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//
// C++ Implementation: phylonode
//
// Description:
//
//
// Author: BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>, (C) 2008
//
// Copyright: See COPYING file that comes with this distribution
//
//
#include "phylonode.h"
void PhyloNeighbor::clearForwardPartialLh(Node *dad) {
clearPartialLh();
for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it ++)
if ((*it)->node != dad)
((PhyloNeighbor*)*it)->clearForwardPartialLh(node);
}
void PhyloNode::clearReversePartialLh(PhyloNode *dad) {
// PhyloNeighbor *node_nei = (PhyloNeighbor*)findNeighbor(dad);
// assert(node_nei);
// node_nei->partial_lh_computed = 0;
for (NeighborVec::iterator it = neighbors.begin(); it != neighbors.end(); it ++)
if ((*it)->node != dad) {
PhyloNeighbor *nei = (PhyloNeighbor*)(*it)->node->findNeighbor(this);
nei->partial_lh_computed = 0;
nei->size = 0;
((PhyloNode*)(*it)->node)->clearReversePartialLh(this);
}
}
void PhyloNode::clearAllPartialLh(bool make_null, PhyloNode *dad) {
PhyloNeighbor *node_nei = (PhyloNeighbor*)findNeighbor(dad);
node_nei->partial_lh_computed = 0;
if (make_null) node_nei->partial_lh = NULL;
if (Params::getInstance().lh_mem_save == LM_MEM_SAVE)
node_nei->size = 0;
node_nei = (PhyloNeighbor*)dad->findNeighbor(this);
node_nei->partial_lh_computed = 0;
if (make_null) node_nei->partial_lh = NULL;
if (Params::getInstance().lh_mem_save == LM_MEM_SAVE)
node_nei->size = 0;
for (NeighborVec::iterator it = neighbors.begin(); it != neighbors.end(); it ++)
if ((*it)->node != dad)
((PhyloNode*)(*it)->node)->clearAllPartialLh(make_null, this);
}
PhyloNode::PhyloNode()
: Node()
{
init();
}
PhyloNode::PhyloNode(int aid) : Node(aid)
{
init();
}
PhyloNode::PhyloNode(int aid, int aname) : Node (aid, aname) {
init();
}
PhyloNode::PhyloNode(int aid, const char *aname) : Node(aid, aname) {
init();
}
void PhyloNode::init() {
//partial_lh = NULL;
}
void PhyloNode::addNeighbor(Node *node, double length, int id) {
neighbors.push_back(new PhyloNeighbor(node, length, id));
}
int PhyloNode::computeSize(Node *dad) {
PhyloNeighbor *nei = (PhyloNeighbor*)dad->findNeighbor(this);
if (nei->size > 0)
return nei->size;
if (isLeaf()) {
nei->size = 1;
return nei->size;
}
nei->size = 0;
FOR_NEIGHBOR_IT(this, dad, it) {
nei->size += ((PhyloNode*)(*it)->node)->computeSize(this);
}
return nei->size;
}
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