Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileWithSub.cpp b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileWithSub.cpp
deleted file mode 100644 (file)
index 9bd6dd2..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileWithSub.cpp
+++ /dev/null
@@ -1,150 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include "ProfileWithSub.h"
-
-namespace clustalw
-{
-
-/**
- * 
- * @param prfLen 
- * @param firstS 
- * @param lastS 
- * @return 
- */
-ProfileWithSub::ProfileWithSub(int prfLen, int firstS, int lastS)
- : ProfileBase(prfLen, firstS, lastS)
-{
-}
-
-/**
- * 
- */
-void ProfileWithSub::resetPrf1()
-{
-    profile.clear();
-}
-
-
-/**
- * 
- * @param seqArray 
- * @param gaps 
- * @param matrix[][] 
- * @param seqWeight 
- */
-void ProfileWithSub::calcProfileWithSub(SeqArray* seqArray, vector<int>* gaps, 
-                              int matrix[NUMRES][NUMRES], vector<int>* seqWeight)
-{
-    vector<vector<int> > weighting;
-    int sum2, aa, seq, res;
-    int _numSeq;
-    int col, pos;
-    int f;
-    float scale;
-    int _maxAA = userParameters->getMaxAA();
-    int _gapPos1 = userParameters->getGapPos1();
-    int _gapPos2 = userParameters->getGapPos2();
-    
-    weighting.resize(NUMRES + 2, vector<int>(prfLength + 2));
-    
-    _numSeq = lastSeq - firstSeq;
-
-    sum2 = 0;
-    for (seq = firstSeq; seq < lastSeq; seq++)
-    {
-        sum2 += (*seqWeight)[seq];
-    }
-
-    for (col = 0; col < prfLength; col++)
-    {
-        for (aa = 0; aa <= _maxAA; aa++)
-        {
-            weighting[aa][col] = 0;
-
-            for (seq = firstSeq; seq < lastSeq; seq++)
-                if (aa == (*seqArray)[seq][col])
-                {
-                    weighting[aa][col] += (*seqWeight)[seq];
-                }
-        }
-        weighting[_gapPos1][col] = 0;
-
-        for (seq = firstSeq; seq < lastSeq; seq++)
-        {
-            if (_gapPos1 == (*seqArray)[seq][col])
-            {
-                weighting[_gapPos1][col] += (*seqWeight)[seq];
-            }
-        }
-
-        weighting[_gapPos2][col] = 0;
-
-        for (seq = firstSeq; seq < lastSeq; seq++)
-        {
-            if (_gapPos2 == (*seqArray)[seq][col])
-            {
-                weighting[_gapPos2][col] += (*seqWeight)[seq];
-            }
-        }
-    }
-
-    for (pos = 0; pos < prfLength; pos++)
-    {
-        if ((*gaps)[pos] == _numSeq) // If all gaps
-        {
-            for (res = 0; res <= _maxAA; res++)
-            {
-                profile[pos + 1][res] = matrix[res][_gapPos1];
-            }
-            profile[pos + 1][_gapPos1] = matrix[_gapPos1][_gapPos1];
-            profile[pos + 1][_gapPos2] = matrix[_gapPos2][_gapPos1];
-        }
-        else
-        {
-            scale = (float)(_numSeq - (*gaps)[pos]) / (float)_numSeq;
-            for (res = 0; res <= _maxAA; res++)
-            {
-                f = 0;
-
-                for (aa = 0; aa <= _maxAA; aa++)
-                {
-                    f += (weighting[aa][pos] * matrix[aa][res]);
-                }
-
-                f += (weighting[_gapPos1][pos] * matrix[_gapPos1][res]);
-                f += (weighting[_gapPos2][pos] * matrix[_gapPos2][res]);
-                profile[pos + 1][res] = (int)(((float)f / (float)sum2) * scale);
-            }
-            f = 0;
-
-            for (aa = 0; aa <= _maxAA; aa++)
-            {
-                f += (weighting[aa][pos] * matrix[aa][_gapPos1]);
-            }
-
-            f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos1]);
-            f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos1]);
-            profile[pos + 1][_gapPos1] = (int)(((float)f / (float)sum2) * scale);
-            f = 0;
-
-            for (aa = 0; aa <= _maxAA; aa++)
-            {
-                f += (weighting[aa][pos] * matrix[aa][_gapPos2]);
-            }
-
-            f += (weighting[_gapPos1][pos] * matrix[_gapPos1][_gapPos2]);
-            f += (weighting[_gapPos2][pos] * matrix[_gapPos2][_gapPos2]);
-            profile[pos + 1][_gapPos2] = (int)(((float)f / (float)sum2) * scale);
-        }
-    }
-}
-                      
-
-}