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#include "libMUSCLE/muscle.h"
#include "libMUSCLE/profile.h"
namespace muscle {
extern void TomHydro(ProfPos *Prof, unsigned Length);
// Apply hydrophobicity heuristic to a profile
void Hydro(ProfPos *Prof, unsigned uLength)
{
if (ALPHA_Amino != g_Alpha.get())
return;
if (g_bTomHydro.get())
{
TomHydro(Prof, uLength);
return;
}
if (0 == g_uHydrophobicRunLength.get())
return;
if (uLength <= g_uHydrophobicRunLength.get())
return;
unsigned uRunLength = 0;
unsigned L2 = g_uHydrophobicRunLength.get()/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.get())
{
Prof[uColIndex-L2].m_scoreGapOpen *= (SCORE) g_dHydroFactor.get();
Prof[uColIndex-L2].m_scoreGapClose *= (SCORE) g_dHydroFactor.get();
}
}
else
uRunLength = 0;
}
}
}
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