Mac binaries

[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
new file mode 100644 (file)
index 0000000..9bd6dd2
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+++ b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileWithSub.cpp
@@ -0,0 +1,150 @@
+/**
+ * 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);
+        }
+    }
+}
+                      
+
+}