1.22.0

[mothur.git] / alnparams.cpp

diff --git a/alnparams.cpp b/alnparams.cpp
index 41ee738027921b1a217544a67a449ff0dc5fb761..d1b90364212dc4aa41bd275166e22cf37afc2038 100644 (file)
--- a/alnparams.cpp
+++ b/alnparams.cpp
@@ -1,5 +1,3 @@
-//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
@@ -8,12 +6,12 @@
 \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
@@ -315,14 +313,14 @@ void AlnParams::SetPenalties(const string &OpenStr, const string &ExtStr)
 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
@@ -363,9 +361,9 @@ void AlnParams::InitFromCmdLine(bool IsNucleo)
 \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