Mac binaries

[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
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+++ b/website/archive/binaries/mac/src/clustalw/src/pairwise/FullPairwiseAlign.h
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+/**
+ * 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