_OUTPUT, ofile);
}
}
void MTree::printTree(ostream &out, int brtype) {
if (root->isLeaf()) {
if (root->neighbors[0]->node->isLeaf()) {
// tree has only 2 taxa!
out << "(";
printTree(out, brtype, root);
out << ",";
if (brtype & WT_TAXON_ID)
out << root->neighbors[0]->node->id;
else
out << root->neighbors[0]->node->name;
if (brtype & WT_BR_LEN)
out << ":0";
out << ")";
} else
// tree has more than 2 taxa
printTree(out, brtype, root->neighbors[0]->node);
} else
printTree(out, brtype, root);
out << ";";
if (brtype & WT_NEWLINE) out << endl;
}
struct IntString {
int id;
string str;
};
/**
nodecmp, for pruning algorithm
*/
struct IntStringCmp
{
/**
nodecmp, for pruning algorithm
*/
bool operator()(const IntString* s1, const IntString* s2) const
{
return (s1->id) < (s2->id);
}
};
typedef set<IntString*, IntStringCmp> IntStringSet;
int MTree::printTree(ostream &out, int brtype, Node *node, Node *dad)
{
int smallest_taxid = leafNum;
out.precision(num_precision);
if (!node) node = root;
if (node->isLeaf()) {
smallest_taxid = node->id;
if (brtype & WT_TAXON_ID)
out << node->id;
else
out << node->name;
if (brtype & WT_BR_LEN) {
double len = node->neighbors[0]->length;
if (brtype & WT_BR_SCALE) len *= len_scale;
if (brtype & WT_BR_LEN_ROUNDING) len = round(len);
if (brtype & WT_BR_LEN_FIXED_WIDTH)
out << ":" << fixed << len;
else
out << ":" << len;
}
} else {
// internal node
out << "(";
bool first = true;
double length = 0.0;
//for (int i = 0; i < node->neighbors.size(); i++)
//if (node->neighbors[i]->node != dad)
if (! (brtype & WT_SORT_TAXA)) {
FOR_NEIGHBOR_IT(node, dad, it) {
if ((*it)->node->name != ROOT_NAME) {
if (!first)
out << ",";
int taxid = printTree(out, brtype, (*it)->node, node);
if (taxid < smallest_taxid) smallest_taxid = taxid;
first = false;
} else
length = (*it)->length;
} else {
length = (*it)->length;
}
} else {
IntStringSet strout;
FOR_NEIGHBOR_IT(node, dad, it) {
if ((*it)->node->name != ROOT_NAME) {
ostringstream ss;
IntString *str = new IntString;
str->id = printTree(ss, brtype, (*it)->node, node);
//ss.flush();
str->str = ss.str();
strout.insert(str);
} else
length = (*it)->length;
} else {
length = (*it)->length;
}
smallest_taxid = (*strout.begin())->id;
IntStringSet::iterator iss;
for (iss = strout.begin(); iss != strout.end(); iss++) {
if (!first) out << ",";
out << (*iss)->str;
first = false;
}
for (iss = strout.begin(); iss != strout.end(); iss++)
delete (*iss);
}
out << ")";
if (!node->name.empty())
out << node->name;
else if (brtype & WT_INT_NODE)
out << node->id;
if (dad != NULL || length > 0.0) {
if (brtype & WT_BR_SCALE) length *= len_scale;
if (brtype & WT_BR_LEN_ROUNDING) length = round(length);
if (brtype & WT_BR_LEN) {
if (brtype & WT_BR_LEN_FIXED_WIDTH)
out << ":" << fixed << length;
else
out << ":" << length;
} else if (brtype & WT_BR_CLADE) {
if (! node->name.empty()) out << "/";
out << length;
}
}
}
return smallest_taxid;
}
void MTree::printSubTree(ostream &out, NodeVector &subtree) {
if (root->isLeaf())
printSubTree(out, subtree, root->neighbors[0]->node);
else
printSubTree(out, subtree, root);
out << ";";
}
void MTree::printSubTree(ostream &out, NodeVector &subtree, Node *node, Node *dad) {
if (!node) node = root;
NeighborVec::iterator it;
double length = 0.0, dad_length = 0.0;
// go down if only 1 child available
Node *child = NULL;
int degree;
do {
degree = 0;
FOR_NEIGHBOR(node, dad, it) {
if (subtree[(*it)->node->id] != NULL) {
degree++;
child = (*it)->node;
}
} else dad_length = (*it)->length;
if (degree == 1) {
dad = node;
