X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=alnparams.cpp;h=41ee738027921b1a217544a67a449ff0dc5fb761;hb=1e8d08e96f4fe99604a6b3502568de464bf60891;hp=d1b90364212dc4aa41bd275166e22cf37afc2038;hpb=fd98ee6efb944d38bbd61fc36ea9fea2557e3830;p=mothur.git

diff --git a/alnparams.cpp b/alnparams.cpp
index d1b9036..41ee738 100644
--- a/alnparams.cpp
+++ b/alnparams.cpp
@@ -1,3 +1,5 @@
+//uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
+
 #include "myutils.h"
 #include <float.h>	// for FLT_MAX
 #include "mx.h"
@@ -6,12 +8,12 @@
 
 #define TEST	0
 
-void SetBLOSUM62();
+void SetBLOSUM62();
 void SetNucSubstMx(double Match, double Mismatch);
 void ReadSubstMx(const string &FileName, Mx<float> &Mxf);
-
-extern Mx<float> g_SubstMxf;
-extern float **g_SubstMx;
+
+extern Mx<float> g_SubstMxf;
+extern float **g_SubstMx;
 
 void AlnParams::Clear()
 	{
@@ -313,14 +315,14 @@ void AlnParams::SetPenalties(const string &OpenStr, const string &ExtStr)
 void AlnParams::SetMxFromCmdLine(bool IsNucleo)
 	{
 	if (IsNucleo)
-		SetNucSubstMx(opt_match, opt_mismatch);
+		SetNucSubstMx(opt_match, opt_mismatch);
 	else
 		{
 		if (opt_matrix == "")
 			{
 			SubstMxName = "BLOSUM62";
-			SetBLOSUM62();
-			}
+			SetBLOSUM62();
+			}
 		else
 			{
 			ReadSubstMx(opt_matrix, g_SubstMxf);
@@ -361,9 +363,9 @@ void AlnParams::InitFromCmdLine(bool IsNucleo)
 
 // Global
 	if (IsNucleo)
-		Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);
+		Init4(g_SubstMx, -10.0, -1.0, -0.5, -0.5);
 	else
-		Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);
+		Init4(g_SubstMx, -17.0, -1.0, -0.5, -0.5);
 	SetPenalties(opt_gapopen, opt_gapext);
 	}