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

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

SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,
  bool bLockLeft, bool bLockRight)
        {
        const unsigned uLengthA = msa1.GetColCount();
        const unsigned uLengthB = msa2.GetColCount();

        ProfPos *PA = ProfileFromMSA(msa1);
        ProfPos *PB = ProfileFromMSA(msa2);

        if (bLockLeft)
                {
                PA[0].m_scoreGapOpen = MINUS_INFINITY;
                PB[0].m_scoreGapOpen = MINUS_INFINITY;
                }

        if (bLockRight)
                {
                PA[uLengthA-1].m_scoreGapClose = MINUS_INFINITY;
                PB[uLengthB-1].m_scoreGapClose = MINUS_INFINITY;
                }

        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);

        AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);

        delete[] PA;
        delete[] PB;

        return Score;
        }