4 * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
7 * This ObjectiveScore class is used to provide an objective function to score
9 * It is used with iteration to improve an alignment.
12 #ifndef OBJECTIVESCORE_H
13 #define OBJECTIVESCORE_H
14 #include "../general/clustalw.h"
15 #include "../substitutionMatrix/globalmatrix.h"
30 long getScore(const Alignment* alnToScore);
33 float scoreLetters(int seq1, int seq2);
34 float scoreGaps(int seq1, int seq2);
35 void calcNormalisedSeqWeights(const vector<int>* seqWeight,
36 vector<float>* normSeqWeight);
38 int matrix[NUMRES][NUMRES];
39 const Alignment* alignToScore;
42 int sagaGapEx, sagaGapOp;
44 static const int BOTHGAPS = 0;
45 static const int NOGAPS = -1;
46 static const int GAPINSEQB = 1;
47 static const int GAPINSEQA = 2;