new mafft v 6.857 with extensions

[jabaws.git] / binaries / src / mafft / extensions / mxscarna_src / probconsRNA / Defaults.h

diff --git a/binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Defaults.h b/binaries/src/mafft/extensions/mxscarna_src/probconsRNA/Defaults.h
new file mode 100644 (file)
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+/////////////////////////////////////////////////////////////////
+// Defaults.h
+//
+// Default constants for use in PROBCONS.  The emission
+// probabilities were computed using the program used to build
+// the BLOSUM62 matrix from the BLOCKS 5.0 dataset.  Transition
+// parameters were obtained via unsupervised EM training on the
+// BALIBASE 2.0 benchmark alignment database.
+/////////////////////////////////////////////////////////////////
+
+#ifndef DEFAULTS_H
+#define DEFAULTS_H
+
+#include <string>
+
+using namespace std;
+/* Default */
+namespace MXSCARNA {
+/*
+float initDistrib1Default[] = { 0.9588437676f, 0.0205782652f, 0.0205782652f };
+float gapOpen1Default[] = { 0.0190259293f, 0.0190259293f };
+float gapExtend1Default[] = { 0.3269913495f, 0.3269913495f };
+*/
+
+/* EMtrainingALL.txt*/
+float initDistrib1Default[] = { 0.9234497547, 0.0385021642, 0.0385021642 };
+float gapOpen1Default[] = { 0.0266662259, 0.0266662259 };
+float gapExtend1Default[] = { 0.3849118352, 0.3849118352 };
+
+
+float initDistrib2Default[] = { 0.9615409374f, 0.0000004538f, 0.0000004538f, 0.0192291681f, 0.0192291681f };
+float gapOpen2Default[] = { 0.0082473317f, 0.0082473317f, 0.0107844425f, 0.0107844425f };
+float gapExtend2Default[] = { 0.3210460842f, 0.3210460842f, 0.3298229277f, 0.3298229277f };
+
+string alphabetDefault = "ACGUTN";
+
+//float emitSingleDefault[6] = {
+//   0.2174750715, 0.2573366761, 0.3005372882, 0.2233072966, 0.2233072966, 0.0004049665
+//};
+
+/* Default */
+/*
+float emitSingleDefault[6] = {
+  0.2270790040f, 0.2422080040f, 0.2839320004f, 0.2464679927f, 0.2464679927f, 0.0003124650f 
+};
+*/
+
+/* EMtrainingALL.txt */
+float emitSingleDefault[6] = {
+    0.2017124593, 0.2590311766, 0.2929603755, 0.2453189045, 0.2453189045, 0.0000873194 };
+
+/* ACGUTN */
+/* Default */
+/*
+float emitPairsDefault[6][6] = {
+  { 0.1487240046f, 0.0184142999f, 0.0361397006f, 0.0238473993f, 0.0238473993f, 0.0000375308f },
+  { 0.0184142999f, 0.1583919972f, 0.0275536999f, 0.0389291011f, 0.0389291011f, 0.0000815823f },
+  { 0.0361397006f, 0.0275536999f, 0.1979320049f, 0.0244289003f, 0.0244289003f, 0.0000824765f },
+  { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+  { 0.0238473993f, 0.0389291011f, 0.0244289003f, 0.1557479948f, 0.1557479948f, 0.0000743985f },
+  { 0.0000375308f, 0.0000815823f, 0.0000824765f, 0.0000743985f, 0.0000743985f, 0.0000263252f }
+};
+*/
+/* EMtrainingALL.txt */
+float emitPairsDefault[6][6] = {
+    { 0.1659344733, 0.0298952684, 0.0543937907, 0.0344539173, 0.0344539173, 0.0000032761 },
+    { 0.0298952684, 0.1817403436, 0.0415624641, 0.0589077808, 0.0589077808, 0.0000117011 },
+    { 0.0543937907, 0.0415624641, 0.2342105955, 0.0410407558, 0.0410407558, 0.0000072893 },
+    { 0.0344539173, 0.0589077808, 0.0410407558, 0.1578272283, 0.1578272283, 0.0000067871 },
+    { 0.0344539173, 0.0589077808, 0.0410407558, 0.1578272283, 0.1578272283, 0.0000067871 },
+    { 0.0344539173, 0.0589077808, 0.0410407558, 0.1578272283, 0.1578272283, 0.0000067871 },
+//    { 0.0000032761, 0.0000117011, 0.0000072893, 0.0000067871, 0.0000067871, 0.0000000166 } 
+};
+
+  /*
+float emitPairsDefault[6][6] = {
+    {0.1731323451, 0.0378843173, 0.0656677559, 0.0450690985, 0.0450690985, 0.0000215275},
+    {0.0378843173, 0.1611578614, 0.0492933467, 0.0651549697, 0.0651549697, 0.0000362353},
+    {0.0656677559, 0.0492933467, 0.1937607974, 0.0464556068, 0.0464556068, 0.0000293904},
+    {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+    {0.0450690985, 0.0651549697, 0.0464556068, 0.1622997671, 0.1622997671, 0.0000352637},
+    {0.0000215275, 0.0000362353, 0.0000293904, 0.0000352637, 0.0000352637, 0.0000000000}
+};
+  */
+}
+#endif