source: tags/arb-6.0/GDE/MAFFT/mafft-7.055-with-extensions/extensions/mxscarna_src/AlifoldMEA.cpp

#include "AlifoldMEA.h"

namespace MXSCARNA{

const int AlifoldMEA::TURN = 3;

void
AlifoldMEA::
Run()
{
    makeProfileBPPMatrix(alignment);
    Initialization();
    DP();
    TraceBack();
}

void
AlifoldMEA::
makeProfileBPPMatrix(const MultiSequence *Sequences)
{
    int length = Sequences->GetSequence(0)->GetLength();

    Trimat<float> *consBppMat = new Trimat<float>(length + 1);
    fill(consBppMat->begin(), consBppMat->end(), 0);

    for(int i = 1; i <= length; i++) 
        for (int j = i; j <= length; j++) 
            bppMat.ref(i, j) = 0;


    int number = Sequences->GetNumSequences();
    for(int seqNum = 0; seqNum < number; seqNum++) {
        SafeVector<int> *tmpMap = Sequences->GetSequence(seqNum)->GetMappingNumber();
        int label = Sequences->GetSequence(seqNum)->GetLabel();
        BPPMatrix *tmpBppMatrix = BPPMatrices[label];
        
        for(int i = 1; i <= length ; i++) {
            int originI = tmpMap->at(i);
            for(int j = i; j <= length; j++) {
                int originJ = tmpMap->at(j);
                if(originI != 0 && originJ != 0) {
                    float tmpProb = tmpBppMatrix->GetProb(originI, originJ);
                    bppMat.ref(i, j) += tmpProb;
                }
            }
        }
    }

        /* compute the mean of base pairing probability  */
    for(int i = 1; i <= length; i++) {
        for(int j = i; j <= length; j++) {
            bppMat.ref(i,j) = bppMat.ref(i,j)/(float)number;
        }
    }

    for (int i = 1; i <= length; i++) {
        float sum = 0;
        for (int j = i; j <= length; j++) {
            sum += bppMat.ref(i,j);
        }
        Qi[i] = 1 - sum;
    }

    for (int i = 1; i <= length; i++) {
        float sum = 0;
        for (int j = i; j >= 1; j--) {
            sum += bppMat.ref(j, i);
        }
        Qj[i] = 1 - sum;
    }
}

void
AlifoldMEA::
Initialization()
{
    int length = alignment->GetSequence(0)->GetLength();

    for (int i = 1; i <= length; i++) {
        for (int j = i; j <= length; j++) {
            M.ref(i,j) = 0;
            traceI.ref(i,j) = 0;
            traceJ.ref(i,j) = 0;
        }
    }

    for (int i = 1; i <= length; i++) {
        M.ref(i,i)   = Qi[i]; 
        traceI.ref(i,i) = 0;
        traceJ.ref(i,i) = 0;
    }

    for (int i = 1; i <= length - 1; i++) {
        M.ref(i, i+1) =  Qi[i+1];
        traceI.ref(i,i + 1) = 0;
        traceJ.ref(i,i + 1) = 0;
    }

    for (int i = 0; i <= length; i++) {
        ssCons[i] = '.';
    }
}

void
AlifoldMEA::
DP()
{
    float g    = BasePairConst; // see scarna.hpp
    int length = alignment->GetSequence(0)->GetLength();
    
    for (int i = length - 1; i >= 1; i--) {
        for (int j = i + TURN + 1; j <= length; j++) {
            float qi       = Qi[i];
            float qj       = Qj[j];
            float p        = bppMat.ref(i,j);

            
            float maxScore = qi + M.ref(i+1, j);
            int tmpI = i+1;
            int tmpJ = j;
            
            float tmpScore = qj + M.ref(i, j-1);
            if (tmpScore > maxScore) {
                maxScore = tmpScore;
                tmpI     = i;
                tmpJ     = j - 1;
            }
            
            tmpScore = g*2*p + M.ref(i+1, j-1);
            if (tmpScore > maxScore) {
                maxScore = tmpScore;
                tmpI     = i + 1;
                tmpJ     = j - 1;
            }
            
            for (int k = i + 1; k < j - 1; k++) {
                tmpScore = M.ref(i,k) + M.ref(k+1,j);
                if (tmpScore > maxScore) {
                    maxScore = tmpScore;
                    tmpI = i;
                    tmpJ = j;
                }
            }
            M.ref(i,j)       = maxScore;
            traceI.ref(i, j) = tmpI;
            traceJ.ref(i, j) = tmpJ;
        }
    }
}

void
AlifoldMEA::
TraceBack()
{

    int length = alignment->GetSequence(0)->GetLength();
    SafeVector<int> stackI((length + 1)*(length+1));
    SafeVector<int> stackJ((length + 1)*(length+1));
    int pt = 0;

    stackI[pt] = traceI.ref(1, length);
    stackJ[pt] = traceJ.ref(1, length);
    ++pt;
    
    while(pt != 0) {
        --pt;
        int tmpI = stackI[pt];
        int tmpJ = stackJ[pt];
        int nextI = traceI.ref(tmpI, tmpJ);
        int nextJ = traceJ.ref(tmpI, tmpJ);

        if (tmpI < tmpJ) {
            if (tmpI + 1  == nextI && tmpJ == nextJ) {
                stackI[pt] = nextI;
                stackJ[pt] = nextJ;
                ++pt;
            }
            else if (tmpI == nextI && tmpJ - 1 == nextJ) {
                stackI[pt] = nextI;
                stackJ[pt] = nextJ;
                ++pt;
            }
            else if (tmpI + 1 == nextI && tmpJ - 1== nextJ) {
                stackI[pt] = nextI;
                stackJ[pt] = nextJ;
                ++pt;
                ssCons[tmpI] = '(';
                ssCons[tmpJ] = ')';
            }
            else if (tmpI == nextI && tmpJ == nextJ) {
                float maxScore = IMPOSSIBLE;
                int maxK = 0;

                for (int k = tmpI + 1; k < tmpJ - 1; k++) {
                    float tmpScore = M.ref(tmpI,k) + M.ref(k+1,tmpJ);
                    if (tmpScore > maxScore) {
                        maxScore = tmpScore;
                        maxK = k;
                    }
                }
                stackI[pt] = traceI.ref(tmpI, maxK);
                stackJ[pt] = traceJ.ref(tmpI, maxK);
                ++pt;
                stackI[pt] = traceI.ref(maxK+1, tmpJ);
                stackJ[pt] = traceJ.ref(maxK+1, tmpJ);
                ++pt;
            }
        }
    }
}
}