binaries/src/muscle/posgap.cpp

   1 #include "muscle.h"\r
   2 \r
   3 //// Pascaralle and Argos gap factors\r
   4 //// after Table 1 in Thompson et. al. ClustalW NAR paper.\r
   5 //static double PAFFacs[20] =\r
   6 //      {\r
   7 //      1.13,           // A\r
   8 //      1.13,           // C\r
   9 //      0.96,           // D\r
  10 //      1.31,           // E\r
  11 //      1.20,           // F\r
  12 //      0.61,           // G\r
  13 //      1.00,           // H\r
  14 //      1.32,           // I\r
  15 //      0.96,           // K\r
  16 //      1.21,           // L\r
  17 //      1.29,           // M\r
  18 //      0.62,           // N\r
  19 //      0.74,           // P\r
  20 //      1.07,           // Q\r
  21 //      0.72,           // R\r
  22 //      0.76,           // S\r
  23 //      0.89,           // T\r
  24 //      1.25,           // V\r
  25 //      1.00,           // Y\r
  26 //      1.23,           // W\r
  27 //      };\r
  28 //\r
  29 //// (Not used: does not appear to work well).\r
  30 //SCORE PAFactor(const FCOUNT fcCounts[])\r
  31 //      {\r
  32 //      if (ALPHA_Amino != g_Alpha)\r
  33 //              Quit("PAFFactor: requires amino acid sequence");\r
  34 //\r
  35 //      FCOUNT fLetterCount = 0;\r
  36 //      double dSum = 0;\r
  37 //      for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
  38 //              {\r
  39 //              const FCOUNT fCount = fcCounts[uLetter];\r
  40 //              dSum += fCount*PAFFacs[uLetter];\r
  41 //              fLetterCount += fCount;\r
  42 //              }\r
  43 //      if (0 == fLetterCount)\r
  44 //              return 0.5;\r
  45 //      return (SCORE) (dSum/fLetterCount);\r
  46 //      }\r
  47 \r
  48 //static bool Hydrophilic[20] =\r
  49 //      {\r
  50 //      false,          // A\r
  51 //      false,          // C\r
  52 //      true,           // D\r
  53 //      true,           // E\r
  54 //      false,          // F\r
  55 //      true,           // G\r
  56 //      false,          // H\r
  57 //      false,          // I\r
  58 //      true,           // K\r
  59 //      false,          // L\r
  60 //      false,          // M\r
  61 //      true,           // N\r
  62 //      true,           // P\r
  63 //      true,           // Q\r
  64 //      true,           // R\r
  65 //      true,           // S\r
  66 //      false,          // T\r
  67 //      false,          // V\r
  68 //      false,          // Y\r
  69 //      false,          // W\r
  70 //      };\r
  71 //\r
  72 //bool IsHydrophilic(const FCOUNT fcCounts[])\r
  73 //      {\r
  74 //      if (ALPHA_Amino != g_Alpha)\r
  75 //              Quit("IsHydrophilic: requires amino acid sequence");\r
  76 //\r
  77 //      for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
  78 //              if (fcCounts[uLetter] > 0 && !Hydrophilic[uLetter])\r
  79 //                      return false;\r
  80 //      return true;\r
  81 //      }\r
  82 //\r
  83 //bool IsHydrophilic(const unsigned uCounts[])\r
  84 //      {\r
  85 //      if (ALPHA_Amino != g_Alpha)\r
  86 //              Quit("IsHydrophilic: requires amino acid sequence");\r
  87 //\r
  88 //      for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
  89 //              if (uCounts[uLetter] > 0 && !Hydrophilic[uLetter])\r
  90 //                      return false;\r
  91 //      return true;\r
  92 //      }\r
  93 \r
  94 // LIVCATMFYWHK\r
  95 // Venn         Pascaralla      B&T             Me\r
  96 // L            y                       y               y\r
  97 // I            y                       y               y\r
  98 // V            y                       y               y\r
  99 // C            y                       n\r
 100 // A            y                       y               y\r
 101 // T            N                       n\r
 102 // M            y                       y               y\r
 103 // F            y                       y               y\r
 104 // Y            n                       n\r
 105 // W            y                       n\r
 106 // H            n                       n\r
 107 // K            n                       n\r
 108 static bool Hydrophobic[20] =\r
 109         {\r
 110         true,           // A\r
 111         true,           // C\r
 112         false,          // D\r
 113         false,          // E\r
 114         true,           // F\r
 115         false,          // G\r
 116         true,           // H\r
 117         true,           // I\r
 118         false,          // K\r
 119         true,           // L\r
 120         true,           // M\r
 121         false,          // N\r
 122         false,          // P\r
 123         false,          // Q\r
 124         false,          // R\r
 125         false,          // S\r
 126         true,           // T\r
 127         true,           // V\r
 128         true,           // Y\r
 129         true,           // W\r
 130         };\r
 131 \r
 132 bool IsHydrophobic(const FCOUNT fcCounts[])\r
 133         {\r
 134         if (ALPHA_Amino != g_Alpha)\r
 135                 Quit("IsHydrophobic: requires amino acid sequence");\r
 136 \r
 137         for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
 138                 if (fcCounts[uLetter] > 0.0 && !Hydrophobic[uLetter])\r
 139                         return false;\r
 140         return true;\r
 141         }\r