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#include "muscle.h"
#include "tree.h"
#include "msa.h"
/***
Compute weights by the CLUSTALW method.
Thompson, Higgins and Gibson (1994), CABIOS (10) 19-29;
see also CLUSTALW paper.
Weights are computed from the edge lengths of a rooted tree.
Define the strength of an edge to be its length divided by the number
of leaves under that edge. The weight of a sequence is then the sum
of edge strengths on the path from the root to the leaf.
Example.
0.2
-----A 0.1
-x ------- B 0.7
--------y ----------- C
0.3 ----------z
0.4 -------------- D
0.8
Edge Length Leaves Strength
---- ----- ------ --------
xy 0.3 3 0.1
xA 0.2 1 0.2
yz 0.4 2 0.2
yB 0.1 1 0.1
zC 0.7 1 0.7
zD 0.8 1 0.8
Leaf Path Strengths Weight
---- ---- --------- ------
A xA 0.2 0.2
B xy-yB 0.1 + 0.1 0.2
C xy-yz-zC 0.1 + 0.2 + 0.7 1.0
D xy-yz-zD 0.1 + 0.2 + 0.8 1.1
***/
#define TRACE 0
static unsigned CountLeaves(const Tree &tree, unsigned uNodeIndex,
unsigned LeavesUnderNode[])
{
if (tree.IsLeaf(uNodeIndex))
{
LeavesUnderNode[uNodeIndex] = 1;
return 1;
}
const unsigned uLeft = tree.GetLeft(uNodeIndex);
const unsigned uRight = tree.GetRight(uNodeIndex);
const unsigned uRightCount = CountLeaves(tree, uRight, LeavesUnderNode);
const unsigned uLeftCount = CountLeaves(tree, uLeft, LeavesUnderNode);
const unsigned uCount = uRightCount + uLeftCount;
LeavesUnderNode[uNodeIndex] = uCount;
return uCount;
}
void CalcClustalWWeights(const Tree &tree, WEIGHT Weights[])
{
#if TRACE
Log("CalcClustalWWeights\n");
tree.LogMe();
#endif
const unsigned uLeafCount = tree.GetLeafCount();
if (0 == uLeafCount)
return;
else if (1 == uLeafCount)
{
Weights[0] = (WEIGHT) 1.0;
return;
}
else if (2 == uLeafCount)
{
Weights[0] = (WEIGHT) 0.5;
Weights[1] = (WEIGHT) 0.5;
return;
}
if (!tree.IsRooted())
Quit("CalcClustalWWeights requires rooted tree");
const unsigned uNodeCount = tree.GetNodeCount();
unsigned *LeavesUnderNode = new unsigned[uNodeCount];
memset(LeavesUnderNode, 0, uNodeCount*sizeof(unsigned));
const unsigned uRootNodeIndex = tree.GetRootNodeIndex();
unsigned uLeavesUnderRoot = CountLeaves(tree, uRootNodeIndex, LeavesUnderNode);
if (uLeavesUnderRoot != uLeafCount)
Quit("WeightsFromTreee: Internal error, root count %u %u",
uLeavesUnderRoot, uLeafCount);
#if TRACE
Log("Node Leaves Length Strength\n");
Log("---- ------ -------- --------\n");
// 1234 123456 12345678 12345678
#endif
double *Strengths = new double[uNodeCount];
for (unsigned uNodeIndex = 0; uNodeIndex < uNodeCount; ++uNodeIndex)
{
if (tree.IsRoot(uNodeIndex))
{
Strengths[uNodeIndex] = 0.0;
continue;
}
const unsigned uParent = tree.GetParent(uNodeIndex);
const double dLength = tree.GetEdgeLength(uNodeIndex, uParent);
const unsigned uLeaves = LeavesUnderNode[uNodeIndex];
const double dStrength = dLength / (double) uLeaves;
Strengths[uNodeIndex] = dStrength;
#if TRACE
Log("%4u %6u %8g %8g\n", uNodeIndex, uLeaves, dLength, dStrength);
#endif
}
#if TRACE
Log("\n");
Log(" Seq Path..Weight\n");
Log("-------------------- ------------\n");
#endif
for (unsigned n = 0; n < uLeafCount; ++n)
{
const unsigned uLeafNodeIndex = tree.LeafIndexToNodeIndex(n);
#if TRACE
Log("%20.20s %4u ", tree.GetLeafName(uLeafNodeIndex), uLeafNodeIndex);
#endif
if (!tree.IsLeaf(uLeafNodeIndex))
Quit("CalcClustalWWeights: leaf");
double dWeight = 0;
unsigned uNode = uLeafNodeIndex;
while (!tree.IsRoot(uNode))
{
dWeight += Strengths[uNode];
uNode = tree.GetParent(uNode);
#if TRACE
Log("->%u(%g)", uNode, Strengths[uNode]);
#endif
}
if (dWeight < 0.0001)
{
#if TRACE
Log("zero->one");
#endif
dWeight = 1.0;
}
Weights[n] = (WEIGHT) dWeight;
#if TRACE
Log(" = %g\n", dWeight);
#endif
}
delete[] Strengths;
delete[] LeavesUnderNode;
Normalize(Weights, uLeafCount);
}
void MSA::SetClustalWWeights(const Tree &tree)
{
const unsigned uSeqCount = GetSeqCount();
const unsigned uLeafCount = tree.GetLeafCount();
WEIGHT *Weights = new WEIGHT[uSeqCount];
CalcClustalWWeights(tree, Weights);
for (unsigned n = 0; n < uLeafCount; ++n)
{
const WEIGHT w = Weights[n];
const unsigned uLeafNodeIndex = tree.LeafIndexToNodeIndex(n);
const unsigned uId = tree.GetLeafId(uLeafNodeIndex);
const unsigned uSeqIndex = GetSeqIndex(uId);
#if DEBUG
if (GetSeqName(uSeqIndex) != tree.GetLeafName(uLeafNodeIndex))
Quit("MSA::SetClustalWWeights: names don't match");
#endif
SetSeqWeight(uSeqIndex, w);
}
NormalizeWeights((WEIGHT) 1.0);
delete[] Weights;
}
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