source: branches/stable/GDE/MUSCLE/src/hydro.cpp

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

extern void TomHydro(ProfPos *Prof, unsigned Length);

// Apply hydrophobicity heuristic to a profile
void Hydro(ProfPos *Prof, unsigned uLength)
        {
        if (ALPHA_Amino != g_Alpha)
                return;

        if (g_bTomHydro)
                {
                TomHydro(Prof, uLength);
                return;
                }

        if (0 == g_uHydrophobicRunLength)
                return;

        if (uLength <= g_uHydrophobicRunLength)
                return;

        unsigned uRunLength = 0;
        unsigned L2 = g_uHydrophobicRunLength/2;
        for (unsigned uColIndex = L2; uColIndex < uLength - L2; ++uColIndex)
                {
                ProfPos &PP = Prof[uColIndex];
                bool bHydro = IsHydrophobic(PP.m_fcCounts);
                if (bHydro)
                        {
                        ++uRunLength;
                        if (uRunLength >= g_uHydrophobicRunLength)
                                {
                                Prof[uColIndex-L2].m_scoreGapOpen *= (SCORE) g_dHydroFactor;
                                Prof[uColIndex-L2].m_scoreGapClose *= (SCORE) g_dHydroFactor;
                                }
                        }
                else
                        uRunLength = 0;
                }
        }