-//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.\r
-\r
#include "myutils.h"\r
#include <float.h> // for FLT_MAX\r
#include "mx.h"\r
\r
#define TEST 0\r
\r
-void SetBLOSUM62();\r
+void SetBLOSUM62();
void SetNucSubstMx(double Match, double Mismatch);\r
void ReadSubstMx(const string &FileName, Mx<float> &Mxf);\r
-\r
-extern Mx<float> g_SubstMxf;\r
-extern float **g_SubstMx;\r
+
+extern Mx<float> g_SubstMxf;
+extern float **g_SubstMx;
\r
void AlnParams::Clear()\r
{\r
void AlnParams::SetMxFromCmdLine(bool IsNucleo)\r
{\r
if (IsNucleo)\r
- SetNucSubstMx(opt_match, opt_mismatch);\r
+ SetNucSubstMx(opt_match, opt_mismatch);
else\r
{\r
if (opt_matrix == "")\r
{\r
SubstMxName = "BLOSUM62";\r
- SetBLOSUM62();\r
- }\r
+ SetBLOSUM62();
+ }
else\r
{\r
ReadSubstMx(opt_matrix, g_SubstMxf);\r
\r
// Global\r
if (IsNucleo)\r
- Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);\r
+ Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);
else\r
- Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);\r
+ Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);
SetPenalties(opt_gapopen, opt_gapext);\r
}\r
\r