Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/tomhydro.cpp b/website/archive/binaries/mac/src/muscle/tomhydro.cpp
deleted file mode 100644 (file)
index 88b664b..0000000
--- a/website/archive/binaries/mac/src/muscle/tomhydro.cpp
+++ /dev/null
@@ -1,109 +0,0 @@
-#include "muscle.h"\r
-#include "profile.h"\r
-\r
-// Original:\r
-//HYDROPHILIC_CONTEXT 0 6 -0.3969495574
-//HYDROPHILIC_CONTEXT 1 6 -0.9407126603
-//HYDROPHILIC_CONTEXT 2 6 -0.4968150972
-//HYDROPHILIC_CONTEXT 3 6 -0.271646023
-//HYDROPHILIC_CONTEXT 4 6 0.006990406416
-//HYDROPHILIC_CONTEXT 5 6 0.1381111256
-//HYDROPHILIC_CONTEXT 6 6 0.2541439872
-\r
-// Blosum62:\r
-//HYDROPHILIC_CONTEXT 0 6 -0.2448419585
-//HYDROPHILIC_CONTEXT 1 6 -0.8734889946
-//HYDROPHILIC_CONTEXT 2 6 -0.5724336598
-//HYDROPHILIC_CONTEXT 3 6 -0.2670439975
-//HYDROPHILIC_CONTEXT 4 6 0.004844647323
-//HYDROPHILIC_CONTEXT 5 6 0.1812057148
-//HYDROPHILIC_CONTEXT 6 6 0.1036540864
-
-static SCORE Factors[7] =\r
-       {\r
-       (SCORE) -0.2448419585,
-       (SCORE) -0.8734889946,
-       (SCORE) -0.5724336598,
-       (SCORE) -0.2670439975,
-       (SCORE) 0.004844647323,
-       (SCORE) 0.1812057148,
-       (SCORE) 0.1036540864
-       };\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
-       for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
-               if (fcCounts[uLetter] > 0.0 && Hydrophilic[uLetter])\r
-                       return false;\r
-       return true;\r
-       }\r
-\r
-static double HydrophilicFraction(const FCOUNT fcCounts[])\r
-       {\r
-       double TotalAll = 0.0;\r
-       double TotalHydrophilic = 0.0;\r
-       for (unsigned uLetter = 0; uLetter < 20; ++uLetter)\r
-               {\r
-               FCOUNT Freq = fcCounts[uLetter];\r
-               TotalAll += Freq;\r
-               if (Hydrophilic[uLetter])\r
-                       TotalHydrophilic += Freq;\r
-               }\r
-       return TotalHydrophilic / TotalAll;\r
-       }\r
-\r
-void TomHydro(ProfPos *Prof, unsigned uLength)\r
-       {\r
-       if (ALPHA_Amino != g_Alpha)\r
-               return;\r
-       if (uLength < 6)\r
-               return;\r
-\r
-       for (unsigned uColIndex = 3; uColIndex < uLength - 2; ++uColIndex)\r
-               {\r
-       // 6-residue window:\r
-       //       xxxxxx\r
-       //      AARNCARNGTAGCATNAC\r
-       //      AARN----------TNAC\r
-\r
-               double dCount = 0.0;\r
-               for (unsigned uColIndexW = uColIndex - 3; uColIndexW < uColIndex + 3;\r
-                 ++uColIndexW)\r
-                       {\r
-                       const ProfPos &PP = Prof[uColIndexW];\r
-                       dCount += HydrophilicFraction(PP.m_fcCounts);\r
-                       }\r
-       // Round to nearest integer\r
-               unsigned uCount = (unsigned) (dCount + 0.5);\r
-               if (uCount > 6)\r
-                       uCount = 6;\r
-               SCORE dFactor = Factors[uCount];\r
-               ProfPos &PP = Prof[uColIndex];\r
-               PP.m_scoreGapOpen += dFactor;\r
-               PP.m_scoreGapClose += dFactor;\r
-               }\r
-       }\r