Delete unneeded directory

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

diff --git a/website/archive/binaries/mac/src/muscle/glbaligndiag.cpp b/website/archive/binaries/mac/src/muscle/glbaligndiag.cpp
deleted file mode 100644 (file)
index ff6f035..0000000
--- a/website/archive/binaries/mac/src/muscle/glbaligndiag.cpp
+++ /dev/null
@@ -1,172 +0,0 @@
-#include "muscle.h"\r
-#include "dpreglist.h"\r
-#include "diaglist.h"\r
-#include "pwpath.h"\r
-#include "profile.h"\r
-#include "timing.h"\r
-\r
-#define TRACE          0\r
-#define TRACE_PATH     0\r
-#define LIST_DIAGS     0\r
-\r
-static double g_dDPAreaWithoutDiags = 0.0;\r
-static double g_dDPAreaWithDiags = 0.0;\r
-\r
-static void OffsetPath(PWPath &Path, unsigned uOffsetA, unsigned uOffsetB)\r
-       {\r
-       const unsigned uEdgeCount = Path.GetEdgeCount();\r
-       for (unsigned uEdgeIndex = 0; uEdgeIndex < uEdgeCount; ++uEdgeIndex)\r
-               {\r
-               const PWEdge &Edge = Path.GetEdge(uEdgeIndex);\r
-\r
-       // Nasty hack -- poke new values back into path, circumventing class\r
-               PWEdge &NonConstEdge = (PWEdge &) Edge;\r
-               NonConstEdge.uPrefixLengthA += uOffsetA;\r
-               NonConstEdge.uPrefixLengthB += uOffsetB;\r
-               }\r
-       }\r
-\r
-static void DiagToPath(const Diag &d, PWPath &Path)\r
-       {\r
-       Path.Clear();\r
-       const unsigned uLength = d.m_uLength;\r
-       for (unsigned i = 0; i < uLength; ++i)\r
-               {\r
-               PWEdge Edge;\r
-               Edge.cType = 'M';\r
-               Edge.uPrefixLengthA = d.m_uStartPosA + i + 1;\r
-               Edge.uPrefixLengthB = d.m_uStartPosB + i + 1;\r
-               Path.AppendEdge(Edge);\r
-               }\r
-       }\r
-\r
-static void AppendRegPath(PWPath &Path, const PWPath &RegPath)\r
-       {\r
-       const unsigned uRegEdgeCount = RegPath.GetEdgeCount();\r
-       for (unsigned uRegEdgeIndex = 0; uRegEdgeIndex < uRegEdgeCount; ++uRegEdgeIndex)\r
-               {\r
-               const PWEdge &RegEdge = RegPath.GetEdge(uRegEdgeIndex);\r
-               Path.AppendEdge(RegEdge);\r
-               }\r
-       }\r
-\r
-SCORE GlobalAlignDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
-  unsigned uLengthB, PWPath &Path)\r
-       {\r
-#if    LIST_DIAGS\r
-       TICKS t1 = GetClockTicks();\r
-#endif\r
-\r
-       DiagList DL;\r
-\r
-       if (ALPHA_Amino == g_Alpha)\r
-               FindDiags(PA, uLengthA, PB, uLengthB, DL);\r
-       else if (ALPHA_DNA == g_Alpha || ALPHA_RNA == g_Alpha)\r
-               FindDiagsNuc(PA, uLengthA, PB, uLengthB, DL);\r
-       else\r
-               Quit("GlobalAlignDiags: bad alpha");\r
-\r
-#if    TRACE\r
-       Log("GlobalAlignDiags, diag list:\n");\r
-       DL.LogMe();\r
-#endif\r
-\r
-       DL.Sort();\r
-       DL.DeleteIncompatible();\r
-\r
-#if    TRACE\r
-       Log("After DeleteIncompatible:\n");\r
-       DL.LogMe();\r
-#endif\r
-\r
-       MergeDiags(DL);\r
-\r
-#if    TRACE\r
-       Log("After MergeDiags:\n");\r
-       DL.LogMe();\r
-#endif\r
-\r
-       DPRegionList RL;\r
