4 char ConsensusChar(const ProfPos &PP)
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6 unsigned uMostCommonLetter = 0;
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7 FCOUNT fcMostCommon = PP.m_fcCounts[0];
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8 bool bMoreThanOneLetter = false;
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9 bool bAnyLetter = false;
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10 for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)
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12 const FCOUNT fc = PP.m_fcCounts[uLetter];
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16 bMoreThanOneLetter = true;
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19 if (fc > fcMostCommon)
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21 uMostCommonLetter = uLetter;
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27 char c = LetterToChar(uMostCommonLetter);
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28 if (bMoreThanOneLetter)
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29 return UnalignChar(c);
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33 SCORE ScoreProfPos2LA(const ProfPos &PPA, const ProfPos &PPB)
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36 for (unsigned n = 0; n < 20; ++n)
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38 const unsigned uLetter = PPA.m_uSortOrder[n];
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39 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
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42 Score += fcLetter*PPB.m_AAScores[uLetter];
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46 SCORE logScore = logf(Score);
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47 return (SCORE) ((logScore - g_scoreCenter)*(PPA.m_fOcc * PPB.m_fOcc));
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50 SCORE ScoreProfPos2NS(const ProfPos &PPA, const ProfPos &PPB)
\r
53 for (unsigned n = 0; n < 20; ++n)
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55 const unsigned uLetter = PPA.m_uSortOrder[n];
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56 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
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59 Score += fcLetter*PPB.m_AAScores[uLetter];
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61 return Score - g_scoreCenter;
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64 SCORE ScoreProfPos2SP(const ProfPos &PPA, const ProfPos &PPB)
\r
67 for (unsigned n = 0; n < 20; ++n)
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69 const unsigned uLetter = PPA.m_uSortOrder[n];
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70 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
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73 Score += fcLetter*PPB.m_AAScores[uLetter];
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75 return Score - g_scoreCenter;
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78 SCORE ScoreProfPos2SPN(const ProfPos &PPA, const ProfPos &PPB)
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81 for (unsigned n = 0; n < 4; ++n)
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83 const unsigned uLetter = PPA.m_uSortOrder[n];
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84 const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];
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87 Score += fcLetter*PPB.m_AAScores[uLetter];
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89 return Score - g_scoreCenter;
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92 SCORE ScoreProfPos2(const ProfPos &PPA, const ProfPos &PPB)
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94 if (PPSCORE_SP == g_PPScore)
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95 return ScoreProfPos2NS(PPA, PPB);
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96 else if (PPSCORE_LE == g_PPScore)
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97 return ScoreProfPos2LA(PPA, PPB);
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98 else if (PPSCORE_SV == g_PPScore)
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99 return ScoreProfPos2SP(PPA, PPB);
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100 else if (PPSCORE_SPN == g_PPScore)
\r
101 return ScoreProfPos2SPN(PPA, PPB);
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102 Quit("Invalid g_PPScore");
\r