node = child;
length += dad_length;
}
} while (degree == 1 && !node->isLeaf());
if (node->isLeaf())
out << node->name << ":" << node->neighbors[0]->length + length;
else
{
// internal node
out << "(";
bool first = true;
FOR_NEIGHBOR(node, dad, it) {
if (subtree[(*it)->node->id] != NULL) {
if ((*it)->node->name != ROOT_NAME) {
if (!first)
out << ",";
printSubTree(out, subtree, (*it)->node, node);
first = false;
} else
length += (*it)->length;
}
} else {
length += (*it)->length;
}
out << ")";
if (!node->name.empty())
out << node->name;
if (dad != NULL || length > 1e-20)
out << ":" << length;
}
}
void MTree::printTaxa(const char *ofile)
{
try {
ofstream out;
out.exceptions(ios::failbit | ios::badbit);
out.open(ofile);
if (root->isLeaf())
printTaxa(out, root->neighbors[0]->node);
else
printTaxa(out);
out.close();
cout << "Taxa list was printed to " << ofile << endl;
} catch (ios::failure) {
outError(ERR_WRITE_OUTPUT, ofile);
}
}
void MTree::printTaxa(ostream &out, Node *node, Node *dad)
{
if (!node) node = root;
if (node->isLeaf())
out << node->name << endl;
else
{
// internal node
//for (int i = 0; i < node->neighbors.size(); i++)
//if (node->neighbors[i]->node != dad)
FOR_NEIGHBOR_IT(node, dad, it) {
printTaxa(out, (*it)->node, node);
}
}
}
void MTree::printTaxa(ostream &out, NodeVector &subtree) {
for (int i = 0; i < leafNum; i++)
if (subtree[i] != NULL) {
out << subtree[i]->name << endl;
}
}
void MTree::readTree(const char *infile, bool &is_rooted) {
ifstream in;
try {
in.exceptions(ios::failbit | ios::badbit);
in.open(infile);
readTree(in, is_rooted);
in.close();
} catch (ios::failure) {
outError(ERR_READ_INPUT, infile);
}
rooted = is_rooted;
if (verbose_mode >= VB_MED)
cout << "Tree contains " << leafNum - is_rooted <<
" taxa and " << nodeNum-1-is_rooted << " branches" << endl;
}
void MTree::readTree(istream &in, bool &is_rooted)
{
in_line = 1;
in_column = 1;
try {
char ch;
ch = readNextChar(in);
if (ch != '(')
throw "Tree file not started with an opening-bracket '('";
leafNum = 0;
double branch_len;
Node *node;
parseFile(in, ch, node, branch_len);
if (is_rooted || branch_len > 0.0) {
if (branch_len == -1.0) branch_len = 0.0;
if (branch_len < 0.0)
throw ERR_NEG_BRANCH;
is_rooted = true;
root = newNode(leafNum, ROOT_NAME);
root->addNeighbor(node, branch_len);
node->addNeighbor(root, branch_len);
leafNum++;
} else { // assign root to one of the neighbor of node, if any
FOR_NEIGHBOR_IT(node, NULL, it)
if ((*it)->node->isLeaf()) {
root = (*it)->node;
break;
}
}
// make sure that root is a leaf
assert(root->isLeaf());
if (in.eof() || ch != ';')
throw "Tree file must be ended with a semi-colon ';'";
} catch (bad_alloc) {
outError(ERR_NO_MEMORY);
} catch (const char *str) {
outError(str, reportInputInfo());
} catch (char *str) {
outError(str, reportInputInfo());
} catch (string str) {
outError(str.c_str(), reportInputInfo());
} catch (ios::failure) {
outError(ERR_READ_INPUT, reportInputInfo());
} catch (...) {
// anything else
outError(ERR_READ_ANY, reportInputInfo());
}
nodeNum = leafNum;
initializeTree();
//bool stop = false;
//checkValidTree(stop);
}
void MTree::initializeTree(Node *node, Node* dad)
{
if (!node) {
node = root;
nodeNum = leafNum;
branchNum = 0;
}
if (!node->isLeaf())
{
node->id = nodeNum;
nodeNum++;
//node->name = node->id;
}
//for (int i = 0; i < node->neighbors.size(); i++)
//if (node->neighbors[i]->node != dad)
FOR_NEIGHBOR_IT(node, dad, it) {
(*it)->id = branchNum;
(*it)->node->findNeighbor(node)->id = branchNum;
branchNum++;
initializeTree((*it)->node, node);
