4 SCORE ScoreSeqPairGaps(const MSA &msa1, unsigned uSeqIndex1,
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5 const MSA &msa2, unsigned uSeqIndex2);
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6 SCORE ScoreSeqPairLetters(const MSA &msa1, unsigned uSeqIndex1,
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7 const MSA &msa2, unsigned uSeqIndex2);
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8 SCORE ScoreGaps(const MSA &msa, const unsigned Cols[], unsigned ColCount);
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10 SCORE ObjScore(const MSA &msa, const unsigned SeqIndexes1[],
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11 unsigned uSeqCount1, const unsigned SeqIndexes2[], unsigned uSeqCount2);
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13 SCORE ObjScoreIds(const MSA &msa, const unsigned Ids1[],
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14 unsigned uCount1, const unsigned Ids2[], unsigned uCount2);
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16 void GetLetterScores(const MSA &msa, SCORE LetterScores[]);
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18 SCORE ObjScoreDP(const MSA &msa1, const MSA &msa2, SCORE MatchScore[] = 0);
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19 SCORE ObjScorePS(const MSA &msa, SCORE MatchScore[] = 0);
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20 SCORE ObjScoreSP(const MSA &msa, SCORE MatchScore[] = 0);
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21 SCORE ObjScoreXP(const MSA &msa, const MSA &msa2);
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22 SCORE ObjScoreSPDimer(const MSA &msa);
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23 SCORE ObjScoreDP_Profs(const ProfPos *PA, const ProfPos *PB, unsigned uColCount,
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24 SCORE MatchScore[] = 0);
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27 const MSA &msa1, const PWPath &Path1, const unsigned Edges1[], unsigned uEdgeCount1,
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28 const MSA &msa2, const PWPath &Path2, const unsigned Edges2[], unsigned uEdgeCount2);
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30 #endif // ObjScore_h
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