--- /dev/null
+#include "muscle.h"\r
+#include "pwpath.h"\r
+#include "timing.h"\r
+#include "textfile.h"\r
+#include "msa.h"\r
+#include "profile.h"\r
+\r
+SCORE GlobalAlign(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
+ unsigned uLengthB, PWPath &Path)\r
+ {\r
+ if (g_bDiags)\r
+ return GlobalAlignDiags(PA, uLengthA, PB, uLengthB, Path);\r
+ else\r
+ return GlobalAlignNoDiags(PA, uLengthA, PB, uLengthB, Path);\r
+ }\r
+\r
+SCORE GlobalAlignNoDiags(const ProfPos *PA, unsigned uLengthA, const ProfPos *PB,\r
+ unsigned uLengthB, PWPath &Path)\r
+ {\r
+ switch (g_PPScore)\r
+ {\r
+ case PPSCORE_LE:\r
+ return GlobalAlignLA(PA, uLengthA, PB, uLengthB, Path);\r
+\r
+ case PPSCORE_SP:\r
+ return GlobalAlignNS(PA, uLengthA, PB, uLengthB, Path);\r
+\r
+ case PPSCORE_SV:\r
+ return GlobalAlignSimple(PA, uLengthA, PB, uLengthB, Path);\r
+ }\r
+ return 0;\r
+ }\r