}
}
void MTree::parseFile(istream &infile, char &ch, Node* &root, double &branch_len)
{
Node *node;
int maxlen = 10000;
char seqname[10000];
int seqlen;
double brlen;
branch_len = -1.0;
root = newNode();
if (ch == '(') {
// internal node
ch = readNextChar(infile);
while (ch != ')' && !infile.eof())
{
node = NULL;
parseFile(infile, ch, node, brlen);
//if (brlen == -1.0)
//throw "Found branch with no length.";
//if (brlen < 0.0)
//throw ERR_NEG_BRANCH;
root->addNeighbor(node, brlen);
node->addNeighbor(root, brlen);
if (infile.eof())
throw "Expecting ')', but end of file instead";
if (ch == ',')
ch = readNextChar(infile);
else if (ch != ')') {
string err = "Expecting ')', but found '";
err += ch;
err += "' instead";
throw err;
}
}
if (!infile.eof()) ch = readNextChar(infile);
}
// now read the node name
seqlen = 0;
char end_ch = 0;
if (ch == '\'' || ch == '"') end_ch = ch;
while (!infile.eof() && seqlen < maxlen)
{
if (end_ch == 0) {
if (is_newick_token(ch) || controlchar(ch)) break;
}
seqname[seqlen++] = ch;
ch = infile.get();
in_column++;
if (end_ch != 0 && ch == end_ch) {
seqname[seqlen++] = ch;
break;
}
}
if ((controlchar(ch) || ch == '[' || ch == end_ch) && !infile.eof())
ch = readNextChar(infile, ch);
if (seqlen == maxlen)
throw "Too long name ( > 100)";
seqname[seqlen] = 0;
if (seqlen == 0 && root->isLeaf())
throw "A taxon has no name.";
if (seqlen > 0)
root->name.append(seqname);
if (root->isLeaf()) {
// is a leaf, assign its ID
root->id = leafNum;
if (leafNum == 0)
MTree::root = root;
leafNum++;
}
if (ch == ';' || infile.eof())
return;
if (ch == ':')
{
ch = readNextChar(infile);
seqlen = 0;
while (!is_newick_token(ch) && !controlchar(ch) && !infile.eof() && seqlen < maxlen)
{
seqname[seqlen] = ch;
seqlen++;
ch = infile.get();
in_column++;
}
if ((controlchar(ch) || ch == '[') && !infile.eof())
ch = readNextChar(infile, ch);
if (seqlen == maxlen || infile.eof())
throw "branch length format error.";
seqname[seqlen] = 0;
branch_len = convert_double(seqname);
}
}
/**
check tree is bifurcating tree (every leaf with level 1 or 3)
*/
void MTree::checkValidTree(bool &stop, Node *node, Node *dad)
{
if (!node) node = root;
if (node->degree() != 1 && node->degree() != 3) {
cout << "Tree is not bifurcating." << endl;
stop = true;
return;
}
//for (int i = 0; i < node->neighbors.size(); i++)
//if (node->neighbors[i]->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
checkValidTree(stop, (*it)->node, node);
if (stop)
return;
}
}
double MTree::treeLength(Node *node, Node *dad)
{
if (!node) node = root;
double sum = 0;
FOR_NEIGHBOR_IT(node, dad, it) {
sum += (*it)->length + treeLength((*it)->node, node);
}
return sum;
}
double MTree::treeLengthInternal( double epsilon, Node *node, Node *dad)
{
if (!node) node = root;
double sum = 0;
FOR_NEIGHBOR_IT(node, dad, it) {
if (!(*it)->node->isLeaf() && !node->isLeaf())
{
if (treeLength((*it)->node, node) > epsilon) {
sum += (*it)->length + treeLengthInternal(epsilon, (*it)->node, node);
}
}
else {
if (treeLength((*it)->node, node) > epsilon) {
sum += treeLengthInternal(epsilon, (*it)->node, node);
}
}
}
return sum;
}
double MTree::treeDepth(Node *node, Node *dad)
{
if (!node) node = root;
double maxsum = 0.0;
FOR_NEIGHBOR_IT(node, dad, it) {
double len = (*it)->length;
if (len < 0.0) len = 0.0;
double sum = len + treeDepth((*it)->node, node);
if (sum > maxsum) maxsum = sum;
}
return maxsum;
}
void MTree::getNonCherryLeaves(NodeVector &noncherry, NodeVector &cherry, Node *node, Node *dad) {
if (!node) node = root;
