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//
// C++ Interface: 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
//
//
#ifndef PHYLONODE_H
#define PHYLONODE_H
#include "node.h"
typedef unsigned short UBYTE;
/**
A neighbor in a phylogenetic tree
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>
*/
class PhyloNeighbor : public Neighbor {
friend class PhyloNode;
friend class PhyloTree;
friend class IQTree;
friend class PhyloSuperTree;
friend class MemSlotVector;
public:
friend class TinaTree;
friend class PhyloSuperTreePlen;
/**
construct class with a node and length @param anode the other end of the branch
@param alength length of branch
*/
PhyloNeighbor(Node *anode, double alength) : Neighbor(anode, alength) {
partial_lh = NULL;
scale_num = NULL;
partial_lh_computed = 0;
lh_scale_factor = 0.0;
partial_pars = NULL;
size = 0;
}
/**
construct class with a node and length
@param anode the other end of the branch
@param alength length of branch
@param aid branch ID
*/
PhyloNeighbor(Node *anode, double alength, int aid) : Neighbor(anode, alength, aid) {
partial_lh = NULL;
scale_num = NULL;
partial_lh_computed = 0;
lh_scale_factor = 0.0;
partial_pars = NULL;
size = 0;
}
/**
tell that the partial likelihood vector is not computed
*/
inline void clearPartialLh() {
partial_lh_computed = 0;
}
/**
* tell that the partial likelihood vector is computed
*/
inline void unclearPartialLh() {
partial_lh_computed = 1;
}
/**
clear all partial likelihood recursively in forward direction
@param dad dad of this neighbor
*/
void clearForwardPartialLh(Node *dad);
/**
DEPRECATED, moved to PhyloTree
if partial_lh is NULL, reorient partial_lh (LM_PER_NODE technique)
@param dad dad of this neighbor
*/
// void reorientPartialLh(Node *dad);
/**
* For Upper Bounds analysis: get partial likelihood and lh scale factor
*/
double* get_partial_lh(){
return partial_lh;
}
double get_lh_scale_factor(){
return lh_scale_factor;
}
int get_partial_lh_computed(){
return partial_lh_computed;
}
int getSize() {
return size;
}
private:
/**
true if the partial likelihood was computed
*/
int partial_lh_computed;
/**
vector containing the partial likelihoods
*/
double *partial_lh;
/**
likelihood scaling factor
*/
double lh_scale_factor;
/**
vector containing number of scaling events per pattern // NEW!
*/
UBYTE *scale_num;
/**
vector containing the partial parsimony scores
*/
UINT *partial_pars;
/** size of subtree below this neighbor in terms of number of taxa */
int size;
};
/**
A node in a phylogenetic tree
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>
*/
class PhyloNode : public Node {
friend class PhyloTree;
public:
/**
constructor
*/
PhyloNode();
/**
constructor
@param aid id of this node
*/
PhyloNode(int aid);
/**
constructor
@param aid id of this node
@param aname name of this node
*/
PhyloNode(int aid, int aname);
/**
constructor
@param aid id of this node
@param aname name of this node
*/
PhyloNode(int aid, const char *aname);
/**
initialization
*/
void init();
/**
add a neighbor
@param node the neighbor node
@param length branch length
@param id branch ID
*/
virtual void addNeighbor(Node *node, double length, int id = -1);
/**
tell that all partial likelihood vectors below this node are not computed
*/
void clearAllPartialLh(bool make_null, PhyloNode *dad);
/**
tell that all partial likelihood vectors (in reverse direction) below this node are not computed
*/
void clearReversePartialLh(PhyloNode *dad);
void computeReversePartialLh(PhyloNode *dad);
/**
compute the size (#taxa) of the subtree rooted at this node
using buffered 'size' attribute if computed beforehand
@param dad dad of this node
*/
int computeSize(Node *dad);
};
/**
Node vector
*/
typedef vector<PhyloNode*> PhyloNodeVector;
#endif
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