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//
// phylonodemixlen.h
// iqtree
//
// Created by Minh Bui on 24/08/15.
//
//
#ifndef __iqtree__phylonodemixlen__
#define __iqtree__phylonodemixlen__
#include <stdio.h>
#include "phylonode.h"
/**
A neighbor in a phylogenetic tree with mixture branch lengths
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>
*/
class PhyloNeighborMixlen : public PhyloNeighbor {
public:
/**
construct class with a node and length
@param anode the other end of the branch
@param alength length of branch
@param aid branch ID
*/
PhyloNeighborMixlen(Node *anode, double alength, int aid = -1) : PhyloNeighbor(anode, alength, aid) {
lengths.clear();
}
PhyloNeighborMixlen(Node *anode, DoubleVector &alength, int aid = -1) : PhyloNeighbor(anode, -1.0, aid) {
lengths = alength;
if (!lengths.empty()) {
length = 0.0;
for (int i = 0; i < lengths.size(); i++)
length += lengths[i];
length /= lengths.size();
}
}
/** branch lengths for mixture */
DoubleVector lengths;
/**
get branch length for a mixture class c, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@param c class index
@return branch length for class c
*/
virtual double getLength(int c) {
if (lengths.empty())
return length;
ASSERT(c < lengths.size());
return lengths[c];
}
/**
get branch lengths, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@return branch length for class c
*/
virtual void getLength(DoubleVector &vec) {
vec = lengths;
}
/**
get branch lengths, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@param vec (OUT) destination branch length vector
@param start_pos starting position in vec to copy to
*/
virtual void getLength(DoubleVector &vec, int start_pos) {
ASSERT(start_pos+lengths.size() <= vec.size());
for (int i = 0; i < lengths.size(); i++)
vec[start_pos+i] = lengths[i];
}
/**
set branch length for a mixture class c, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@param c class index
@return branch length for class c
*/
virtual void setLength(int c, double len) {
if (lengths.empty()) {
length = len;
return;
}
ASSERT(c < lengths.size());
lengths[c] = len;
}
/**
get branch lengths, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@return branch length for class c
*/
virtual void setLength(DoubleVector &vec) {
lengths = vec;
}
/**
set branch length by length of a Neighbor, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@param nei source neigbor to copy branch lengths
@return branch length for class c
*/
virtual void setLength(Neighbor *nei) {
length = nei->length;
lengths = ((PhyloNeighborMixlen*)nei)->lengths;
}
/**
set branch lengths, used by heterotachy model (PhyloNeighborMixlen)
the default is just to return a single branch length
@param vec source branch length vector
@param start_pos starting position in vec to copy from
*/
virtual void setLength(DoubleVector &vec, int start_pos, int num_elem) {
ASSERT(start_pos+num_elem <= vec.size());
lengths.clear();
lengths.insert(lengths.begin(), vec.begin()+start_pos, vec.begin()+start_pos+num_elem);
}
protected:
};
class PhyloNodeMixlen : public PhyloNode {
public:
/**
constructor
*/
PhyloNodeMixlen() : PhyloNode() {}
/**
constructor
@param aid id of this node
*/
PhyloNodeMixlen(int aid) : PhyloNode(aid) {}
/**
constructor
@param aid id of this node
@param aname name of this node
*/
PhyloNodeMixlen(int aid, int aname) : PhyloNode(aid, aname) {}
/**
constructor
@param aid id of this node
@param aname name of this node
*/
PhyloNodeMixlen(int aid, const char *aname) : PhyloNode(aid, aname) {}
/**
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);
/**
add a neighbor for heterotachy model
@param node the neighbor node
@param length branch length
@param id branch ID
*/
virtual void addNeighbor(Node *node, DoubleVector &length, int id = -1);
protected:
};
#endif /* defined(__iqtree__phylonodemixlen__) */
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