if (node->isLeaf()) {
if (node->isInCherry()) {
cherry.push_back(node);
} else {
noncherry.push_back(node);
}
}
FOR_NEIGHBOR_IT(node, dad, it) {
getNonCherryLeaves(noncherry, cherry, (*it)->node, node);
}
}
void MTree::getTaxa(NodeVector &taxa, Node *node, Node *dad) {
if (!node) node = root;
if (node->isLeaf()) {
taxa.push_back(node);
}
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
getTaxa(taxa, (*it)->node, node);
}
}
void MTree::getAllNodesInSubtree(Node *node, Node *dad, NodeVector &nodeList) {
assert(node && dad);
nodeList.push_back(node);
if (node->isLeaf()) {
return;
}
FOR_NEIGHBOR_IT(node, dad, it) {
getAllNodesInSubtree((*it)->node, node, nodeList);
}
}
int MTree::getNumTaxa(Node *node, Node *dad) {
if (!node) node = root;
if (node->isLeaf()) {
return 1;
}
int numLeaf = 0;
FOR_NEIGHBOR_IT(node, dad, it) {
numLeaf += getNumTaxa((*it)->node, node);
}
return numLeaf;
}
void MTree::getInternalNodes(NodeVector &nodes, Node *node, Node *dad) {
if (!node) node = root;
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it)
if (!(*it)->node->isLeaf()) {
getInternalNodes(nodes, (*it)->node, node);
nodes.push_back((*it)->node);
}
}
void MTree::getInternalBranches(NodeVector &nodes, NodeVector &nodes2, Node *node, Node *dad) {
if (!node) node = root;
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it)
if (!(*it)->node->isLeaf()) {
getInternalBranches(nodes, nodes2, (*it)->node, node);
if (!node->isLeaf()) {
if (node->id < (*it)->node->id) {
nodes.push_back(node);
nodes2.push_back((*it)->node);
} else {
nodes.push_back((*it)->node);
nodes2.push_back(node);
}
}
}
}
void MTree::getBranches(NodeVector &nodes, NodeVector &nodes2, Node *node, Node *dad) {
if (!node) node = root;
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
if (node->id < (*it)->node->id) {
nodes.push_back(node);
nodes2.push_back((*it)->node);
} else {
nodes.push_back((*it)->node);
nodes2.push_back(node);
}
getBranches(nodes, nodes2, (*it)->node, node);
}
}
void MTree::getBranchLengths(DoubleVector &len, Node *node, Node *dad) {
if (!node) {
node = root;
assert(len.size() == branchNum);
}
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
len[(*it)->id] = (*it)->length;
getBranchLengths(len, (*it)->node, node);
}
}
void MTree::setBranchLengths(DoubleVector &len, Node *node, Node *dad) {
if (!node) {
node = root;
assert(len.size() == branchNum);
}
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
(*it)->length = (*it)->node->findNeighbor(node)->length = len[(*it)->id];
setBranchLengths(len, (*it)->node, node);
}
}
void MTree::getOrderedTaxa(NodeVector &taxa, Node *node, Node *dad) {
if (!node) node = root;
if (node->isLeaf()) {
if (taxa.empty()) taxa.resize(leafNum);
taxa[node->id] = node;
}
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
getOrderedTaxa(taxa, (*it)->node, node);
}
}
void MTree::getTaxaName(vector<string> &taxname, Node *node, Node *dad) {
if (!node) node = root;
if (node->isLeaf()) {
if (taxname.empty()) taxname.resize(leafNum);
taxname[node->id] = node->name;
}
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
getTaxaName(taxname, (*it)->node, node);
}
}
void MTree::getTaxaID(vector<int> &taxa, Node *node, Node *dad) {
if (!node) node = root;
if (node->isLeaf()) {
taxa.push_back(node->id);
}
//for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
//if ((*it)->node != dad) {
FOR_NEIGHBOR_IT(node, dad, it) {
getTaxaID(taxa, (*it)->node, node);
}
}
void MTree::convertSplits(SplitGraph &sg, Split *resp, NodeVector *nodes, Node *node, Node *dad) {
