Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / muscle / types.h

diff --git a/website/archive/binaries/mac/src/muscle/types.h b/website/archive/binaries/mac/src/muscle/types.h
new file mode 100644 (file)
index 0000000..b93eb84
--- /dev/null
+++ b/website/archive/binaries/mac/src/muscle/types.h
@@ -0,0 +1,117 @@
+#ifndef types_h\r
+#define types_h\r
+\r
+typedef unsigned char byte;\r
+typedef unsigned short ushort;\r
+\r
+typedef float SCOREMATRIX[32][32];\r
+typedef SCOREMATRIX *PTR_SCOREMATRIX;\r
+\r
+class MSA;\r
+class Seq;\r
+class ClusterTree;\r
+class DistFunc;\r
+class TextFile;\r
+class PWPath;\r
+class Tree;\r
+class SeqVect;\r
+class DistCalc;\r
+\r
+struct ProgNode;\r
+struct ProfPos;\r
+\r
+#if    SINGLE_AFFINE\r
+// Compress M, D and I trace-back matrices into 4 bits\r
+enum\r
+       {\r
+       BIT_MM = 0x00,\r
+       BIT_DM = 0x01,\r
+       BIT_IM = 0x02,\r
+       BIT_xM = 0x03,\r
+\r
+       BIT_DD = 0x00,\r
+       BIT_MD = 0x04,\r
+       //  ID not allowed\r
+       BIT_xD = 0x04,\r
+\r
+       BIT_II = 0x00,\r
+       BIT_MI = 0x08,\r
+       //  DI not allowed\r
+       BIT_xI = 0x08,\r
+       };\r
+\r
+#endif\r
+\r
+#if    DOUBLE_AFFINE\r
+// Compress M, D, E, I and J trace-back matrices into 7 bits\r
+enum\r
+       {\r
+       BIT_MM = 0x00,\r
+       BIT_DM = 0x01,\r
+       BIT_EM = 0x02,\r
+       BIT_IM = 0x03,\r
+       BIT_JM = 0x04,\r
+       BIT_xM = 0x07,\r
+\r
+       BIT_DD = 0x00,\r
+       BIT_MD = 0x08,\r
+       // [EIJ]D not sallowed\r
+       BIT_xD = 0x08,\r
+\r
+       BIT_EE = 0x00,\r
+       BIT_ME = 0x10,\r
+       //  [DDJ]E not allowed\r
+       BIT_xE = 0x10,\r
+\r
+       BIT_II = 0x00,\r
+       BIT_MI = 0x20,\r
+       //  [EDJ]I not allowed\r
+       BIT_xI = 0x20,\r
+\r
+       BIT_JJ = 0x00,\r
+       BIT_MJ = 0x40,\r
+       //  [EDI]J not allowed\r
+       BIT_xJ = 0x40,\r
+       };\r
+#endif\r
+\r
+enum EXIT\r
+       {\r
+       EXIT_Success = 0,\r
+       EXIT_NotStarted = 1,\r
+       EXIT_FatalError = 2,\r
+       EXIT_Except = 3,\r
+       };\r
+\r
+enum NODECMP\r
+       {\r
+       NODECMP_Undefined = 0,\r
+       NODECMP_Same = 0,               // equivalent to node in old tree\r
+       NODECMP_Diff = 1,               // equivalent & parent is changed\r
+       NODECMP_Changed = 2             // no equivalent node in old tree\r
+       };\r
+\r
+// Declare enums using macro hacks (see enums.h).\r
+#define s(t)   enum t { t##_Undefined = 0,\r
+#define c(t, x)        t##_##x,\r
+#define e(t)   };\r
+#include "enums.h"\r
+\r
+// Declare conversion function XXXToStr(XXX x)\r
+// for each enum type XXX.\r
+#define        s(t)    const char *t##ToStr(t x);\r
+#define c(t, x)        /* empty */\r
+#define e(t)   /* empty */\r
+#include "enums.h"\r
+\r
+// Declare conversion function StrToXXX(const char *Str)\r
+// for each enum type XXX.\r
+#define        s(t)    t StrTo##t(const char *Str);\r
+#define c(t, x)        /* empty */\r
+#define e(t)   /* empty */\r
+#include "enums.h"\r
+\r
+const char *BoolToStr(bool b);\r
+const char *SecsToStr(unsigned long Secs);\r
+\r
+#endif // types_h\r