Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/scorepp.cpp b/website/archive/binaries/mac/src/muscle/scorepp.cpp
deleted file mode 100644 (file)
index 541e7ff..0000000
--- a/website/archive/binaries/mac/src/muscle/scorepp.cpp
+++ /dev/null
@@ -1,104 +0,0 @@
-#include "muscle.h"\r
-#include "profile.h"\r
-\r
-char ConsensusChar(const ProfPos &PP)\r
-       {\r
-       unsigned uMostCommonLetter = 0;\r
-       FCOUNT fcMostCommon = PP.m_fcCounts[0];\r
-       bool bMoreThanOneLetter = false;\r
-       bool bAnyLetter = false;\r
-       for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter)\r
-               {\r
-               const FCOUNT fc = PP.m_fcCounts[uLetter];\r
-               if (fc > 0)\r
-                       {\r
-                       if (bAnyLetter)\r
-                               bMoreThanOneLetter = true;\r
-                       bAnyLetter = true;\r
-                       }\r
-               if (fc > fcMostCommon)\r
-                       {\r
-                       uMostCommonLetter = uLetter;\r
-                       fcMostCommon = fc;\r
-                       }\r
-               }\r
-       if (!bAnyLetter)\r
-               return '-';\r
-       char c = LetterToChar(uMostCommonLetter);\r
-       if (bMoreThanOneLetter)\r
-               return UnalignChar(c);\r
-       return c;\r
-       }\r
-\r
-SCORE ScoreProfPos2LA(const ProfPos &PPA, const ProfPos &PPB)\r
-       {\r
-       SCORE Score = 0;\r
-       for (unsigned n = 0; n < 20; ++n)\r
-               {\r
-               const unsigned uLetter = PPA.m_uSortOrder[n];\r
-               const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
-               if (0 == fcLetter)\r
-                       break;\r
-               Score += fcLetter*PPB.m_AAScores[uLetter];\r
-               }\r
-       if (0 == Score)\r
-               return -2.5;\r
-       SCORE logScore = logf(Score);\r
-       return (SCORE) ((logScore - g_scoreCenter)*(PPA.m_fOcc * PPB.m_fOcc));\r
-       }\r
-\r
-SCORE ScoreProfPos2NS(const ProfPos &PPA, const ProfPos &PPB)\r
-       {\r
-       SCORE Score = 0;\r
-       for (unsigned n = 0; n < 20; ++n)\r
-               {\r
-               const unsigned uLetter = PPA.m_uSortOrder[n];\r
-               const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
-               if (0 == fcLetter)\r
-                       break;\r
-               Score += fcLetter*PPB.m_AAScores[uLetter];\r
-               }\r
-       return Score - g_scoreCenter;\r
-       }\r
-\r
-SCORE ScoreProfPos2SP(const ProfPos &PPA, const ProfPos &PPB)\r
-       {\r
-       SCORE Score = 0;\r
-       for (unsigned n = 0; n < 20; ++n)\r
-               {\r
-               const unsigned uLetter = PPA.m_uSortOrder[n];\r
-               const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
-               if (0 == fcLetter)\r
-                       break;\r
-               Score += fcLetter*PPB.m_AAScores[uLetter];\r
-               }\r
-       return Score - g_scoreCenter;\r
-       }\r
-\r
-SCORE ScoreProfPos2SPN(const ProfPos &PPA, const ProfPos &PPB)\r
-       {\r
-       SCORE Score = 0;\r
-       for (unsigned n = 0; n < 4; ++n)\r
-               {\r
-               const unsigned uLetter = PPA.m_uSortOrder[n];\r
-               const FCOUNT fcLetter = PPA.m_fcCounts[uLetter];\r
-               if (0 == fcLetter)\r
-                       break;\r
-               Score += fcLetter*PPB.m_AAScores[uLetter];\r
-               }\r
-       return Score - g_scoreCenter;\r
-       }\r
-\r
-SCORE ScoreProfPos2(const ProfPos &PPA, const ProfPos &PPB)\r
-       {\r
-       if (PPSCORE_SP == g_PPScore)\r
-               return ScoreProfPos2NS(PPA, PPB);\r
-       else if (PPSCORE_LE == g_PPScore)\r
-               return ScoreProfPos2LA(PPA, PPB);\r
-       else if (PPSCORE_SV == g_PPScore)\r
-               return ScoreProfPos2SP(PPA, PPB);\r
-       else if (PPSCORE_SPN == g_PPScore)\r
-               return ScoreProfPos2SPN(PPA, PPB);\r
-       Quit("Invalid g_PPScore");\r
-       return 0;\r
-       }\r