if (!node) node = root;
assert(resp->getNTaxa() == leafNum);
bool has_child = false;
FOR_NEIGHBOR_IT(node, dad, it) {
//vector<int> taxa;
//getTaxaID((*it)->node, node, taxa);
Split *sp = new Split(leafNum, (*it)->length);
convertSplits(sg, sp, nodes, (*it)->node, node);
*resp += *sp;
if (sp->shouldInvert())
sp->invert();
/* ignore nodes with degree of 2 because such split will be added before */
if (node->degree() != 2) {
sg.push_back(sp);
if (nodes) nodes->push_back((*it)->node);
}
has_child = true;
}
if (!has_child)
resp->addTaxon(node->id);
}
void MTree::convertSplits(vector<string> &taxname, SplitGraph &sg, NodeVector *nodes, Node *node, Node *dad) {
if (!sg.taxa) {
sg.taxa = new NxsTaxaBlock();
for (vector<string>::iterator it = taxname.begin(); it != taxname.end(); it++)
sg.taxa->AddTaxonLabel(NxsString(it->c_str()));
}
if (!sg.splits)
sg.splits = new MSplitsBlock(&sg);
if (!sg.pda)
sg.pda = new MPdaBlock(&sg);
// make the cycle
getTaxaID(sg.splits->cycle);
// make the splits
Split sp(leafNum);
convertSplits(sg, &sp, nodes, node, dad);
}
void MTree::convertSplits(SplitGraph &sg, NodeVector *nodes, Node *node, Node *dad) {
// make the taxa name
vector<string> taxname;
taxname.resize(leafNum);
getTaxaName(taxname);
convertSplits(taxname, sg, nodes, node, dad);
}
inline int splitnumtaxacmp(const Split* a, const Split* b)
{
return (a->countTaxa() < b->countTaxa());
}
void MTree::convertToTree(SplitGraph &sg) {
SplitGraph::iterator it;
int taxid;
int count;
BoolVector has_tax;
has_tax.resize(sg.getNTaxa(), false);
// first add trivial splits if not existed
for (it = sg.begin(); it != sg.end(); it++) {
taxid = (*it)->trivial();
if (taxid >= 0) has_tax[taxid] = true;
}
for (count = 0; count < has_tax.size(); count++)
if (!has_tax[count]) {
Split *sp = new Split(sg.getNTaxa());
sp->addTaxon(count);
sg.push_back(sp);
}
// sort splits by the number of taxa they contain
sort(sg.begin(), sg.end(), splitnumtaxacmp);
// initialize the tree
rooted = false;
leafNum = sg.getNTaxa();
nodeNum = leafNum;
// create the ground nodes, first as the leaves
NodeVector leaves;
vector<Split*> cladetaxa;
leaves.resize(leafNum, NULL);
cladetaxa.resize(leafNum, NULL);
// first add all trivial splits into tree
for (it = sg.begin(), count = 0; it != sg.end(); it++, count++) {
//(*it)->report(cout);
taxid = (*it)->trivial();
if (taxid < 0) break;
assert(leaves[taxid] == NULL);
leaves[taxid] = newNode(taxid, sg.getTaxa()->GetTaxonLabel(taxid).c_str());
leaves[taxid]->addNeighbor(NULL, (*it)->getWeight());
cladetaxa[taxid] = (*it);
}
// now fill in all missing taxa with zero terminal branch
for (taxid = 0; taxid < leafNum; taxid++)
assert(leaves[taxid]);
// now add non-trivial splits, cotinue with the interrupted iterator
for (/*it = sg.begin()*/; it != sg.end(); it++) {
//(*it)->report(cout);
Split *mysp = *it;
Node *newnode = newNode(nodeNum);
int count = 0;
for (taxid = 0; taxid < leaves.size(); )
if (cladetaxa[taxid]->subsetOf(*mysp)) // clade is a subset of current split
{
count += cladetaxa[taxid]->countTaxa();
double len = leaves[taxid]->updateNeighbor(NULL, newnode);
newnode->addNeighbor(leaves[taxid], len);
leaves[taxid] = leaves.back();
leaves.pop_back();
cladetaxa[taxid] = cladetaxa.back();
cladetaxa.pop_back();
} else taxid++;
assert(count == mysp->countTaxa());
cladetaxa.push_back(mysp);
leaves.push_back(newnode);
newnode->addNeighbor(NULL, mysp->getWeight());
nodeNum++;
}
assert(leaves.size() >= 3);
Node *newnode = newNode(nodeNum);
for (taxid = 0; taxid < leaves.size(); taxid++) {