| 1 | #ifndef ObjScore_h |
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| 2 | #define ObjScore_h |
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| 3 | |
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| 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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| 9 | |
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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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| 12 | |
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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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| 15 | |
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| 16 | void GetLetterScores(const MSA &msa, SCORE LetterScores[]); |
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| 17 | |
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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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| 25 | |
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| 26 | SCORE DiffObjScore( |
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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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| 29 | |
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| 30 | #endif // ObjScore_h |
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