source: branches/alilink/GDE/MUSCLE/src/scorepp.cpp

#include "muscle.h"
#include "profile.h"

char ConsensusChar(const ProfPos &PP)
        {
        unsigned uMostCommonLetter = 0;
        FCOUNT fcMostCommon = PP.m_fcCounts[0];
        bool bMoreThanOneLetter = false;
        bool bAnyLetter = false;
        for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)
                {
                const FCOUNT fc = PP.m_fcCounts[uLetter];
                if (fc > 0)
                        {
                        if (bAnyLetter)
                                bMoreThanOneLetter = true;
                        bAnyLetter = true;
                        }
                if (fc > fcMostCommon)
                        {
                        uMostCommonLetter = uLetter;
                        fcMostCommon = fc;
                        }
                }
        if (!bAnyLetter)
                return '-';
        char c = LetterToChar(uMostCommonLetter);
        if (bMoreThanOneLetter)
                return UnalignChar(c);
        return c;
        }

SCORE ScoreProfPos2LA(const ProfPos &PPA, const ProfPos &PPB)
        {
        SCORE Score = 0;
        for (unsigned n = 0; n < 20; ++n)
                {
                const unsigned uLetter = PPA.m_uSortOrder[n];
                const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
                if (0 == fcLetter)
                        break;
                Score += fcLetter*PPB.m_AAScores[uLetter];
                }
        if (0 == Score)
                return -2.5;
        SCORE logScore = logf(Score);
        return (SCORE) ((logScore - g_scoreCenter)*(PPA.m_fOcc * PPB.m_fOcc));
        }

SCORE ScoreProfPos2NS(const ProfPos &PPA, const ProfPos &PPB)
        {
        SCORE Score = 0;
        for (unsigned n = 0; n < 20; ++n)
                {
                const unsigned uLetter = PPA.m_uSortOrder[n];
                const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
                if (0 == fcLetter)
                        break;
                Score += fcLetter*PPB.m_AAScores[uLetter];
                }
        return Score - g_scoreCenter;
        }

SCORE ScoreProfPos2SP(const ProfPos &PPA, const ProfPos &PPB)
        {
        SCORE Score = 0;
        for (unsigned n = 0; n < 20; ++n)
                {
                const unsigned uLetter = PPA.m_uSortOrder[n];
                const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
                if (0 == fcLetter)
                        break;
                Score += fcLetter*PPB.m_AAScores[uLetter];
                }
        return Score - g_scoreCenter;
        }

SCORE ScoreProfPos2SPN(const ProfPos &PPA, const ProfPos &PPB)
        {
        SCORE Score = 0;
        for (unsigned n = 0; n < 4; ++n)
                {
                const unsigned uLetter = PPA.m_uSortOrder[n];
                const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
                if (0 == fcLetter)
                        break;
                Score += fcLetter*PPB.m_AAScores[uLetter];
                }
        return Score - g_scoreCenter;
        }

SCORE ScoreProfPos2(const ProfPos &PPA, const ProfPos &PPB)
        {
        if (PPSCORE_SP == g_PPScore)
                return ScoreProfPos2NS(PPA, PPB);
        else if (PPSCORE_LE == g_PPScore)
                return ScoreProfPos2LA(PPA, PPB);
        else if (PPSCORE_SV == g_PPScore)
                return ScoreProfPos2SP(PPA, PPB);
        else if (PPSCORE_SPN == g_PPScore)
                return ScoreProfPos2SPN(PPA, PPB);
        Quit("Invalid g_PPScore");
        return 0;
        }