Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/mhack.cpp b/website/archive/binaries/mac/src/muscle/mhack.cpp
deleted file mode 100644 (file)
index 5a38f90..0000000
--- a/website/archive/binaries/mac/src/muscle/mhack.cpp
+++ /dev/null
@@ -1,64 +0,0 @@
-#include "muscle.h"\r
-#include "seqvect.h"\r
-#include "msa.h"\r
-\r
-/***\r
-Methionine hack.\r
-Most proteins start with M.\r
-This results in odd-looking alignments with the terminal Ms aligned followed\r
-immediately by gaps.\r
-Hack this by treating terminal M like X.\r
-***/\r
-\r
-static bool *M;\r
-\r
-void MHackStart(SeqVect &v)\r
-       {\r
-       if (ALPHA_Amino != g_Alpha)\r
-               return;\r
-\r
-       const unsigned uSeqCount = v.Length();\r
-       M = new bool[uSeqCount];\r
-       memset(M, 0, uSeqCount*sizeof(bool));\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               Seq &s = v.GetSeq(uSeqIndex);\r
-               if (0 == s.Length())\r
-                       continue;\r
-               unsigned uId = s.GetId();\r
-               if (s[0] == 'M' || s[0] == 'm')\r
-                       {\r
-                       M[uId] = true;\r
-                       s[0] = 'X';\r
-                       }\r
-               }\r
-       }\r
-\r
-void MHackEnd(MSA &msa)\r
-       {\r
-       if (ALPHA_Amino != g_Alpha)\r
-               return;\r
-       if (0 == M)\r
-               return;\r
-\r
-       const unsigned uSeqCount = msa.GetSeqCount();\r
-       const unsigned uColCount = msa.GetColCount();\r
-       for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
-               {\r
-               unsigned uId = msa.GetSeqId(uSeqIndex);\r
-               if (M[uId])\r
-                       {\r
-                       for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
-                               {\r
-                               if (!msa.IsGap(uSeqIndex, uColIndex))\r
-                                       {\r
-                                       msa.SetChar(uSeqIndex, uColIndex, 'M');\r
-                                       break;\r
-                                       }\r
-                               }\r
-                       }\r
-               }\r
-\r
-       delete[] M;\r
-       M = 0;\r
-       }\r