Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / multipleAlign / MyersMillerProfileAlign.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/MyersMillerProfileAlign.h b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/MyersMillerProfileAlign.h
deleted file mode 100644 (file)
index 0a932fd..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/MyersMillerProfileAlign.h
+++ /dev/null
@@ -1,70 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifndef MYERSMILLERPROFILEALIGN_H
-#define MYERSMILLERPROFILEALIGN_H
-
-#include <vector>
-#include "ProfileAlignAlgorithm.h"
-#include "ProfileStandard.h"
-#include "ProfileWithSub.h"
-namespace clustalw
-{
-
-class MyersMillerProfileAlign : public ProfileAlignAlgorithm
-{
-    public:
-  virtual ~MyersMillerProfileAlign(){};
-
-    /* Functions */
-        MyersMillerProfileAlign();
-        virtual int profileAlign(Alignment* alnPtr, DistMatrix* distMat, 
-                                 vector<int>* group, int* aligned);
-    /* Attributes */
-    
-    private:
-    /* Functions */
-        void addGGaps(Alignment* alnPtr, SeqArray* seqArray);
-        void addGGapsMask(vector<char>* mask,int len, vector<int>* path1, vector<int>* path2);
-        int prfScore(int n, int m);
-        int progTracepath();
-        void progDel(int k);
-        void progAdd(int k);
-        void progAlign();
-        int progDiff(int A, int B, int M, int N, int go1, int go2);
-        int openPenalty1(int i, int j);
-        int extPenalty1(int i, int j);
-        int gapPenalty1(int i, int j, int k);
-        int openPenalty2(int i, int j);
-        int extPenalty2(int i, int j);
-        int gapPenalty2(int i, int j, int k);    
-    /* Attributes */
-        ProfileWithSub* profileWithSub;
-        ProfileStandard* profileStandard;
-        int gapcoef1;
-        int gapcoef2;
-        int lencoef1;
-        int lencoef2;
-        vector<int> displ;
-        vector<int> gS;
-        vector<int> HH;
-        vector<int> DD;
-        vector<int> RR;
-        vector<int> SS;
-        vector<int> alnPath1;
-        vector<int> alnPath2;
-        int printPtr;
-        int lastPrint;                        
-        int matrix[32][32];
-        vector<int> gaps;
-        bool switchProfiles;
-        const SeqArray* profile1;
-        const SeqArray* profile2;
-        int _gapPos1, _gapPos2;
-        int alignmentLength;                   
-};
-
-}
-#endif