Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / muscle / fastscorepath2.cpp

diff --git a/website/archive/binaries/mac/src/muscle/fastscorepath2.cpp b/website/archive/binaries/mac/src/muscle/fastscorepath2.cpp
deleted file mode 100644 (file)
index 37a5b3b..0000000
--- a/website/archive/binaries/mac/src/muscle/fastscorepath2.cpp
+++ /dev/null
@@ -1,165 +0,0 @@
-#include "muscle.h"\r
-#include "profile.h"\r
-#include "pwpath.h"\r
-\r
-SCORE FastScorePath2(const ProfPos *PA, unsigned uLengthA,\r
-  const ProfPos *PB, unsigned uLengthB, const PWPath &Path)\r
-       {\r
-       const unsigned uEdgeCount = Path.GetEdgeCount();\r
-       Log("Edge  SS     PLA   PLB   Match     Gap    Total\n");\r
-       Log("----  --     ---   ---   -----     ---    -----\n");\r
-       char cType = 'S';\r
-       SCORE scoreTotal = 0;\r
-       for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)\r
-               {\r
-               const PWEdge &Edge = Path.GetEdge(uEdgeIndex);\r
-               const char cPrevType = cType;\r
-               cType = Edge.cType;\r
-               const unsigned uPrefixLengthA = Edge.uPrefixLengthA;\r
-               const unsigned uPrefixLengthB = Edge.uPrefixLengthB;\r
-               bool bGap = false;\r
-               bool bMatch = false;\r
-               SCORE scoreGap = 0;\r
-               SCORE scoreMatch = 0;\r
-\r
-               switch (cType)\r
-                       {\r
-               case 'M':\r
-                       {\r
-                       if (0 == uPrefixLengthA || 0 == uPrefixLengthB)\r
-                               Quit("FastScorePath2, M zero length");\r
-\r
-                       const ProfPos &PPA = PA[uPrefixLengthA - 1];\r
-                       const ProfPos &PPB = PB[uPrefixLengthB - 1];\r
-\r
-                       bMatch = true;\r
-                       scoreMatch = ScoreProfPos2(PPA, PPB);\r
-\r
-                       if ('D' == cPrevType)\r
-                               {\r
-                               bGap = true;\r
-                               assert(uPrefixLengthA > 1);\r
-                               scoreGap = PA[uPrefixLengthA-2].m_scoreGapClose;\r
-                               }\r
-                       else if ('I' == cPrevType)\r
-                               {\r
-                               bGap = true;\r
-                               assert(uPrefixLengthB > 1);\r
-                               scoreGap = PB[uPrefixLengthB-2].m_scoreGapClose;\r
-                               }\r
-                       break;\r
-                       }\r
-\r
-               case 'D':\r
-                       {\r
-                       if (0 == uPrefixLengthA)\r
-                               Quit("FastScorePath2, D zero length");\r
-\r
-                       const ProfPos &PPA = PA[uPrefixLengthA - 1];\r
-                       bGap = true;\r
-                       switch (cPrevType)\r
-                               {\r
-                       case 'S':\r
-                               scoreGap = PPA.m_scoreGapOpen;\r
-                               break;\r
-                       case 'M':\r
-                               scoreGap = PPA.m_scoreGapOpen;\r
-                               break;\r
-                       case 'D':\r
-//                             scoreGap = g_scoreGapExtend;\r
-                               scoreGap = 0;\r
-                               break;\r
-                       case 'I':\r
-                               Quit("FastScorePath2 DI");\r
-                               }\r
-                       break;\r
-                       }\r
-\r
-               case 'I':\r
-                       {\r
-                       if (0 == uPrefixLengthB)\r
-                               Quit("FastScorePath2, I zero length");\r
-\r
-                       const ProfPos &PPB = PB[uPrefixLengthB - 1];\r
-                       bGap = true;\r
-                       switch (cPrevType)\r
-                               {\r
-                       case 'S':\r
-                               scoreGap = PPB.m_scoreGapOpen;\r
-                               break;\r
-                       case 'M':\r
-                               scoreGap = PPB.m_scoreGapOpen;\r
-                               break;\r
-                       case 'I':\r
-                               scoreGap = 0;\r
-//                             scoreGap = g_scoreGapExtend;\r
-                               break;\r
-                       case 'D':\r
-                               Quit("FastScorePath2 DI");\r
-                               }\r
-                       break;\r
-                       }\r
-\r
-               case 'U':\r
-                       {\r
-                       Quit("FastScorePath2 U");\r
-                       }\r
-\r
-               default:\r
-                       Quit("FastScorePath2: invalid type %c", cType);\r
-                       }\r
-\r
-               Log("%4u  %c%c  %4u  %4u  ", uEdgeIndex, cPrevType, cType,\r
-                 uPrefixLengthA, uPrefixLengthB);\r
-               if (bMatch)\r
-                       Log("%7.1f  ", scoreMatch);\r
-               else\r
-                       Log("         ");\r
-               if (bGap)\r
-                       Log("%7.1f  ", scoreGap);\r
-               else\r
-                       Log("         ");\r
-               SCORE scoreEdge = scoreMatch + scoreGap;\r
-               scoreTotal += scoreEdge;\r
-               Log("%7.1f  %7.1f", scoreEdge, scoreTotal);\r
-               Log("\n");\r
-               }\r
-\r
-       SCORE scoreGap = 0;\r
-//     if (!g_bTermGapsHalf)\r
-               switch (cType)\r
-                       {\r
-               case 'M':\r
-                       scoreGap = 0;\r
-                       break;\r
-\r
-               case 'D':\r
-                       {\r
-                       const ProfPos &LastPPA = PA[uLengthA - 1];\r
-                       scoreGap = LastPPA.m_scoreGapClose;\r
-                       break;\r
-                       }\r
-\r
-               case 'I':\r
-                       {\r
-                       const ProfPos &LastPPB = PB[uLengthB - 1];\r
-                       scoreGap = LastPPB.m_scoreGapClose;\r
-                       break;\r
-                       }\r
-\r
-               case 'U':\r
-                       Quit("Unaligned regions not supported");\r
-\r
-               case 'S':\r
-                       break;\r
-\r
-               default:\r
-                       Quit("Invalid type %c", cType);\r
-                       }\r
-\r
-       Log("      %cE  %4u  %4u           %7.1f\n", cType, uLengthA, uLengthB, scoreGap);\r
-       scoreTotal += scoreGap;\r
-\r
-       Log("Total = %g\n", scoreTotal);\r
-       return scoreTotal;\r
-       }\r