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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 "greedy.h"
/*********************************************
class Greedy
*********************************************/
/**
run the algorithm
*/
void Greedy::run(Params ¶ms, vector<PDTaxaSet> &taxa_set)
{
Node *node1, *node2;
NodeVector subtree;
subtree.resize(nodeNum, NULL);
//if (params.is_rooted) subsize++;
if (params.min_size < 2)
params.min_size = params.sub_size;
taxa_set.resize(params.sub_size - params.min_size + 1);
if (initialset.empty()) {
taxa_set[0].score = root->longestPath2(node1, node2);
root = node1;
// initialize the subtree length
subtree[root->id] = root;
// update the current PD set
taxa_set[0].push_back(root);
list_size = params.sub_size-2;
updateOnLongestPath(root->highestNei->node, subtree, taxa_set[0]);
} else if (initialset.size() == 1) {
root = initialset[0];
subtree[root->id] = root;
root->calcHeight();
// initialize the subtree length
taxa_set[0].score = root->height;
taxa_set[0].push_back(root);
list_size = params.sub_size-2;
updateOnLongestPath(root->highestNei->node, subtree, taxa_set[0]);
} else {
root = initialset[0];
int included = initialset.size();
// put all taxa on the initial set into subtree
for (NodeVector::iterator it = initialset.begin(); it != initialset.end(); it++) {
if (subtree[(*it)->id]) {
cout << "Duplicated " << (*it)->name << endl;
included--;
continue;
}
subtree[(*it)->id] = (*it);
taxa_set[0].push_back(*it);
}
list_size = params.sub_size - included;
cout << included - rooted << " distinct taxa included, adding " << list_size << " more taxa" << endl;
// initialize maximal distance set
root->calcHeight();
NodeVector nodestack;
buildOnInitialSet(subtree, nodestack);
taxa_set[0].score = updateOnInitialSet(subtree);
//taxa_set[0].insert(taxa_set[0].end(), initialset.begin(), initialset.end());
}
// greedy step
if (list_size < 0) outError("Too small k");
int ts;
for (ts = 0; list_size > 0; list_size--)
{
if (params.sub_size - list_size >= params.min_size) {
taxa_set[ts].setSubTree(*this, subtree);
ts++;
taxa_set[ts] = taxa_set[ts-1];
}
NeighborSet::iterator itneigh = highestNeighbor();
Neighbor* neigh = *itneigh;
neighset.erase(itneigh);
// update the subtree length
taxa_set[ts].score += neigh->length + neigh->node->height;
// update the subtree
updateOnLongestPath(neigh->node, subtree, taxa_set[ts]);
}
taxa_set[ts].setSubTree(*this, subtree);
}
/**
initialize the ordered list based on the initial tree structure
*/
void Greedy::buildOnInitialSet(NodeVector &subtree, NodeVector &nodestack, Node *node, Node *dad) {
if (!node) node = root;
FOR_NEIGHBOR_IT(node, dad, it) {
Node *next = (*it)->node;
nodestack.push_back(next);
if (next->isLeaf() && subtree[next->id] != NULL) {
// the next node is a leaf and is in the initial set
// put all node on the stack into the subtree
for (NodeVector::iterator itnode = nodestack.begin(); itnode != nodestack.end(); itnode++) {
subtree[(*itnode)->id] = (*itnode);
}
}
buildOnInitialSet(subtree, nodestack, next, node);
nodestack.pop_back();
}
}
/**
initialize the ordered list based on the initial subtree structure
@param subtree vector containing nodes in the subtree
@return the subtree length
*/
double Greedy::updateOnInitialSet(NodeVector &subtree) {
int i;
// scan through interior nodes
for (i = leafNum; i < nodeNum; i++)
if (subtree[i] != NULL) {
Node *node = subtree[i];
for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
if (subtree[(*it)->node->id] == NULL){
addNeighbor((*it));
}
}
double len = 0.0;
for (i = 0; i < nodeNum; i++)
if (subtree[i] != NULL) {
Node *node = subtree[i];
for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
if (subtree[(*it)->node->id] != NULL){
len += (*it)->length;
}
}
return len / 2.0;
}
void Greedy::updateOnLongestPath(Node *node, NodeVector &subtree, PDTaxaSet &cur_set)
{
Node* next;
Node* current;
for (current = node; !current->isLeaf(); current = next)
{
subtree[current->id] = current;
next = current->highestNei->node;
// redirect the highest neighbor of the current
//for (int i = 0; i < current->neighbors.size(); i++)
//if (subtree[current->neighbors[i]->node->id] == NULL && current->neighbors[i]->node != next)
FOR_NEIGHBOR_IT(current, next, it)
if (subtree[(*it)->node->id] == NULL) {
addNeighbor((*it));
}
}
subtree[current->id] = current;
cur_set.push_back(current);
}
NeighborSet::iterator Greedy::highestNeighbor()
{
return neighset.begin();
}
/**
add an edge into the NeighborSet
*/
void Greedy::addNeighbor(Neighbor* neigh) {
if (list_size <= 0)
return;
if (neighset.size() < list_size)
neighset.insert(neigh);
else {
NeighborSet::iterator last = neighset.end();
last--;
Neighbor* endn = *last;
if ((neigh->length + neigh->node->height) > (endn->length + endn->node->height)) {
neighset.erase(last);
neighset.insert(neigh);
}
}
}
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