Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/glbalign.cpp b/website/archive/binaries/mac/src/muscle/glbalign.cpp
deleted file mode 100644 (file)
index a22d6a1..0000000
--- a/website/archive/binaries/mac/src/muscle/glbalign.cpp
+++ /dev/null
@@ -1,165 +0,0 @@
-#include "muscle.h"\r
-#include "pwpath.h"\r
-#include "timing.h"\r
-#include "textfile.h"\r
-#include "msa.h"\r
-#include "profile.h"\r
-\r
-#if    !VER_3_52\r
-\r
-#define COMPARE_SIMPLE 0\r
-\r
-#if    TIMING\r
-TICKS g_ticksDP = 0;\r
-#endif\r
-\r
-#if    1\r
-extern bool g_bKeepSimpleDP;\r
-SCORE NWSmall(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path);\r
-SCORE NWDASmall(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path);\r
-SCORE NWDASimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path);\r
-SCORE NWDASimple2(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path);\r
-SCORE GlobalAlignSimple(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path);\r
-\r
-SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path)\r
-       {\r
-       return GlobalAlign(PA, uLengthA, PB, uLengthB, Path);\r
-       }\r
-\r
-#if    COMPARE_SIMPLE\r
-\r
-SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path)\r
-       {\r
-#if    TIMING\r
-       TICKS t1 = GetClockTicks();\r
-#endif\r
-       g_bKeepSimpleDP = true;\r
-       PWPath SimplePath;\r
-       GlobalAlignSimple(PA, uLengthA, PB, uLengthB, SimplePath);\r
-\r
-       SCORE Score = NWSmall(PA, uLengthA, PB, uLengthB, Path);\r
-\r
-       if (!Path.Equal(SimplePath))\r
-               {\r
-               Log("Simple:\n");\r
-               SimplePath.LogMe();\r
-               Log("Small:\n");\r
-               Path.LogMe();\r
-               Quit("Paths differ");\r
-               }\r
-\r
-#if    TIMING\r
-       TICKS t2 = GetClockTicks();\r
-       g_ticksDP += (t2 - t1);\r
-#endif\r
-       return Score;\r
-       }\r
-\r
-#else // COMPARE_SIMPLE\r
-\r
-SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path)\r
-       {\r
-#if    TIMING\r
-       TICKS t1 = GetClockTicks();\r
-#endif\r
-       SCORE Score = NWSmall(PA, uLengthA, PB, uLengthB, Path);\r
-#if    TIMING\r
-       TICKS t2 = GetClockTicks();\r
-       g_ticksDP += (t2 - t1);\r
-#endif\r
-       return Score;\r
-       }\r
-\r
-#endif\r
-\r
-#else // 1\r
-\r
-static void AllInserts(PWPath &Path, unsigned uLengthB)\r
-       {\r
-       Path.Clear();\r
-       PWEdge Edge;\r
-       Edge.cType = 'I';\r
-       Edge.uPrefixLengthA = 0;\r
-       for (unsigned uPrefixLengthB = 1; uPrefixLengthB <= uLengthB; ++uPrefixLengthB)\r
-               {\r
-               Edge.uPrefixLengthB = uPrefixLengthB;\r
-               Path.AppendEdge(Edge);\r
-               }\r
-       }\r
-\r
-static void AllDeletes(PWPath &Path, unsigned uLengthA)\r
-       {\r
-       Path.Clear();\r
-       PWEdge Edge;\r
-       Edge.cType = 'D';\r
-       Edge.uPrefixLengthB = 0;\r
-       for (unsigned uPrefixLengthA = 1; uPrefixLengthA <= uLengthA; ++uPrefixLengthA)\r
-               {\r
-               Edge.uPrefixLengthA = uPrefixLengthA;\r
-               Path.AppendEdge(Edge);\r
-               }\r
-       }\r
-\r
-SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path)\r
-       {\r
-#if    TIMING\r
-       TICKS t1 = GetClockTicks();\r
-#endif\r
-       if (0 == uLengthA)\r
-               {\r
-               AllInserts(Path, uLengthB);\r
-               return 0;\r
-               }\r
-       else if (0 == uLengthB)\r
-               {\r
-               AllDeletes(Path, uLengthA);\r
-               return 0;\r
-               }\r
-\r
-       SCORE Score = 0;\r
-       if (g_bDiags)\r
-               Score = GlobalAlignDiags(PA, uLengthA, PB, uLengthB, Path);\r
-       else\r
-               Score = GlobalAlignNoDiags(PA, uLengthA, PB, uLengthB, Path);\r
-#if    TIMING\r
-       TICKS t2 = GetClockTicks();\r
-       g_ticksDP += (t2 - t1);\r
-#endif\r
-       return Score;\r
-       }\r
-\r
-SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path)\r
-       {\r
-       if (g_bDimer)\r
-               return GlobalAlignDimer(PA, uLengthA, PB, uLengthB, Path);\r
-\r
-       switch (g_PPScore)\r
-               {\r
-       case PPSCORE_LE:\r
-               return GlobalAlignLE(PA, uLengthA, PB, uLengthB, Path);\r
-\r
-       case PPSCORE_SP:\r
-       case PPSCORE_SV:\r
-               return GlobalAlignSP(PA, uLengthA, PB, uLengthB, Path);\r
-\r
-       case PPSCORE_SPN:\r
-               return GlobalAlignSPN(PA, uLengthA, PB, uLengthB, Path);\r
-               }\r
-\r
-       Quit("Invalid PP score (GlobalAlignNoDiags)");\r
-       return 0;\r
-       }\r
-\r
-#endif\r
-\r
-#endif // !VER_3_52\r