Mac binaries

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

diff --git a/website/archive/binaries/mac/src/muscle/bittraceback.cpp b/website/archive/binaries/mac/src/muscle/bittraceback.cpp
new file mode 100644 (file)
index 0000000..9165985
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/bittraceback.cpp
@@ -0,0 +1,206 @@
+#include "muscle.h"\r
+#include "pwpath.h"\r
+\r
+#define TRACE 0\r
+\r
+static char XlatEdgeType(char c)\r
+       {\r
+       if ('E' == c)\r
+               return 'D';\r
+       if ('J' == c)\r
+               return 'I';\r
+       return c;\r
+       }\r
+\r
+static const char *BitsToStr(char Bits)\r
+       {\r
+       static char Str[] = "xM xD xI";\r
+\r
+       switch (Bits & BIT_xM)\r
+               {\r
+       case BIT_MM:\r
+               Str[0] = 'M';\r
+               break;\r
+       case BIT_DM:\r
+               Str[0] = 'D';\r
+               break;\r
+       case BIT_IM:\r
+               Str[0] = 'I';\r
+               break;\r
+               }\r
+\r
+       switch (Bits & BIT_xD)\r
+               {\r
+       case BIT_MD:\r
+               Str[3] = 'M';\r
+               break;\r
+       case BIT_DD:\r
+               Str[3] = 'D';\r
+               break;\r
+               }\r
+\r
+       switch (Bits & BIT_xI)\r
+               {\r
+       case BIT_MI:\r
+               Str[6] = 'M';\r
+               break;\r
+       case BIT_II:\r
+               Str[6] = 'I';\r
+               break;\r
+               }\r
+\r
+       return Str;\r
+       }\r
+\r
+static inline char XChar(char Bits, char cType)\r
+       {\r
+       switch (cType)\r
+               {\r
+       case 'M':\r
+               {\r
+               switch (Bits & BIT_xM)\r
+                       {\r
+               case BIT_MM:\r
+                       return 'M';\r
+               case BIT_DM:\r
+                       return 'D';\r
+               case BIT_IM:\r
+                       return 'I';\r
+#if    DOUBLE_AFFINE\r
+               case BIT_EM:\r
+                       return 'E';\r
+               case BIT_JM:\r
+                       return 'J';\r
+#endif\r
+                       }\r
+               Quit("Huh!?");\r
+               return '?';\r
+               }\r
+       case 'D':\r
+               {\r
+               switch (Bits & BIT_xD)\r
+                       {\r
+               case BIT_MD:\r
+                       return 'M';\r
+               case BIT_DD:\r
+                       return 'D';\r
+                       }\r
+               Quit("Huh!?");\r
+               return '?';\r
+               }\r
+       case 'I':\r
+               {\r
+               switch (Bits & BIT_xI)\r
+                       {\r
+               case BIT_MI:\r
+                       return 'M';\r
+               case BIT_II:\r
+                       return 'I';\r
+                       }\r
+               Quit("Huh!?");\r
+               return '?';\r
+               }\r
+#if    DOUBLE_AFFINE\r
+       case 'E':\r
+               {\r
+               switch (Bits & BIT_xE)\r
+                       {\r
+               case BIT_ME:\r
+                       return 'M';\r
+               case BIT_EE:\r
+                       return 'E';\r
+                       }\r
+               Quit("Huh!?");\r
+               return '?';\r
+               }\r
+       case 'J':\r
+               {\r
+               switch (Bits & BIT_xJ)\r
+                       {\r
+               case BIT_MJ:\r
+                       return 'M';\r
+               case BIT_JJ:\r
+                       return 'J';\r
+                       }\r
+               Quit("Huh!?");\r
+               return '?';\r
+               }\r
+#endif\r
+       default:\r
+               Quit("Huh?");\r
+               return '?';\r
+               }\r
+       }\r
+\r
+void BitTraceBack(char **TraceBack, unsigned uLengthA, unsigned uLengthB,\r
+  char LastEdge, PWPath &Path)\r
+       {\r
+#if    TRACE\r
+       Log("BitTraceBack\n");\r
+#endif\r
+       Path.Clear();\r
+\r
+       PWEdge Edge;\r
+       Edge.uPrefixLengthA = uLengthA;\r
+       Edge.uPrefixLengthB = uLengthB;\r
+       char Bits = TraceBack[uLengthA][uLengthB];\r
+       Edge.cType = LastEdge;\r
+       for (;;)\r
+               {\r
+#if    TRACE\r
+               Log("Prepend %c%d.%d\n", Edge.cType, Edge.uPrefixLengthA, Edge.uPrefixLengthB);\r
+#endif\r
+               char cSave = Edge.cType;\r
+               Edge.cType = XlatEdgeType(cSave);\r
+               Path.PrependEdge(Edge);\r
+               Edge.cType = cSave;\r
+\r
+               unsigned PLA = Edge.uPrefixLengthA;\r
+               unsigned PLB = Edge.uPrefixLengthB;\r
+               char Bits = TraceBack[PLA][PLB];\r
+               char NextEdgeType = XChar(Bits, Edge.cType);\r
+#if    TRACE\r
+               Log("XChar(%s, %c) = %c\n", BitsToStr(Bits), Edge.cType, NextEdgeType);\r
+#endif\r
+               switch (Edge.cType)\r
+                       {\r
+               case 'M':\r
+                       {\r
+                       if (Edge.uPrefixLengthA == 0)\r
+                               Quit("BitTraceBack MA=0");\r
+                       if (Edge.uPrefixLengthB == 0)\r
+                               Quit("BitTraceBack MA=0");\r
+                       --(Edge.uPrefixLengthA);\r
+                       --(Edge.uPrefixLengthB);\r
+                       break;\r
+                       }\r
+               case 'D':\r
+               case 'E':\r
+                       {\r
+                       if (Edge.uPrefixLengthA == 0)\r
+                               Quit("BitTraceBack DA=0");\r
+                       --(Edge.uPrefixLengthA);\r
+                       break;\r
+                       }\r
+               case 'I':\r
+               case 'J':\r
+                       {\r
+                       if (Edge.uPrefixLengthB == 0)\r
+                               Quit("BitTraceBack IB=0");\r
+                       --(Edge.uPrefixLengthB);\r
+                       break;\r
+                       }\r
+               default:\r
+                       Quit("BitTraceBack: Invalid edge %c", Edge);\r
+                       }\r
+\r
+               if (0 == Edge.uPrefixLengthA && 0 == Edge.uPrefixLengthB)\r
+                       break;\r
+\r
+               Edge.cType = NextEdgeType;\r
+               }\r
+\r
+#if    TRACE\r
+       Path.LogMe();\r
+#endif\r
+       }\r