binaries/src/muscle/gapscoredimer.h

   1 // source code generated by dimer.py\r
   2 \r
   3 static SCORE GapScoreMM(const ProfPos &PPA, const ProfPos &PPB)\r
   4         {\r
   5         return\r
   6           g_scoreGapOpen*(PPA.m_LL*PPB.m_LG + PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_LG) +\r
   7           g_scoreGapExtend*(PPA.m_LL*PPB.m_GG + PPA.m_GG*PPB.m_LL) +\r
   8           g_scoreGapAmbig*(PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_GL);\r
   9         }\r
  10 \r
  11 static SCORE GapScoreMD(const ProfPos &PPA, const ProfPos &PPB)\r
  12         {\r
  13         return\r
  14           g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +\r
  15           g_scoreGapExtend*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG) +\r
  16           g_scoreGapAmbig*(PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG);\r
  17         }\r
  18 \r
  19 static SCORE GapScoreMI(const ProfPos &PPA, const ProfPos &PPB)\r
  20         {\r
  21         return\r
  22           g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +\r
  23           g_scoreGapExtend*(PPA.m_LG*PPB.m_LL + PPA.m_GG*PPB.m_LL) +\r
  24           g_scoreGapAmbig*(PPA.m_LG*PPB.m_GL + PPA.m_GG*PPB.m_GL);\r
  25         }\r
  26 \r
  27 static SCORE GapScoreDM(const ProfPos &PPA, const ProfPos &PPB)\r
  28         {\r
  29         return\r
  30           g_scoreGapOpen*(PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL) +\r
  31           g_scoreGapExtend*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG) +\r
  32           g_scoreGapAmbig*(PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_LL + PPA.m_GG*PPB.m_GL);\r
  33         }\r
  34 \r
  35 static SCORE GapScoreDD(const ProfPos &PPA, const ProfPos &PPB)\r
  36         {\r
  37         return\r
  38           g_scoreGapExtend*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GL + PPA.m_LL*PPB.m_GG) +\r
  39           g_scoreGapAmbig*(PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GL + PPA.m_GL*PPB.m_GG);\r
  40         }\r
  41 \r
  42 static SCORE GapScoreDI(const ProfPos &PPA, const ProfPos &PPB)\r
  43         {\r
  44         return\r
  45           g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +\r
  46           g_scoreGapAmbig*(PPA.m_LG*PPB.m_LL + PPA.m_LG*PPB.m_GL + PPA.m_GG*PPB.m_LL + PPA.m_GG*PPB.m_GL);\r
  47         }\r
  48 \r
  49 static SCORE GapScoreIM(const ProfPos &PPA, const ProfPos &PPB)\r
  50         {\r
  51         return\r
  52           g_scoreGapOpen*(PPA.m_LL*PPB.m_LG + PPA.m_GL*PPB.m_LG) +\r
  53           g_scoreGapExtend*(PPA.m_LG*PPB.m_LL + PPA.m_GG*PPB.m_LL) +\r
  54           g_scoreGapAmbig*(PPA.m_LL*PPB.m_GG + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_GG + PPA.m_GG*PPB.m_GL);\r
  55         }\r
  56 \r
  57 static SCORE GapScoreID(const ProfPos &PPA, const ProfPos &PPB)\r
  58         {\r
  59         return\r
  60           g_scoreGapOpen*(PPA.m_LL*PPB.m_LL + PPA.m_LL*PPB.m_GL + PPA.m_GL*PPB.m_LL + PPA.m_GL*PPB.m_GL) +\r
  61           g_scoreGapAmbig*(PPA.m_LL*PPB.m_LG + PPA.m_LL*PPB.m_GG + PPA.m_GL*PPB.m_LG + PPA.m_GL*PPB.m_GG);\r
  62         }\r
  63 \r
  64 static SCORE GapScoreII(const ProfPos &PPA, const ProfPos &PPB)\r
  65         {\r
  66         return\r
  67           g_scoreGapExtend*(PPA.m_LL*PPB.m_LL + PPA.m_LG*PPB.m_LL + PPA.m_GL*PPB.m_LL + PPA.m_GG*PPB.m_LL) +\r
  68           g_scoreGapAmbig*(PPA.m_LL*PPB.m_GL + PPA.m_LG*PPB.m_GL + PPA.m_GL*PPB.m_GL + PPA.m_GG*PPB.m_GL);\r
  69         }\r