new mafft v 6.857 with extensions

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / GlobalParameters.cpp

diff --git a/binaries/src/mafft/extensions/mxscarna_src/GlobalParameters.cpp b/binaries/src/mafft/extensions/mxscarna_src/GlobalParameters.cpp
new file mode 100644 (file)
index 0000000..4d32c8e
--- /dev/null
+++ b/binaries/src/mafft/extensions/mxscarna_src/GlobalParameters.cpp
@@ -0,0 +1,27 @@
+//////////////////////////////////////////////////////////////
+// GlobalParameters.cpp
+// This file include Global Parameters, command line options, etc.
+//////////////////////////////////////////////////////////////
+
+#include "scarna.hpp"
+
+// These paramenters are defined in scarna.hpp
+
+float RNA_Match_AA      = RNAMATCHAA;
+float RNA_Match_AT      = RNAMATCHAT;
+float RNA_Match_AG      = RNAMATCHAG;
+float RNA_Match_AC      = RNAMATCHAC;
+float RNA_Match_TT      = RNAMATCHTT;
+float RNA_Match_TG      = RNAMATCHTG;
+float RNA_Match_TC      = RNAMATCHTC;
+float RNA_Match_GG      = RNAMATCHGG;
+float RNA_Match_GC      = RNAMATCHGC;
+float RNA_Match_CC      = RNAMATCHCC;
+float RNA_Gap_Penalty   = GAPPENALTY;
+float RNA_Gap_Extension = GAPEXTENTIONPENALTY;
+
+int   numIterativeRefinementReps = REFINEMENTREPS;
+bool  PostProcessAlignment = false;
+int   scsLength = SCSLENGTH;
+float BaseProbThreshold = BASEPROBTHRESHOLD;
+float BasePairConst     = BASEPAIRCONST;