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

#include "muscle.h"
#include "msa.h"
#include "profile.h"
#include "pwpath.h"

SCORE GlobalAlign4(ProfPos *PA, unsigned uLengthA, ProfPos *PB,
  unsigned uLengthB, PWPath &Path);

SCORE AlignTwoProfs(
  const ProfPos *PA, unsigned uLengthA, WEIGHT wA,
  const ProfPos *PB, unsigned uLengthB, WEIGHT wB,
  PWPath &Path, ProfPos **ptrPout, unsigned *ptruLengthOut)
        {
        assert(uLengthA < 100000);
        assert(uLengthB < 100000);

        float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0
        if (r < 1)
                r = 1/r;

        SCORE Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);

        AlignTwoProfsGivenPath(Path, PA, uLengthB, wA/(wA + wB), PB, uLengthB, wB/(wA + wB),
          ptrPout, ptruLengthOut);

#if     HYDRO
        if (ALPHA_Amino == g_Alpha)
                Hydro(*ptrPout, *ptruLengthOut);
#endif
        return Score;
        }