source: branches/lib/GDE/MUSCLE/src/henikoffweight.cpp

#include "muscle.h"
#include "msa.h"

/***
Compute Henikoff weights.
Steven Henikoff and Jorja G. Henikoff (1994), Position-based sequence weights.
J. Mol. Biol., 243(4):574-578.

Award each different residue an equal share of the weight, and then to divide up
that weight equally among the sequences sharing the same residue. So if in a
position of a multiple alignment, r different residues are represented, a residue
represented in only one sequence contributes a score of 1/r to that sequence, whereas a
residue represented in s sequences contributes a score of 1/rs to each of the s
sequences. For each sequence, the contributions from each position are summed to give
a sequence weight.

See also HenikoffWeightPB.
***/

void MSA::CalcHenikoffWeightsCol(unsigned uColIndex) const
        {
        const unsigned uSeqCount = GetSeqCount();

// Compute letter counts in this column
        unsigned uLetterCount[MAX_ALPHA];
        memset(uLetterCount, 0, sizeof(uLetterCount));
        unsigned uDifferentLetterCount = 0;
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                {
                unsigned uLetter = GetLetterEx(uSeqIndex, uColIndex);
                if (uLetter >= 20)
                        continue;
                unsigned uNewCount = uLetterCount[uLetter] + 1;
                uLetterCount[uLetter] = uNewCount;
                if (1 == uNewCount)
                        ++uDifferentLetterCount;
                }

// Compute weight contributions
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                {
                unsigned uLetter = GetLetterEx(uSeqIndex, uColIndex);
                if (uLetter >= 20)
                        continue;
                const unsigned uCount = uLetterCount[uLetter];
                unsigned uDenom = uCount*uDifferentLetterCount;
                if (uDenom == 0)
                        continue;
                m_Weights[uSeqIndex] += (WEIGHT) (1.0/uDenom);
                }
        }

void MSA::SetHenikoffWeights() const
        {
        const unsigned uColCount = GetColCount();
        const unsigned uSeqCount = GetSeqCount();

        if (0 == uSeqCount)
                return;
        else if (1 == uSeqCount)
                {
                m_Weights[0] = (WEIGHT) 1.0;
                return;
                }
        else if (2 == uSeqCount)
                {
                m_Weights[0] = (WEIGHT) 0.5;
                m_Weights[1] = (WEIGHT) 0.5;
                return;
                }

        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                m_Weights[uSeqIndex] = 0.0;

        for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)
                CalcHenikoffWeightsCol(uColIndex);

// Set all-gap seqs weight to 0
        for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)
                if (IsGapSeq(uSeqIndex))
                        m_Weights[uSeqIndex] = 0.0;

        Normalize(m_Weights, uSeqCount);
        }