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/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include <iostream>
#include "RootedGuideTree.h"
#include "../../general/userparams.h"
using namespace std;
namespace clustalw
{
RootedGuideTree::RootedGuideTree()
: root(0){ }
RootedGuideTree::RootedGuideTree(Node* r)
: root(r) { }
RootedGuideTree::~RootedGuideTree()
{
root->makeEmpty();
}
void RootedGuideTree::setRoot(Node* r)
{
makeEmpty();
root = r;
}
void RootedGuideTree::makeEmpty()
{
root->makeEmpty();
}
void RootedGuideTree::orderNodes()
{
calcOrderNode(root);
}
int RootedGuideTree::calcOrderNode(Node* node)
{
if(node != 0)
{
if(node->getLeft() == 0 && node->getRight() == 0) // Leaf Node
{
node->setOrder(1);
return 1;
}
else // Internal node
{
node->setOrder(calcOrderNode(node->getLeft()) + calcOrderNode(node->getRight()));
return node->getOrder();
}
}
return 0;
}
void RootedGuideTree::calcSeqWeights(int firstSeq, int lastSeq, vector<int>* seqWeights)
{
if((int)seqWeights->size() < lastSeq - 1)
{
seqWeights->resize(lastSeq - 1);
}
int i = 0, _nSeqs = 0;
int temp = 0, sum = 0;
//
// If there are more than three sequences....
//
_nSeqs = lastSeq - firstSeq;
if ((_nSeqs >= 2) && (userParameters->getDistanceTree() == true) &&
(userParameters->getNoWeights() == false))
{
//
// Calculate sequence weights based on Phylip tree.
//
orderNodes();
calcWeights(seqWeights);
//
// Normalise the weights, such that the sum of the weights = INT_SCALE_FACTOR
//
sum = 0;
for (i = firstSeq; i < lastSeq; i++)
{
sum += (*seqWeights)[i];
}
if (sum == 0)
{
for (i = firstSeq; i < lastSeq; i++)
{
(*seqWeights)[i] = 1;
}
sum = i;
}
for (i = firstSeq; i < lastSeq; i++)
{
(*seqWeights)[i] = ((*seqWeights)[i] * INT_SCALE_FACTOR) / sum;
if ((*seqWeights)[i] < 1)
{
(*seqWeights)[i] = 1;
}
}
}
else
{
//
// Otherwise, use identity weights.
//
temp = INT_SCALE_FACTOR / _nSeqs;
// AW 2009-07-09: goes wrong if we have more than
// INT_SCALE_FACTOR seqs. if so, set to 1, just as above
// same as in Tree.cpp
if (temp < 1)
temp = 1;
for (i = firstSeq; i < lastSeq; i++)
{
(*seqWeights)[i] = temp;
}
}
}
void RootedGuideTree::calcWeights(vector<int>* seqWeights)
{
vector<float> weights;
int sizeSeqWeights = seqWeights->size();
weights.resize(sizeSeqWeights, 0.0);
doWeightCalc(0.0, &weights, root);
for(int i = 0; i < sizeSeqWeights; i++)
{
(*seqWeights)[i] = static_cast<int>(weights[i] * 100);
}
}
void RootedGuideTree::doWeightCalc(float weightSoFar, vector<float>* weights, Node* t)
{
if(t != 0)
{
if(t->getLeft() == 0 && t->getRight() == 0) // Leaf Node
{
(*weights)[t->getSeqNum() - 1] = weightSoFar;
}
else // Internal node
{
float w = weightSoFar + (t->getHeight() / t->getOrder());
doWeightCalc(w, weights, t->getLeft());
doWeightCalc(w, weights, t->getRight());
}
}
}
}
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