Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileStandard.cpp b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileStandard.cpp
deleted file mode 100644 (file)
index 650ad11..0000000
--- a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/ProfileStandard.cpp
+++ /dev/null
@@ -1,117 +0,0 @@
-/**
- * Author: Mark Larkin
- * 
- * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
- */
-#ifdef HAVE_CONFIG_H
-    #include "config.h"
-#endif
-#include "ProfileStandard.h"
-
-namespace clustalw
-{
-
-/**
- * 
- * @param prfLen 
- * @param firstS 
- * @param lastS 
- * @return 
- */
-ProfileStandard::ProfileStandard(int prfLen, int firstS, int lastS)
- : ProfileBase(prfLen, firstS, lastS)
-{
-
-}
-
-/**
- * 
- */
-void ProfileStandard::resetPrf2()
-{
-    profile.clear();
-}
-
-
-/**
- * 
- * @param seqArray 
- * @param seqWeight 
- */
-void ProfileStandard::calcStandardProfile(SeqArray* seqArray, vector<int>* seqWeight)
-{
-    /** DONT FORGET TO CHECK THE SIZES ARE CORRECT */
-    
-    int sum1, sum2;
-    int i, d;
-    int r;
-    int _maxAA = userParameters->getMaxAA();
-    profile.resize(prfLength + 2, vector<int>(LENCOL + 2));
-    int _gapPos1 = userParameters->getGapPos1();
-    int _gapPos2 = userParameters->getGapPos2();
-    
-    for (r = 0; r < prfLength; r++)
-    {
-        /*
-         * calculate sum2 = number of residues found in this column
-         */
-        sum2 = 0;
-        for (i = firstSeq; i < lastSeq; i++)
-        {
-            sum2 += (*seqWeight)[i];
-        }
-        /*
-         * only include matrix comparison scores for those residue types found in this
-         * column
-         */
-        if (sum2 == 0)
-        {
-            for (d = 0; d <= _maxAA; d++)
-            {
-                profile[r + 1][d] = 0;
-            }
-
-            profile[r + 1][_gapPos1] = 0;
-            profile[r + 1][_gapPos2] = 0;
-        }
-        else
-        {
-            for (d = 0; d <= _maxAA; d++)
-            {
-                sum1 = 0;
-                for (i = firstSeq; i < lastSeq; i++)
-                {
-                    if (d == (*seqArray)[i][r])
-                    {
-                        sum1 += (*seqWeight)[i];
-                    }
-                }
-                profile[r + 1][d] = (int)(10 *(float)sum1 / (float)sum2);
-            }
-            sum1 = 0;
-
-            for (i = firstSeq; i < lastSeq; i++)
-            {
-                if (_gapPos1 == (*seqArray)[i][r])
-                {
-                    sum1 += (*seqWeight)[i];
-                }
-            }
-            profile[r + 1][_gapPos1] = (int)(10 *(float)sum1 / (float)sum2);
-            sum1 = 0;
-
-            for (i = firstSeq; i < lastSeq; i++)
-            {
-                if (_gapPos2 == (*seqArray)[i][r])
-                {
-                    sum1 += (*seqWeight)[i];
-                }
-            }
-            profile[r + 1][_gapPos2] = (int)(10 *(float)sum1 / (float)sum2);
-        }
-    }
-
-}
-                      
-
-}