1 // source code generated by dimer.py
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3 static SCORE GapScoreMM(const ProfPos &PPA, const ProfPos &PPB)
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6 g_scoreGapOpen*(PPA.m_LL*PPB.m_LG + PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_LG) +
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7 g_scoreGapExtend*(PPA.m_LL*PPB.m_GG + PPA.m_GG*PPB.m_LL) +
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8 g_scoreGapAmbig*(PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_GL);
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11 static SCORE GapScoreMD(const ProfPos &PPA, const ProfPos &PPB)
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14 g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
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15 g_scoreGapExtend*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG) +
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16 g_scoreGapAmbig*(PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG);
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19 static SCORE GapScoreMI(const ProfPos &PPA, const ProfPos &PPB)
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22 g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
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23 g_scoreGapExtend*(PPA.m_LG*PPB.m_LL + PPA.m_GG*PPB.m_LL) +
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24 g_scoreGapAmbig*(PPA.m_LG*PPB.m_GL + PPA.m_GG*PPB.m_GL);
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27 static SCORE GapScoreDM(const ProfPos &PPA, const ProfPos &PPB)
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30 g_scoreGapOpen*(PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL) +
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31 g_scoreGapExtend*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG) +
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32 g_scoreGapAmbig*(PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_LL + PPA.m_GG*PPB.m_GL);
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35 static SCORE GapScoreDD(const ProfPos &PPA, const ProfPos &PPB)
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38 g_scoreGapExtend*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GL + PPA.m_LL*PPB.m_GG) +
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39 g_scoreGapAmbig*(PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GL + PPA.m_GL*PPB.m_GG);
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42 static SCORE GapScoreDI(const ProfPos &PPA, const ProfPos &PPB)
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45 g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
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46 g_scoreGapAmbig*(PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL + PPA.m_GG*PPB.m_LL + PPA.m_GG*PPB.m_GL);
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49 static SCORE GapScoreIM(const ProfPos &PPA, const ProfPos &PPB)
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52 g_scoreGapOpen*(PPA.m_LL*PPB.m_LG + PPA.m_GL*PPB.m_LG) +
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53 g_scoreGapExtend*(PPA.m_LG*PPB.m_LL + PPA.m_GG*PPB.m_LL) +
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54 g_scoreGapAmbig*(PPA.m_LL*PPB.m_GG + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_GL);
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57 static SCORE GapScoreID(const ProfPos &PPA, const ProfPos &PPB)
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60 g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +
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61 g_scoreGapAmbig*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG + PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG);
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64 static SCORE GapScoreII(const ProfPos &PPA, const ProfPos &PPB)
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67 g_scoreGapExtend*(PPA.m_LL*PPB.m_LL + PPA.m_LG*PPB.m_LL + PPA.m_GL*PPB.m_LL + PPA.m_GG*PPB.m_LL) +
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68 g_scoreGapAmbig*(PPA.m_LL*PPB.m_GL + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_GL + PPA.m_GG*PPB.m_GL);
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