Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / pairwise / FullPairwiseAlign.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/pairwise/FullPairwiseAlign.h b/website/archive/binaries/mac/src/clustalw/src/pairwise/FullPairwiseAlign.h
deleted file mode 100644 (file)
index 10c5283..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/pairwise/FullPairwiseAlign.h
+++ /dev/null
@@ -1,66 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifndef FULLPAIRWISEALIGN_H
-#define FULLPAIRWISEALIGN_H
-
-#include "PairwiseAlignBase.h"
-
-namespace clustalw
-{
-
-class FullPairwiseAlign : public PairwiseAlignBase
-{
-    public:
-        /* Functions */
-        FullPairwiseAlign();
-       virtual ~FullPairwiseAlign(){};
-
-        virtual void pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart, 
-                                   int iEnd, int jStart, int jEnd); 
-        /* Attributes */
-
-    private:
-        /* Functions */
-        void add(int v);
-        int calcScore(int iat, int jat, int v1, int v2); 
-        float tracePath(int tsb1, int tsb2);
-        void forwardPass(const vector<int>* seq1, const vector<int>* seq2, int n, int m);
-        void reversePass(const vector<int>* ia, const vector<int>* ib);
-        int diff(int A, int B, int M, int N, int tb, int te);
-        void del(int k);
-        int gap(int k);
-        int tbgap(int k, int tb);
-        int tegap(int k, int te);
-        /* Attributes */
-        // I have constant pointers to the data. This allows for the fastest access.
-        const vector<int>* _ptrToSeq1;
-        const vector<int>* _ptrToSeq2;
-        int _maxAlnLength;
-        int intScale;
-        float mmScore;
-        int printPtr;
-        int lastPrint;
-        vector<int> displ;
-        vector<int> HH;
-        vector<int> DD;
-        vector<int> RR;
-        vector<int> SS;
-
-        int _gapOpen; // scaled to be an integer, this is not a mistake
-        int _gapExtend; // scaled to be an integer, not a mistake
-        int seq1;
-        int seq2;
-        int matrix[NUMRES][NUMRES];
-        int maxScore;
-        int sb1;
-        int sb2;
-        int se1;
-        int se2;
-
-};
-
-}
-#endif