website/archive/binaries/mac/src/muscle/aligntwomsas.cpp

   1 #include "muscle.h"\r
   2 #include "msa.h"\r
   3 #include "profile.h"\r
   4 #include "pwpath.h"\r
   5 #include "textfile.h"\r
   6 #include "timing.h"\r
   7 \r
   8 SCORE AlignTwoMSAs(const MSA &msa1, const MSA &msa2, MSA &msaOut, PWPath &Path,\r
   9   bool bLockLeft, bool bLockRight)\r
  10         {\r
  11         const unsigned uLengthA = msa1.GetColCount();\r
  12         const unsigned uLengthB = msa2.GetColCount();\r
  13 \r
  14         ProfPos *PA = ProfileFromMSA(msa1);\r
  15         ProfPos *PB = ProfileFromMSA(msa2);\r
  16 \r
  17         if (bLockLeft)\r
  18                 {\r
  19                 PA[0].m_scoreGapOpen = MINUS_INFINITY;\r
  20                 PB[0].m_scoreGapOpen = MINUS_INFINITY;\r
  21                 }\r
  22 \r
  23         if (bLockRight)\r
  24                 {\r
  25                 PA[uLengthA-1].m_scoreGapClose = MINUS_INFINITY;\r
  26                 PB[uLengthB-1].m_scoreGapClose = MINUS_INFINITY;\r
  27                 }\r
  28 \r
  29         float r = (float) uLengthA/ (float) (uLengthB + 1); // +1 to prevent div 0\r
  30         if (r < 1)\r
  31                 r = 1/r;\r
  32 \r
  33         SCORE Score = GlobalAlign(PA, uLengthA, PB, uLengthB, Path);\r
  34 \r
  35         AlignTwoMSAsGivenPath(Path, msa1, msa2, msaOut);\r
  36 \r
  37         delete[] PA;\r
  38         delete[] PB;\r
  39 \r
  40         return Score;\r
  41         }\r