Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / multipleAlign / LowScoreSegProfile.cpp

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/LowScoreSegProfile.cpp b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/LowScoreSegProfile.cpp
deleted file mode 100644 (file)
index a239c12..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/LowScoreSegProfile.cpp
+++ /dev/null
@@ -1,116 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include "LowScoreSegProfile.h"
-
-namespace clustalw
-{
-
-LowScoreSegProfile::LowScoreSegProfile(int prfLen, int firstS, int lastS)
-    : prfLength(prfLen),
-      firstSeq(firstS),
-      lastSeq(lastS)
-{
-    profile.resize(prfLength + 2, vector<int>(LENCOL + 2));
-}
-
-void LowScoreSegProfile::calcLowScoreSegProfile(const SeqArray* seqArray, 
-                                int matrix[NUMRES][NUMRES], vector<int>* seqWeight)
-{
-    vector<vector<int> > weighting; 
-    int d, i, res; 
-    int r, pos;
-    int f;
-    int _gapPos1 = userParameters->getGapPos1();
-    int _gapPos2 = userParameters->getGapPos2();
-    int _maxAA = userParameters->getMaxAA();
-
-    weighting.resize(NUMRES + 2, vector<int>(prfLength + 2));
-    
-    for (r = 0; r < prfLength; r++)
-    {
-        for (d = 0; d <= _maxAA; d++)
-        {
-            weighting[d][r] = 0;
-            for (i = firstSeq; i < lastSeq; i++)
-            {
-                if (r + 1 < (int)(*seqArray)[i + 1].size() - 1)
-                {
-                    if (d == (*seqArray)[i + 1][r + 1])
-                    { 
-                        weighting[d][r] += (*seqWeight)[i];
-                    }
-                }
-            }
-        }
-        
-        weighting[_gapPos1][r] = 0;
-        
-        for (i = firstSeq; i < lastSeq; i++)
-        {
-            if (r + 1 < (int)(*seqArray)[i + 1].size() - 1)
-            {
-                if (_gapPos1 == (*seqArray)[i + 1][r + 1])
-                { 
-                    weighting[_gapPos1][r] += (*seqWeight)[i];
-                }
-            }
-        }
-        
-        weighting[_gapPos2][r] = 0;
-        
-        for (i = firstSeq; i < lastSeq; i++)
-        {
-            if (r + 1 < (int)(*seqArray)[i + 1].size() - 1)
-            {
-                if (_gapPos2 == (*seqArray)[i + 1][r + 1])
-                { 
-                    weighting[_gapPos2][r] += (*seqWeight)[i];
-                }
-            }
-        }
-    }
-
-    for (pos = 0; pos < prfLength; pos++)
-    {
-        for (res = 0; res <= _maxAA; res++)
-        {
-            f = 0;
-            
-            for (d = 0; d <= _maxAA; d++)
-            {
-                f += (weighting[d][pos] * matrix[d][res]);
-            }
-            
-            f += (weighting[_gapPos1][pos] * matrix[_gapPos1][res]);
-            f += (weighting[_gapPos2][pos] * matrix[_gapPos2][res]);
-            profile[pos + 1][res] = f;
-        }
-        f = 0;
-        
-        for (d = 0; d <= _maxAA; d++)
-        {
-            f += (weighting[d][pos] * matrix[d][_gapPos1]);
-        }   
-        
-        f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos1]);
-        f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos1]);
-        profile[pos + 1][_gapPos1] = f;
-        f = 0;
-           
-        for (d = 0; d <= _maxAA; d++)
-        {
-            f += (weighting[d][pos] * matrix[d][_gapPos2]);
-        }   
-        f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos2]);
-        f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos2]);
-        profile[pos + 1][_gapPos2] = f;
-    }
-}                                
-
-}