binaries/src/muscle/mhack.cpp

   1 #include "muscle.h"\r
   2 #include "seqvect.h"\r
   3 #include "msa.h"\r
   4 \r
   5 /***\r
   6 Methionine hack.\r
   7 Most proteins start with M.\r
   8 This results in odd-looking alignments with the terminal Ms aligned followed\r
   9 immediately by gaps.\r
  10 Hack this by treating terminal M like X.\r
  11 ***/\r
  12 \r
  13 static bool *M;\r
  14 \r
  15 void MHackStart(SeqVect &v)\r
  16         {\r
  17         if (ALPHA_Amino != g_Alpha)\r
  18                 return;\r
  19 \r
  20         const unsigned uSeqCount = v.Length();\r
  21         M = new bool[uSeqCount];\r
  22         memset(M, 0, uSeqCount*sizeof(bool));\r
  23         for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
  24                 {\r
  25                 Seq &s = v.GetSeq(uSeqIndex);\r
  26                 if (0 == s.Length())\r
  27                         continue;\r
  28                 unsigned uId = s.GetId();\r
  29                 if (s[0] == 'M' || s[0] == 'm')\r
  30                         {\r
  31                         M[uId] = true;\r
  32                         s[0] = 'X';\r
  33                         }\r
  34                 }\r
  35         }\r
  36 \r
  37 void MHackEnd(MSA &msa)\r
  38         {\r
  39         if (ALPHA_Amino != g_Alpha)\r
  40                 return;\r
  41         if (0 == M)\r
  42                 return;\r
  43 \r
  44         const unsigned uSeqCount = msa.GetSeqCount();\r
  45         const unsigned uColCount = msa.GetColCount();\r
  46         for (unsigned uSeqIndex = 0; uSeqIndex < uSeqCount; ++uSeqIndex)\r
  47                 {\r
  48                 unsigned uId = msa.GetSeqId(uSeqIndex);\r
  49                 if (M[uId])\r
  50                         {\r
  51                         for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex)\r
  52                                 {\r
  53                                 if (!msa.IsGap(uSeqIndex, uColIndex))\r
  54                                         {\r
  55                                         msa.SetChar(uSeqIndex, uColIndex, 'M');\r
  56                                         break;\r
  57                                         }\r
  58                                 }\r
  59                         }\r
  60                 }\r
  61 \r
  62         delete[] M;\r
  63         M = 0;\r
  64         }\r