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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 "pruning.h"
#include <algorithm>
/*********************************************
class Pruning
*********************************************/
/**
Steffen Klaere's pruning algorithm
*/
void Pruning::run(Params ¶ms, vector<PDTaxaSet> &taxa_set)
{
//if (params.min_size < 2)
params.min_size = params.sub_size;
list_size = 2*(leafNum-params.sub_size)-1;
if (!initialset.empty()) {
doInitialSet();
}
buildLeaves();
for (int step = leafNum; step > params.sub_size; step--)
{
deleteExNode(nearestLeaf());
list_size -= 2;
}
taxa_set.resize(1);
taxa_set[0].setTree(*this);
}
void Pruning::doInitialSet() {
for (NodeVector::iterator it = initialset.begin(); it != initialset.end(); it++) {
(*it)->height = 1;
}
}
void Pruning::printLeaves()
{
// print info
for (LeafSet::iterator it = leaves.begin(); it != leaves.end(); it++)
{
Node *node = *it;
cout << node->id << " " << node->neighbors[0]->length << endl;
}
}
void Pruning::buildLeaves(Node *node, Node *dad)
{
if (!node) node = root;
if (node->isLeaf())
addLeaf(node);
FOR_NEIGHBOR_IT(node, dad, it)
buildLeaves((*it)->node, node);
}
LeafSet::iterator Pruning::findNode(Node *node)
{
pair<LeafSet::iterator, LeafSet::iterator>
range = leaves.equal_range(node);
for (LeafSet::iterator it = range.first; it != range.second; it++)
if (*it == node)
return it;
return leaves.end();
}
void Pruning::deleteExNode(LeafSet::iterator pos)
{
// delete from the tree
Node *node = *pos;
Node *innode = node->neighbors[0]->node;
Node *othernodes[2] = { NULL, NULL };
int i;
NeighborVec::iterator it;
double length = 0;
bool should_merge = true;
//for (it = innode->neighbors.begin(); it != innode->neighbors.end(); it++)
//if ((*it)->node != node)
FOR_NEIGHBOR(innode, node, it) {
length += (*it)->length;
if (othernodes[0] == NULL)
othernodes[0] = (*it)->node;
else if (othernodes[1] == NULL)
othernodes[1] = (*it)->node;
else
should_merge = false;
}
if (should_merge)
{
// merge two branches
for (i = 0; i < 2; i++)
if (othernodes[i]->isLeaf()) {
LeafSet::iterator temp = findNode(othernodes[i]);
if (temp != leaves.end())
leaves.erase(temp);
}
for (i = 0; i < 2; i++)
for (it = othernodes[i]->neighbors.begin(); it != othernodes[i]->neighbors.end(); it++)
if ((*it)->node == innode)
{
(*it)->node = othernodes[1-i];
(*it)->length = length;
}
} else {
// simple delete the neighbor of innode
for (it = innode->neighbors.begin(); it != innode->neighbors.end(); it++)
if ((*it)->node == node) {
innode->neighbors.erase(it);
break;
}
}
// delete the first element
leaves.erase(pos);
if (should_merge)
for (i = 0; i < 2; i++)
if (othernodes[i]->isLeaf())
addLeaf(othernodes[i]);
// also delete the last element if necessary
if (leaves.size() > list_size && leaves.size() > 1) {
LeafSet::iterator last = leaves.end();
last--;
leaves.erase(last);
}
if (node == root)
{ // find another root
root = *(leaves.begin());
}
}
LeafSet::iterator Pruning::nearestLeaf()
{
return leaves.begin();
}
/**
insert a leaf into the LeafSet
*/
void Pruning::addLeaf(Node* leaf) {
// if leaf in the initial set
if (leaf->height == 1) {
return;
}
if (list_size <= 0)
return;
if (leaves.size() < list_size)
leaves.insert(leaf);
else {
LeafSet::iterator last = leaves.end();
last--;
Node* endp = *last;
if (leaf->neighbors[0]->length < endp->neighbors[0]->length) {
leaves.erase(last);
leaves.insert(leaf);
}
}
}
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