Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / alignment / ObjectiveScore.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/alignment/ObjectiveScore.h b/website/archive/binaries/mac/src/clustalw/src/alignment/ObjectiveScore.h
deleted file mode 100644 (file)
index 8e99bbf..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/alignment/ObjectiveScore.h
+++ /dev/null
@@ -1,51 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-/**
- * This ObjectiveScore class is used to provide an objective function to score 
- * an alignment.
- * It is used with iteration to improve an alignment.
- */
- 
-#ifndef OBJECTIVESCORE_H
-#define OBJECTIVESCORE_H
-#include "../general/clustalw.h"
-#include "../substitutionMatrix/globalmatrix.h" 
-namespace clustalw
-{
-
-class Alignment;
-typedef struct
-{
-    int first;
-    int second; 
-} Pair;  
-
-class ObjectiveScore
-{   
-    public:
-        ObjectiveScore();
-        long getScore(const Alignment* alnToScore);    
-    private:
-        
-        float scoreLetters(int seq1, int seq2);
-        float scoreGaps(int seq1, int seq2);
-        void calcNormalisedSeqWeights(const vector<int>* seqWeight, 
-                                      vector<float>* normSeqWeight);
-        long score;
-        int matrix[NUMRES][NUMRES];
-        const Alignment* alignToScore;
-        long scale;
-        int weightScale;
-        int sagaGapEx, sagaGapOp;
-        int gapPos1, gapPos2;
-        static const int BOTHGAPS = 0;
-        static const int NOGAPS = -1;
-        static const int GAPINSEQB = 1;
-        static const int GAPINSEQA = 2;
-};
-
-}
-#endif