binaries/src/muscle/fastscorepath2.cpp

   1 #include "muscle.h"\r
   2 #include "profile.h"\r
   3 #include "pwpath.h"\r
   4 \r
   5 SCORE FastScorePath2(const ProfPos *PA, unsigned uLengthA,\r
   6   const ProfPos *PB, unsigned uLengthB, const PWPath &Path)\r
   7         {\r
   8         const unsigned uEdgeCount = Path.GetEdgeCount();\r
   9         Log("Edge  SS     PLA   PLB   Match     Gap    Total\n");\r
  10         Log("----  --     ---   ---   -----     ---    -----\n");\r
  11         char cType = 'S';\r
  12         SCORE scoreTotal = 0;\r
  13         for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)\r
  14                 {\r
  15                 const PWEdge &Edge = Path.GetEdge(uEdgeIndex);\r
  16                 const char cPrevType = cType;\r
  17                 cType = Edge.cType;\r
  18                 const unsigned uPrefixLengthA = Edge.uPrefixLengthA;\r
  19                 const unsigned uPrefixLengthB = Edge.uPrefixLengthB;\r
  20                 bool bGap = false;\r
  21                 bool bMatch = false;\r
  22                 SCORE scoreGap = 0;\r
  23                 SCORE scoreMatch = 0;\r
  24 \r
  25                 switch (cType)\r
  26                         {\r
  27                 case 'M':\r
  28                         {\r
  29                         if (0 == uPrefixLengthA || 0 == uPrefixLengthB)\r
  30                                 Quit("FastScorePath2, M zero length");\r
  31 \r
  32                         const ProfPos &PPA = PA[uPrefixLengthA - 1];\r
  33                         const ProfPos &PPB = PB[uPrefixLengthB - 1];\r
  34 \r
  35                         bMatch = true;\r
  36                         scoreMatch = ScoreProfPos2(PPA, PPB);\r
  37 \r
  38                         if ('D' == cPrevType)\r
  39                                 {\r
  40                                 bGap = true;\r
  41                                 assert(uPrefixLengthA > 1);\r
  42                                 scoreGap = PA[uPrefixLengthA-2].m_scoreGapClose;\r
  43                                 }\r
  44                         else if ('I' == cPrevType)\r
  45                                 {\r
  46                                 bGap = true;\r
  47                                 assert(uPrefixLengthB > 1);\r
  48                                 scoreGap = PB[uPrefixLengthB-2].m_scoreGapClose;\r
  49                                 }\r
  50                         break;\r
  51                         }\r
  52 \r
  53                 case 'D':\r
  54                         {\r
  55                         if (0 == uPrefixLengthA)\r
  56                                 Quit("FastScorePath2, D zero length");\r
  57 \r
  58                         const ProfPos &PPA = PA[uPrefixLengthA - 1];\r
  59                         bGap = true;\r
  60                         switch (cPrevType)\r
  61                                 {\r
  62                         case 'S':\r
  63                                 scoreGap = PPA.m_scoreGapOpen;\r
  64                                 break;\r
  65                         case 'M':\r
  66                                 scoreGap = PPA.m_scoreGapOpen;\r
  67                                 break;\r
  68                         case 'D':\r
  69 //                              scoreGap = g_scoreGapExtend;\r
  70                                 scoreGap = 0;\r
  71                                 break;\r
  72                         case 'I':\r
  73                                 Quit("FastScorePath2 DI");\r
  74                                 }\r
  75                         break;\r
  76                         }\r
  77 \r
  78                 case 'I':\r
  79                         {\r
  80                         if (0 == uPrefixLengthB)\r
  81                                 Quit("FastScorePath2, I zero length");\r
  82 \r
  83                         const ProfPos &PPB = PB[uPrefixLengthB - 1];\r
  84                         bGap = true;\r
  85                         switch (cPrevType)\r
  86                                 {\r
  87                         case 'S':\r
  88                                 scoreGap = PPB.m_scoreGapOpen;\r
  89                                 break;\r
  90                         case 'M':\r
  91                                 scoreGap = PPB.m_scoreGapOpen;\r
  92                                 break;\r
  93                         case 'I':\r
  94                                 scoreGap = 0;\r
  95 //                              scoreGap = g_scoreGapExtend;\r
  96                                 break;\r
  97                         case 'D':\r
  98                                 Quit("FastScorePath2 DI");\r
  99                                 }\r
 100                         break;\r
 101                         }\r
 102 \r
 103                 case 'U':\r
 104                         {\r
 105                         Quit("FastScorePath2 U");\r
 106                         }\r
 107 \r
 108                 default:\r
 109                         Quit("FastScorePath2: invalid type %c", cType);\r
 110                         }\r
 111 \r
 112                 Log("%4u  %c%c  %4u  %4u  ", uEdgeIndex, cPrevType, cType,\r
 113                   uPrefixLengthA, uPrefixLengthB);\r
 114                 if (bMatch)\r
 115                         Log("%7.1f  ", scoreMatch);\r
 116                 else\r
 117                         Log("         ");\r
 118                 if (bGap)\r
 119                         Log("%7.1f  ", scoreGap);\r
 120                 else\r
 121                         Log("         ");\r
 122                 SCORE scoreEdge = scoreMatch + scoreGap;\r
 123                 scoreTotal += scoreEdge;\r
 124                 Log("%7.1f  %7.1f", scoreEdge, scoreTotal);\r
 125                 Log("\n");\r
 126                 }\r
 127 \r
 128         SCORE scoreGap = 0;\r
 129 //      if (!g_bTermGapsHalf)\r
 130                 switch (cType)\r
 131                         {\r
 132                 case 'M':\r
 133                         scoreGap = 0;\r
 134                         break;\r
 135 \r
 136                 case 'D':\r
 137                         {\r
 138                         const ProfPos &LastPPA = PA[uLengthA - 1];\r
 139                         scoreGap = LastPPA.m_scoreGapClose;\r
 140                         break;\r
 141                         }\r
 142 \r
 143                 case 'I':\r
 144                         {\r
 145                         const ProfPos &LastPPB = PB[uLengthB - 1];\r
 146                         scoreGap = LastPPB.m_scoreGapClose;\r
 147                         break;\r
 148                         }\r
 149 \r
 150                 case 'U':\r
 151                         Quit("Unaligned regions not supported");\r
 152 \r
 153                 case 'S':\r
 154                         break;\r
 155 \r
 156                 default:\r
 157                         Quit("Invalid type %c", cType);\r
 158                         }\r
 159 \r
 160         Log("      %cE  %4u  %4u           %7.1f\n", cType, uLengthA, uLengthB, scoreGap);\r
 161         scoreTotal += scoreGap;\r
 162 \r
 163         Log("Total = %g\n", scoreTotal);\r
 164         return scoreTotal;\r
 165         }\r