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/***************************************************************************
* Copyright (C) 2009-2015 by *
* BUI Quang Minh <minh.bui@univie.ac.at> *
* Lam-Tung Nguyen <nltung@gmail.com> *
* *
* *
* 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. *
***************************************************************************/
#ifndef NODE_H
#define NODE_H
#include <vector>
#include <string>
#include <set>
#include <map>
#include <iostream>
#include <fstream>
#include <stdio.h>
#include <stdlib.h>
//#include <sys/time.h>
//#include <time.h>
#include <math.h>
#include "ncl/ncl.h"
#include "tools.h"
#include "split.h"
using namespace std;
/*--------------------------------------------------------------*/
class Node;
/**
Neighbor list of a node in the tree
*/
class Neighbor {
public:
/**
the other end of the branch
*/
Node *node;
/**
branch length
*/
double length;
/**
branch ID
*/
int id;
/**
* The set of taxa underneath the neighbor
*/
Split* split;
/**
construct class with a node and length
@param anode the other end of the branch
@param alength length of branch
*/
Neighbor(Node *anode, double alength) {
node = anode;
length = alength;
id = -1;
split = NULL;
}
/**
construct class with a node and length
@param anode the other end of the branch
@param alength length of branch
@param id branch ID
*/
Neighbor(Node *anode, double alength, int aid) {
node = anode;
length = alength;
id = aid;
split = NULL;
}
/**
construct class with another Neighbor
@param nei another Neighbor
*/
Neighbor(Neighbor *nei) {
node = nei->node;
length = nei->length;
id = nei->id;
split = NULL;
}
/**
destructor
*/
virtual ~Neighbor() {
}
};
/**
Neighbor vector
*/
typedef vector<Neighbor*> NeighborVec;
/**
Node vector
*/
typedef vector<Node*> NodeVector;
typedef pair<Node*, Node*> Branch;
typedef map<int, Branch> Branches;
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/**
A Node in the tree
@author BUI Quang Minh, Steffen Klaere, Arndt von Haeseler
*/
class Node {
public:
/**
node id.
*/
int id;
/**
node name
*/
string name;
/**
list of neighbors
*/
NeighborVec neighbors;
/**
the height of subtree rooted at this node, used for greedy algorithm
*/
double height;
/**
child of maximal height of subtree rooted at this node, used for greedy algorithm
*/
Neighbor *highestNei;
/**
* List of closest leaves to the current node.
*/
NodeVector closestLeaves;
/**
constructor
*/
Node() {
id = -1;
height = -1;
};
/**
constructor
@param aid id of this node
*/
Node(int aid);
/**
constructor
@param aid id of this node
@param aname name of this node
*/
Node(int aid, int aname);
/**
constructor
@param aid id of this node
@param aname name of this node
*/
Node(int aid, const char *aname);
/**
destructor
*/
virtual ~Node();
/**
used for the destructor
*/
virtual void deleteNode();
/**
@return true of this is a leaf
*/
bool isLeaf();
/**
* @return TRUE if this node is a leaf in a cherry
*/
bool isInCherry();
/**
@return TRUE if this node is a cherry, FALSE otherwise
*/
bool isCherry();
/**
@return the number of adjacent nodes
*/
int degree();
/** calculate the height of the subtree rooted at this node,
given the dad. Also return the lowestLeaf.
@param dad the dad of this node
@return the leaf at the lowest level. Also modify the height, highestNei of this class.
*/
Node *calcHeight(Node *dad = NULL);
/**
* Calculate the distance between 2 nodes. Only for binary tree.
