Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / cons.cpp

diff --git a/website/archive/binaries/mac/src/muscle/cons.cpp b/website/archive/binaries/mac/src/muscle/cons.cpp
deleted file mode 100644 (file)
index c1507c5..0000000
--- a/website/archive/binaries/mac/src/muscle/cons.cpp
+++ /dev/null
@@ -1,118 +0,0 @@
-/***\r
-Conservation value for a column in an MSA is defined as the number\r
-of times the most common letter appears divided by the number of\r
-sequences.\r
-***/\r
-\r
-#include "muscle.h"\r
-#include "msa.h"\r
-#include <math.h>\r
-\r
-double MSA::GetAvgCons() const\r
-       {\r
-       assert(GetSeqCount() > 0);\r
-       double dSum = 0;\r
-       unsigned uNonGapColCount = 0;\r
-       for (unsigned uColIndex = 0; uColIndex < GetColCount(); ++uColIndex)\r
-               {\r
-               if (!IsGapColumn(uColIndex))\r
-                       {\r
-                       dSum += GetCons(uColIndex);\r
-                       ++uNonGapColCount;\r
-                       }\r
-               }\r
-       assert(uNonGapColCount > 0);\r
-       double dAvg = dSum / uNonGapColCount;\r
-       assert(dAvg > 0 && dAvg <= 1);\r
-       return dAvg;\r
-       }\r
-\r
-double MSA::GetCons(unsigned uColIndex) const\r
-       {\r
-       unsigned Counts[MAX_ALPHA];\r
-       for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)\r
-               Counts[uLetter] = 0;\r
-\r
-       unsigned uMaxCount = 0;\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex)\r
-               {\r
-               if (IsGap(uSeqIndex, uColIndex))\r
-                       continue;\r
-               char c = GetChar(uSeqIndex, uColIndex);\r
-               c = toupper(c);\r
-               if ('X' == c || 'B' == c || 'Z' == c)\r
-                       continue;\r
-               unsigned uLetter = GetLetter(uSeqIndex, uColIndex);\r
-               unsigned uCount = Counts[uLetter] + 1;\r
-               if (uCount > uMaxCount)\r
-                       uMaxCount = uCount;\r
-               Counts[uLetter] = uCount;\r
-               }\r
-\r
-// Cons is undefined for all-gap column\r
-       if (0 == uMaxCount)\r
-               {\r
-//             assert(false);\r
-               return 1;\r
-               }\r
-\r
-       double dCons = (double) uMaxCount / (double) GetSeqCount();\r
-       assert(dCons > 0 && dCons <= 1);\r
-       return dCons;\r
-       }\r
-\r
-// Perecent identity of a pair of sequences.\r
-// Positions with one or both gapped are ignored.\r
-double MSA::GetPctIdentityPair(unsigned uSeqIndex1, unsigned uSeqIndex2) const\r
-       {\r
-       const unsigned uColCount = GetColCount();\r
-       unsigned uPosCount = 0;\r
-       unsigned uSameCount = 0;\r
-       for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-               {\r
-               const char c1 = GetChar(uSeqIndex1, uColIndex);\r
-               const char c2 = GetChar(uSeqIndex2, uColIndex);\r
-               if (IsGapChar(c1) || IsGapChar(c2))\r
-                       continue;\r
-               if (c1 == c2)\r
-                       ++uSameCount;\r
-               ++uPosCount;\r
-               }\r
-       if (0 == uPosCount)\r
-               return 0;\r
-       return (double) uSameCount / (double) uPosCount;\r
-       }\r
-\r
-// Perecent group identity of a pair of sequences.\r
-// Positions with one or both gapped are ignored.\r
-double MSA::GetPctGroupIdentityPair(unsigned uSeqIndex1,\r
-  unsigned uSeqIndex2) const\r
-       {\r
-       extern unsigned ResidueGroup[];\r
-\r
-       const unsigned uColCount = GetColCount();\r
-       unsigned uPosCount = 0;\r
-       unsigned uSameCount = 0;\r
-       for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-               {\r
-               if (IsGap(uSeqIndex1, uColIndex))\r
-                       continue;\r
-               if (IsGap(uSeqIndex2, uColIndex))\r
-                       continue;\r
-               if (IsWildcard(uSeqIndex1, uColIndex))\r
-                       continue;\r
-               if (IsWildcard(uSeqIndex2, uColIndex))\r
-                       continue;\r
-\r
-               const unsigned uLetter1 = GetLetter(uSeqIndex1, uColIndex);\r
-               const unsigned uLetter2 = GetLetter(uSeqIndex2, uColIndex);\r
-               const unsigned uGroup1 = ResidueGroup[uLetter1];\r
-               const unsigned uGroup2 = ResidueGroup[uLetter2];\r
-               if (uGroup1 == uGroup2)\r
-                       ++uSameCount;\r
-               ++uPosCount;\r
-               }\r
-       if (0 == uPosCount)\r
-               return 0;\r
-       return (double) uSameCount / (double) uPosCount;\r
-       }\r