-       DiagListToDPRegionList(DL, RL, uLengthA, uLengthB);\r
-\r
-#if    TRACE\r
-       Log("RegionList:\n");\r
-       RL.LogMe();\r
-#endif\r
-\r
-#if    LIST_DIAGS\r
-       {\r
-       TICKS t2 = GetClockTicks();\r
-       unsigned uArea = RL.GetDPArea();\r
-       Log("ticks=%ld\n", (long) (t2 - t1));\r
-       Log("area=%u\n", uArea);\r
-       }\r
-#endif\r
-\r
-       g_dDPAreaWithoutDiags += uLengthA*uLengthB;\r
-\r
-       double dDPAreaWithDiags = 0.0;\r
-       const unsigned uRegionCount = RL.GetCount();\r
-       for (unsigned uRegionIndex = 0; uRegionIndex < uRegionCount; ++uRegionIndex)\r
-               {\r
-               const DPRegion &r = RL.Get(uRegionIndex);\r
-\r
-               PWPath RegPath;\r
-               if (DPREGIONTYPE_Diag == r.m_Type)\r
-                       {\r
-                       DiagToPath(r.m_Diag, RegPath);\r
-#if    TRACE_PATH\r
-                       Log("DiagToPath, path=\n");\r
-                       RegPath.LogMe();\r
-#endif\r
-                       }\r
-               else if (DPREGIONTYPE_Rect == r.m_Type)\r
-                       {\r
-                       const unsigned uRegStartPosA = r.m_Rect.m_uStartPosA;\r
-                       const unsigned uRegStartPosB = r.m_Rect.m_uStartPosB;\r
-                       const unsigned uRegLengthA = r.m_Rect.m_uLengthA;\r
-                       const unsigned uRegLengthB = r.m_Rect.m_uLengthB;\r
-                       const ProfPos *RegPA = PA + uRegStartPosA;\r
-                       const ProfPos *RegPB = PB + uRegStartPosB;\r
-\r
-                       dDPAreaWithDiags += uRegLengthA*uRegLengthB;\r
-                       GlobalAlignNoDiags(RegPA, uRegLengthA, RegPB, uRegLengthB, RegPath);\r
-#if    TRACE_PATH\r
-                       Log("GlobalAlignNoDiags RegPath=\n");\r
-                       RegPath.LogMe();\r
-#endif\r
-                       OffsetPath(RegPath, uRegStartPosA, uRegStartPosB);\r
-#if    TRACE_PATH\r
-                       Log("After offset path, RegPath=\n");\r
-                       RegPath.LogMe();\r
-#endif\r
-                       }\r
-               else\r
-                       Quit("GlobalAlignDiags, Invalid region type %u", r.m_Type);\r
-\r
-               AppendRegPath(Path, RegPath);\r
-#if    TRACE_PATH\r
-               Log("After AppendPath, path=");\r
-               Path.LogMe();\r
-#endif\r
-               }\r
-\r
-#if    TRACE\r
-       {\r
-       double dDPAreaWithoutDiags = uLengthA*uLengthB;\r
-       Log("DP area with diags %.3g without %.3g pct saved %.3g %%\n",\r
-         dDPAreaWithDiags, dDPAreaWithoutDiags, (1.0 - dDPAreaWithDiags/dDPAreaWithoutDiags)*100.0);\r
-       }\r
-#endif\r
-       g_dDPAreaWithDiags += dDPAreaWithDiags;\r
-       return 0;\r
-       }\r
-\r
-void ListDiagSavings()\r
-       {\r
-       if (!g_bVerbose || !g_bDiags)\r
-               return;\r
-       double dAreaSaved = g_dDPAreaWithoutDiags - g_dDPAreaWithDiags;\r
-       double dPct = dAreaSaved*100.0/g_dDPAreaWithoutDiags;\r
-       Log("DP area saved by diagonals %-4.1f%%\n", dPct);\r
-       }\r