new version of muscle 3.8.31

[jabaws.git] / binaries / src / muscle / scoremx.cpp

diff --git a/binaries/src/muscle/scoremx.cpp b/binaries/src/muscle/scoremx.cpp
new file mode 100644 (file)
index 0000000..ca36c4d
--- /dev/null
+++ b/binaries/src/muscle/scoremx.cpp
@@ -0,0 +1,45 @@
+#include "muscle.h"\r
+#include "profile.h"\r
+\r
+extern SCOREMATRIX VTML_LA;\r
+extern SCOREMATRIX PAM200;\r
+extern SCOREMATRIX PAM200NoCenter;\r
+extern SCOREMATRIX VTML_SP;\r
+extern SCOREMATRIX VTML_SPNoCenter;\r
+extern SCOREMATRIX NUC_SP;\r
+\r
+PTR_SCOREMATRIX g_ptrScoreMatrix;\r
+\r
+void SetScoreMatrix()\r
+       {\r
+       switch (g_PPScore)\r
+               {\r
+       case PPSCORE_LE:\r
+               g_ptrScoreMatrix = &VTML_LA;\r
+               break;\r
+\r
+       case PPSCORE_SP:\r
+               if (g_bPrecompiledCenter)\r
+                       g_ptrScoreMatrix = &PAM200;\r
+               else\r
+                       g_ptrScoreMatrix = &PAM200NoCenter;\r
+               break;\r
+\r
+       case PPSCORE_SV:\r
+               if (g_bPrecompiledCenter)\r
+                       g_ptrScoreMatrix = &VTML_SP;\r
+               else\r
+                       g_ptrScoreMatrix = &VTML_SPNoCenter;\r
+               break;\r
+\r
+       case PPSCORE_SPN:\r
+               if (g_bPrecompiledCenter)\r
+                       g_ptrScoreMatrix = &NUC_SP;\r
+               else\r
+                       Quit("SPN requires precompiled center");\r
+               break;\r
+\r
+       default:\r
+               Quit("Invalid g_PPScore");\r
+               }\r
+       }\r