| 1 | // source code generated by dimer.py |
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| 2 | |
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| 3 | static SCORE GapScoreMM(const ProfPos &PPA, const ProfPos &PPB) |
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| 4 | { |
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| 5 | return |
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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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| 9 | } |
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| 10 | |
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| 11 | static SCORE GapScoreMD(const ProfPos &PPA, const ProfPos &PPB) |
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| 12 | { |
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| 13 | return |
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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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| 17 | } |
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| 18 | |
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| 19 | static SCORE GapScoreMI(const ProfPos &PPA, const ProfPos &PPB) |
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| 20 | { |
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| 21 | return |
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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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| 25 | } |
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| 26 | |
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| 27 | static SCORE GapScoreDM(const ProfPos &PPA, const ProfPos &PPB) |
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| 28 | { |
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| 29 | return |
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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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| 33 | } |
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| 34 | |
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| 35 | static SCORE GapScoreDD(const ProfPos &PPA, const ProfPos &PPB) |
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| 36 | { |
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| 37 | return |
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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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| 40 | } |
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| 41 | |
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| 42 | static SCORE GapScoreDI(const ProfPos &PPA, const ProfPos &PPB) |
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| 43 | { |
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| 44 | return |
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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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| 47 | } |
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| 48 | |
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| 49 | static SCORE GapScoreIM(const ProfPos &PPA, const ProfPos &PPB) |
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| 50 | { |
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| 51 | return |
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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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| 55 | } |
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| 56 | |
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| 57 | static SCORE GapScoreID(const ProfPos &PPA, const ProfPos &PPB) |
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| 58 | { |
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| 59 | return |
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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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| 62 | } |
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| 63 | |
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| 64 | static SCORE GapScoreII(const ProfPos &PPA, const ProfPos &PPB) |
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| 65 | { |
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| 66 | return |
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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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| 69 | } |
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