added uchime_src folder. added biom parameter to make.shared. added biom as a current...

[mothur.git] / uchime_src / setnucmx.cpp

diff --git a/uchime_src/setnucmx.cpp b/uchime_src/setnucmx.cpp
new file mode 100644 (file)
index 0000000..030ff5a
--- /dev/null
+++ b/uchime_src/setnucmx.cpp
@@ -0,0 +1,77 @@
+#include "myutils.h"
+#include "mx.h"
+
+Mx<float> g_SubstMxf;
+float **g_SubstMx;
+
+static const char Alphabet[] = "ACGTU";
+
+void SetNucSubstMx(double Match, double Mismatch)\r
+       {\r
+       static bool Done = false;\r
+       if (Done)\r
+               return;\r
+       Done = true;\r
+\r
+       if (Match <= 0.0)\r
+               Die("Match score should be +ve");\r
+       if (Mismatch >= 0.0)\r
+               Die("Mismatch score should be -ve");\r
+\r
+       unsigned N = unsigned(strlen(Alphabet));\r
+\r
+       g_SubstMxf.Alloc("NUCMX", 256, 256);\r
+       strcpy(g_SubstMxf.m_Alpha, "ACGT");\r
+       g_SubstMxf.Init(0);\r
+       g_SubstMx = g_SubstMxf.GetData();\r
+       for (unsigned i = 0; i < N; ++i)\r
+               {\r
+               for (unsigned j = 0; j < N; ++j)\r
+                       {\r
+                       float v = float(i == j ? Match : Mismatch);\r
+\r
+                       byte ui = (byte) toupper(Alphabet[i]);\r
+                       byte uj = (byte) toupper(Alphabet[j]);\r
+                       byte li = (byte) tolower(ui);\r
+                       byte lj = (byte) tolower(uj);\r
+                       ui = (byte) toupper(ui);\r
+                       uj = (byte) toupper(uj);\r
+\r
+                       g_SubstMx[ui][uj] = v;\r
+                       g_SubstMx[uj][ui] = v;\r
+\r
+                       g_SubstMx[ui][lj] = v;\r
+                       g_SubstMx[uj][li] = v;\r
+\r
+                       g_SubstMx[li][uj] = v;\r
+                       g_SubstMx[lj][ui] = v;\r
+\r
+                       g_SubstMx[li][lj] = v;\r
+                       g_SubstMx[lj][li] = v;\r
+                       }\r
+               }\r
+\r
+       for (unsigned j = 0; j < N; ++j)\r
+               {\r
+               float v = 0.0f;\r
+\r
+               byte ui = (byte) 'N';\r
+               byte uj = (byte) toupper(Alphabet[j]);\r
+               byte li = (byte) 'n';\r
+               byte lj = (byte) tolower(uj);\r
+               ui = (byte) toupper(ui);\r
+               uj = (byte) toupper(uj);\r
+\r
+               g_SubstMx[ui][uj] = v;\r
+               g_SubstMx[uj][ui] = v;\r
+\r
+               g_SubstMx[ui][lj] = v;\r
+               g_SubstMx[uj][li] = v;\r
+\r
+               g_SubstMx[li][uj] = v;\r
+               g_SubstMx[lj][ui] = v;\r
+\r
+               g_SubstMx[li][lj] = v;\r
+               g_SubstMx[lj][li] = v;\r
+               }\r
+       }\r