Add GLprobs and MSAprobs to binaries

[jabaws.git] / binaries / src / MSAProbs-0.9.7 / MSAProbs / MSAReadMatrix.h

diff --git a/binaries/src/MSAProbs-0.9.7/MSAProbs/MSAReadMatrix.h b/binaries/src/MSAProbs-0.9.7/MSAProbs/MSAReadMatrix.h
new file mode 100644 (file)
index 0000000..8d15ce5
--- /dev/null
+++ b/binaries/src/MSAProbs-0.9.7/MSAProbs/MSAReadMatrix.h
@@ -0,0 +1,87 @@
+/////////////////////////////////////////////////////////////////
+//  Matrix.h
+//
+//  Specifies scoring matrices and their structure
+//  
+//
+//
+/////////////////////////////////////////////////////////////////
+
+#ifndef _MSA_READ_MATRIX_H
+#define _MSA_READ_MATRIX_H
+
+typedef struct {
+       char monomers[26]; /* amino or nucleic acid order */
+       float matrix[676]; /* entries of the score matix, 26*26=676 */
+} score_matrix;
+
+//default protein sequence scoring matrix as well as default scoring matrix of the PROBALIGN
+//also used when -prot option is used
+
+score_matrix gonnet_160 = { "ABCDEFGHIKLMNPQRSTVWXYZ",
+
+{ 4.6, 0.0, 0.0, 0.3, 0.0, 13.5, -1.1, 0.0, -5.3, 7.0, -0.4, 0.0, -5.2, 3.4,
+               5.9, -3.8, 0.0, -1.8, -7.0, -6.2, 9.1, 0.2, 0.0, -3.4, -0.7, -2.1, -7.6,
+               8.2, -1.8, 0.0, -2.3, -0.1, -0.1, -0.7, -2.7, 9.3, -1.8, 0.0, -2.5,
+               -6.2, -4.3, 0.3, -7.0, -3.7, 5.9, -1.2, 0.0, -4.8, -0.1, 1.3, -5.3,
+               -2.4, 0.2, -3.5, 5.5, -2.2, 0.0, -2.9, -6.5, -4.5, 1.9, -6.7, -3.2, 3.0,
+               -3.4, 5.7, -1.2, 0.0, -1.9, -5.0, -3.1, 1.4, -5.2, -2.1, 2.9, -2.1, 3.4,
+               7.6, -1.2, 0.0, -3.1, 2.6, 0.5, -4.7, -0.2, 1.5, -4.4, 0.8, -4.8, -3.6,
+               6.5, -0.1, 0.0, -5.2, -1.9, -1.4, -5.8, -3.0, -2.2, -4.3, -1.6, -3.5,
+               -4.2, -2.2, 9.6, -0.7, 0.0, -4.2, 0.6, 2.3, -4.1, -2.1, 1.7, -3.2, 2.0,
+               -2.4, -1.2, 0.5, -0.8, 5.6, -1.6, 0.0, -3.5, -1.6, -0.3, -5.3, -2.1,
+               0.3, -4.1, 3.5, -3.5, -2.9, -0.4, -2.1, 1.7, 7.1, 1.6, 0.0, -0.2, 0.0,
+               -0.3, -4.5, -0.1, -0.8, -3.3, -0.4, -3.6, -2.3, 1.1, 0.0, -0.2, -0.9,
+               4.4, 0.5, 0.0, -1.4, -0.6, -0.8, -3.6, -2.4, -0.8, -1.2, -0.2, -2.4,
+               -1.1, 0.3, -0.4, -0.4, -0.9, 2.3, 5.0, 0.1, 0.0, -0.6, -4.9, -3.0, -0.8,
+               -5.2, -3.5, 4.0, -3.0, 1.7, 1.4, -3.8, -3.2, -2.7, -3.4, -2.0, 0.0, 5.3,
+               -5.5, 0.0, -2.1, -7.8, -6.4, 3.2, -5.5, -1.9, -3.4, -5.4, -2.0, -2.2,
+               -5.5, -7.4, -4.0, -2.4, -4.7, -5.4, -4.5, 15.8, 0.0, 0.0, 0.0, 0.0, 0.0,
+               0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+               0.0, 0.0, -3.7, 0.0, -1.3, -4.2, -4.4, 5.6, -6.0, 2.7, -2.0, -3.5, -1.1,
+               -1.3, -2.2, -4.8, -2.9, -2.9, -2.8, -3.2, -2.4, 3.8, 0.0, 10.0, 0.0,
+               0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+               0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 }
+
+};
+
+//default nucleotide sequence scoring matrix
+//used when -nuc option is used
+score_matrix nuc_simple = {
+
+"ABCDGHKMNRSTUVWXY",
+
+{ 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+               0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+               0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+               0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
+               0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+               0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+               0, 0, 0, 0, 0, 0, 0 }
+
+//Ribosum85-60
+               /*
+                {
+                2.22,
+                0,  0,
+                -1.86,  0,  1.16,
+                0,  0,  0,  0,
+                -1.46,  0,  -2.48,  0,  1.03,
+                0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+                -1.39,  0,  -1.05,  0,  -1.74,  0,  0,  0,  0,  0,  0,  1.65,
+                -1.39,  0,  -1.05,  0,  -1.74,  0,  0,  0,  0,  0,  0,  0,  1.65,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,
+                0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0
+                }
+                */
+
+               };
+
+#endif