Mac binaries

[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
new file mode 100644 (file)
index 0000000..a239c12
--- /dev/null
+++ b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/LowScoreSegProfile.cpp
@@ -0,0 +1,116 @@
+/**
+ * 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;
+    }
+}                                
+
+}