Project: s41467-024-54392-x | Function: Viterbi_PSSM (cpp)

system: You are an expert C++ programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow C++ best practices and maintain consistent code style.
Return **only** the complete C++ function code.

user: Complete this C++ function:

**DESCRIPTION:** Implements the Viterbi algorithm for aligning amino acid sequences to Position-Specific Scoring Matrices (PSSMs) to identify nifH genes using dynamic programming

**KEY TERMS:** {
  "PSSM": "Position-Specific Scoring Matrix for nifH",
  "Mrow": "match state scores",
  "Drow": "deletion state scores",
  "I0": "insertion state scores",
  "OpenA/OpenB": "gap opening penalties",
  "ExtA/ExtB": "gap extension penalties",
  "TraceBits": "traceback information for alignment",
  "LA/LB": "sequence/profile lengths"
}

**CONTEXT CODE:** #include "myutils.h"
#include "xdpmem.h"
#include "tracebit.h"
#include "pathinfo.h"
#include "alnparams.h"
#include "pssm.h"
#include <iostream>
#include <stdexcept>

void TraceBackBitMem(XDPMem &Mem, unsigned LA, unsigned LB, char State, PathInfo &PI);

// A is a.a. query seq
#include "myutils.h"
#include "xdpmem.h"
#include "tracebit.h"
#include "pathinfo.h"
#include "alnparams.h"
#include "pssm.h"
#include <iostream>
#include <stdexcept>

void TraceBackBitMem(XDPMem &Mem, unsigned LA, unsigned LB, char State, PathInfo &PI);

float Viterbi_PSSM(XDPMem &Mem, const char *A, unsigned LA,
  const PSSM &P, const AlnParams &AP, PathInfo &PI)
{
    Mem.Alloc(LA, LB);
    PI.Alloc(LA, LB);

    StartTimer(ViterbiFastMem);

    float OpenA = AP.LOpenA;
    float ExtA = AP.LExtA;

    float *Mrow = Mem.GetDPRow1();
    float *Drow = Mem.GetDPRow2();
    byte **TB = Mem.GetTBBit();

    Mrow[-1] = MINUS_INFINITY;
    for (unsigned j = 0; j <= LB; ++j)
    {
        Mrow[j] = MINUS_INFINITY;
        Drow[j] = MINUS_INFINITY;
    }

    float M0 = float (0);
    for (unsigned i = 0; i < LA; ++i)
    {
        byte a = A[i];
        float OpenB = AP.LOpenB;
        float ExtB = AP.LExtB;
        float I0 = MINUS_INFINITY;

        byte *TBrow = TB[i];
        for (unsigned j = 0; j < LB; ++j)
        {
            byte TraceBits = 0;
            float SavedM0 = M0;

            // MATCH
            {
                float xM = M0;
                if (Drow[j] > xM)
                {
                    xM = Drow[j];
                    TraceBits = TRACEBITS_DM;
                }
                if (I0 > xM)
                {
                    xM = I0;
                    TraceBits = TRACEBITS_IM;
                }
                M0 = Mrow[j];

                Mrow[j] = xM + P.GetScore1(j, a);
            }

            // DELETE
            {
                float md = SavedM0 + OpenB;
                Drow[j] += ExtB;
                if (md >= Drow[j])
                {
                    Drow[j] = md;
                    TraceBits |= TRACEBITS_MD;
                }
            }

            // INSERT
            {
                float mi = SavedM0 + OpenA;
                I0 += ExtA;
                if (mi >= I0)
                {
                    I0 = mi;
                    TraceBits |= TRACEBITS_MI;
                }
            }

            TBrow[j] = TraceBits;
            OpenB = AP.OpenB;
            ExtB = AP.ExtB;
        }
    }

    float Score = M0;
    for (unsigned j = 0; j < LB; ++j)
    {
        if (Mrow[j] > Score)
        {
            Score = Mrow[j];
            PI.SetEndPos(LA, j + 1, 'M');
        }
        if (Drow[j] > Score)
        {
            Score = Drow[j];
            PI.SetEndPos(LA, j, 'D');
        }
    }

    TraceBackBitMem(Mem, LA, LB, PI.GetEndState(), PI);
    return Score;
}


Complete the function implementation replacing "throw std::runtime_error("Not implemented");".