+++ /dev/null
-#ifndef ObjScore_h\r
-#define ObjScore_h\r
-\r
-SCORE ScoreSeqPairGaps(const MSA &msa1, unsigned uSeqIndex1,\r
- const MSA &msa2, unsigned uSeqIndex2);\r
-SCORE ScoreSeqPairLetters(const MSA &msa1, unsigned uSeqIndex1,\r
- const MSA &msa2, unsigned uSeqIndex2);\r
-SCORE ScoreGaps(const MSA &msa, const unsigned Cols[], unsigned ColCount);\r
-\r
-SCORE ObjScore(const MSA &msa, const unsigned SeqIndexes1[],\r
- unsigned uSeqCount1, const unsigned SeqIndexes2[], unsigned uSeqCount2);\r
-\r
-SCORE ObjScoreIds(const MSA &msa, const unsigned Ids1[],\r
- unsigned uCount1, const unsigned Ids2[], unsigned uCount2);\r
-\r
-void GetLetterScores(const MSA &msa, SCORE LetterScores[]);\r
-\r
-SCORE ObjScoreDP(const MSA &msa1, const MSA &msa2, SCORE MatchScore[] = 0);\r
-SCORE ObjScorePS(const MSA &msa, SCORE MatchScore[] = 0);\r
-SCORE ObjScoreSP(const MSA &msa, SCORE MatchScore[] = 0);\r
-SCORE ObjScoreXP(const MSA &msa, const MSA &msa2);\r
-SCORE ObjScoreSPDimer(const MSA &msa);\r
-SCORE ObjScoreDP_Profs(const ProfPos *PA, const ProfPos *PB, unsigned uColCount,\r
- SCORE MatchScore[] = 0);\r
-\r
-SCORE DiffObjScore(\r
- const MSA &msa1, const PWPath &Path1, const unsigned Edges1[], unsigned uEdgeCount1, \r
- const MSA &msa2, const PWPath &Path2, const unsigned Edges2[], unsigned uEdgeCount2);\r
-\r
-#endif // ObjScore_h\r