Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/pairwise/FastPairwiseAlign.h b/website/archive/binaries/mac/src/clustalw/src/pairwise/FastPairwiseAlign.h
deleted file mode 100644 (file)
index c20cd44..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/pairwise/FastPairwiseAlign.h
+++ /dev/null
@@ -1,54 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifndef FASTPAIRWISEALIGN_H
-#define FASTPAIRWISEALIGN_H
-
-#include "PairwiseAlignBase.h"
-
-namespace clustalw
-{
-
-class FastPairwiseAlign : public PairwiseAlignBase
-{
-    public:
-        /* Functions */
-        FastPairwiseAlign();
-       virtual ~FastPairwiseAlign(){};
-
-        virtual void pairwiseAlign(Alignment *alignPtr, DistMatrix *distMat, int iStart, 
-                                   int iEnd, int jStart, int jEnd);
-        /* Attributes */
-
-    private:
-        /* Functions */
-        void pairAlign(const vector<int>* seq, int l1, int l2); 
-        void makePPtrs(vector<int>& tptr, vector<int>& pl, const vector<int>* seq, 
-                       int length); 
-        void makeNPtrs(vector<int>& tptr, vector<int>& pl, const vector<int>* seq, 
-                       int length);
-        void putFrag(int fs, int v1, int v2, int flen);
-        int fragRelPos(int a1, int b1, int a2, int b2);
-        void desQuickSort(vector<int>& array1, vector<int>& array2, int arraySize);
-
-        /* Attributes */
-        
-        vector<int> displ;
-        vector<int> zza;
-        vector<int> zzb;
-        vector<int> zzc;
-        vector<int> zzd;        
-        int next;
-        int currFrag;
-        int maxSoFar;
-        int vatend;
-        
-        Array2D<int> accum;
-        vector<int> diagIndex;
-        vector<int> slopes;
-        int _maxAlnLength;        
-};
-}
-#endif