Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / posgap.cpp

diff --git a/website/archive/binaries/mac/src/muscle/posgap.cpp b/website/archive/binaries/mac/src/muscle/posgap.cpp
deleted file mode 100644 (file)
index 863edc6..0000000
--- a/website/archive/binaries/mac/src/muscle/posgap.cpp
+++ /dev/null
@@ -1,141 +0,0 @@
-#include "muscle.h"\r
-\r
-//// Pascaralle and Argos gap factors\r
-//// after Table 1 in Thompson et. al. ClustalW NAR paper.\r
-//static double PAFFacs[20] =\r
-//     {\r
-//     1.13,           // A\r
-//     1.13,           // C\r
-//     0.96,           // D\r
-//     1.31,           // E\r
-//     1.20,           // F\r
-//     0.61,           // G\r
-//     1.00,           // H\r
-//     1.32,           // I\r
-//     0.96,           // K\r
-//     1.21,           // L\r
-//     1.29,           // M\r
-//     0.62,           // N\r
-//     0.74,           // P\r
-//     1.07,           // Q\r
-//     0.72,           // R\r
-//     0.76,           // S\r
-//     0.89,           // T\r
-//     1.25,           // V\r
-//     1.00,           // Y\r
-//     1.23,           // W\r
-//     };\r
-//\r
-//// (Not used: does not appear to work well).\r
-//SCORE PAFactor(const FCOUNT fcCounts[])\r
-//     {\r
-//     if (ALPHA_Amino != g_Alpha)\r
-//             Quit("PAFFactor: requires amino acid sequence");\r
-//\r
-//     FCOUNT fLetterCount = 0;\r
-//     double dSum = 0;\r
-//     for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
-//             {\r
-//             const FCOUNT fCount = fcCounts[uLetter];\r
-//             dSum += fCount*PAFFacs[uLetter];\r
-//             fLetterCount += fCount;\r
-//             }\r
-//     if (0 == fLetterCount)\r
-//             return 0.5;\r
-//     return (SCORE) (dSum/fLetterCount);\r
-//     }\r
-\r
-//static bool Hydrophilic[20] =\r
-//     {\r
-//     false,          // A\r
-//     false,          // C\r
-//     true,           // D\r
-//     true,           // E\r
-//     false,          // F\r
-//     true,           // G\r
-//     false,          // H\r
-//     false,          // I\r
-//     true,           // K\r
-//     false,          // L\r
-//     false,          // M\r
-//     true,           // N\r
-//     true,           // P\r
-//     true,           // Q\r
-//     true,           // R\r
-//     true,           // S\r
-//     false,          // T\r
-//     false,          // V\r
-//     false,          // Y\r
-//     false,          // W\r
-//     };\r
-//\r
-//bool IsHydrophilic(const FCOUNT fcCounts[])\r
-//     {\r
-//     if (ALPHA_Amino != g_Alpha)\r
-//             Quit("IsHydrophilic: requires amino acid sequence");\r
-//\r
-//     for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
-//             if (fcCounts[uLetter] > 0 && !Hydrophilic[uLetter])\r
-//                     return false;\r
-//     return true;\r
-//     }\r
-//\r
-//bool IsHydrophilic(const unsigned uCounts[])\r
-//     {\r
-//     if (ALPHA_Amino != g_Alpha)\r
-//             Quit("IsHydrophilic: requires amino acid sequence");\r
-//\r
-//     for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
-//             if (uCounts[uLetter] > 0 && !Hydrophilic[uLetter])\r
-//                     return false;\r
-//     return true;\r
-//     }\r
-\r
-// LIVCATMFYWHK\r
-// Venn                Pascaralla      B&T             Me\r
-// L           y                       y               y\r
-// I           y                       y               y\r
-// V           y                       y               y\r
-// C           y                       n\r
-// A           y                       y               y\r
-// T           N                       n\r
-// M           y                       y               y\r
-// F           y                       y               y\r
-// Y           n                       n\r
-// W           y                       n\r
-// H           n                       n\r
-// K           n                       n\r
-static bool Hydrophobic[20] =\r
-       {\r
-       true,           // A\r
-       true,           // C\r
-       false,          // D\r
-       false,          // E\r
-       true,           // F\r
-       false,          // G\r
-       true,           // H\r
-       true,           // I\r
-       false,          // K\r
-       true,           // L\r
-       true,           // M\r
-       false,          // N\r
-       false,          // P\r
-       false,          // Q\r
-       false,          // R\r
-       false,          // S\r
-       true,           // T\r
-       true,           // V\r
-       true,           // Y\r
-       true,           // W\r
-       };\r
-\r
-bool IsHydrophobic(const FCOUNT fcCounts[])\r
-       {\r
-       if (ALPHA_Amino != g_Alpha)\r
-               Quit("IsHydrophobic: requires amino acid sequence");\r
-\r
-       for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
-               if (fcCounts[uLetter] > 0.0 && !Hydrophobic[uLetter])\r
-                       return false;\r
-       return true;\r
-       }\r