* @param parner the other node
* @return the distance
*/
int calDist(Node *parner, Node *dad = NULL, int curLen = 0);
/** calculate the longest path in the subtree (version 2: more efficient)
@param node1 the returned node1 of the one end of the path
@param node2 the returned node2 of the one end of the path
@return the length of the longest path
*/
double longestPath2(Node* &node1, Node* &node2);
/**
@param node the target node
@return the iterator to the neighbor that has the node. If not found, return NULL
*/
Neighbor *findNeighbor(Node *node);
/**
* @brief check whether the two nodes are neighbors
* @param[in] node the other node
*/
bool isNeighbor(Node *node);
/**
@param node the target node
@return the iterator to the neighbor that has the node. If not found, return neighbors.end()
*/
NeighborVec::iterator findNeighborIt(Node *node);
/**
update the neighbor node with the newnode
@param node old neighbor node
@param newnode new neighbor node
@param newlen new length applied for the corresponding branch
*/
void updateNeighbor(Node* node, Node *newnode, double newlen);
/**
update the neighbor node with the newnode
@param node old neighbor node
@param newnode new neighbor node
@return length applied for the corresponding branch
*/
double updateNeighbor(Node* node, Node *newnode);
/**
update the neighbor node with the newnode
@param nei_it iterator to the neighbor
@param newnei new neighbor
*/
void updateNeighbor(NeighborVec::iterator nei_it, Neighbor *newnei);
/**
update the neighbor node with the newnode
@param nei_it iterator to the neighbor
@param newnei new neighbor
@param newlen new branch length
*/
void updateNeighbor(NeighborVec::iterator nei_it, Neighbor *newnei, double newlen);
/**
update the neighbor node with the newnode
@param node old neighbor node
@param newnei new neighbor
*/
void updateNeighbor(Node *node, Neighbor *newnei);
/**
update the neighbor node with the newnode
@param node old neighbor node
@param newnei new neighbor
@param newlen new branch length
*/
void updateNeighbor(Node *node, Neighbor *newnei, double newlen);
/**
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);
};
/*
class Branch {
public:
Node* node1;
Node* node2;
string key;
Branch(Node* node1, Node* node2) {
assert(node1->isNeighbor(node2));
assert(node2->isNeighbor(node1));
if (node1->id < node2->id) {
this->node1 = node1;
this->node2 = node2;
} else {
this->node1 = node2;
this->node2 = node1;
}
key = convertIntToString(this->node1->id) + convertIntToString(this->node2->id);
}
inline string getKey() {
return key;
}
};
*/
/*
some macros to transverse neighbors of a node
*/
#define FOR_NEIGHBOR(mynode, mydad, it) \
for (it = (mynode)->neighbors.begin(); it != (mynode)->neighbors.end(); it++) \
if ((*it)->node != (mydad))
#define FOR_NEIGHBOR_IT(mynode, mydad, it) \
for (NeighborVec::iterator it = (mynode)->neighbors.begin(); it != (mynode)->neighbors.end(); it++) \
if ((*it)->node != (mydad))
#define FOR_NEIGHBOR_DECLARE(mynode, mydad, it) \
NeighborVec::iterator it; \
for (it = (mynode)->neighbors.begin(); it != (mynode)->neighbors.end(); it++) \
if ((*it)->node != (mydad))
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/**
nodecmp, for pruning algorithm
*/
struct nodecmp {
/**
nodecmp, for pruning algorithm
*/
bool operator()(const Node* s1, const Node* s2) const {
return (s1->neighbors[0]->length) < (s2->neighbors[0]->length);
}
};
inline int nodenamecmp(const Node* a, const Node* b) {
return (a->name < b->name);
}
/**
set of leaves, sorted in ascending order by the length of the incident branch.
For pruning algorithm
*/
typedef multiset<Node*, nodecmp> LeafSet;
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/**
map from leaf name to node class
*/
typedef map<const string, Node*> LeafMapName;
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
/**
neighborcmp, for greedy algorithm
*/
struct neighborcmp {
/**
neighborcmp, for greedy algorithm
*/
bool operator()(const Neighbor* s1, const Neighbor* s2) const {
return ((s1->length + s1->node->height) > (s2->length + s2->node->height));
}
};
/**
set of branches, sorted in descending order by the height of the corresponding subtree.
For greedy algorithm.
*/
typedef multiset<Neighbor*, neighborcmp> NeighborSet;
#endif
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