6 double GetScoreDist(const MSA &msa, unsigned SeqIndex1, unsigned SeqIndex2);
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11 MSADist(DISTANCE Distance)
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13 m_Distance = Distance;
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16 double ComputeDist(const MSA &msa, unsigned uSeqIndex1, unsigned uSeqIndex2)
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18 if (m_Distance == DISTANCE_ScoreDist)
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19 return GetScoreDist(msa, uSeqIndex1, uSeqIndex2);
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21 double dPctId = msa.GetPctIdentityPair(uSeqIndex1, uSeqIndex2);
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24 case DISTANCE_PctIdKimura:
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25 return KimuraDist(dPctId);
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26 case DISTANCE_PctIdLog:
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29 return -log(dPctId);
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31 Quit("MSADist::ComputeDist, invalid DISTANCE_%u", m_Distance);
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36 DISTANCE m_Distance;
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