JAL-1632 JAL-2416 load score matrices from file, as float[][]

[jalview.git] / resources / scoreModel / dna.scm

diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm
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+ScoreMatrix DNA
+ACGTUIXRYN -
+#
+# A DNA substitution matrix.
+# This is an ad-hoc matrix which, in addition to penalising mutations between the common 
+# nucleotides (ACGT), includes T/U equivalence in order to allow both DNA and/or RNA. 
+# In addition, it encodes weak equivalence between R and Y with AG and CTU, respectively, 
+# and N is allowed to match any other base weakly. 
+# This matrix also includes I (Inosine) and X (Xanthine), but encodes them to weakly match
+# any of (ACGTU), and unfavourably match each other.
+#
+# The first line declares a ScoreMatrix with the name DNA (shown in menus)
+# The second line gives the symbols for which scores are held in the matrix
+# These may include a space (but not as the first or last character)
+# Scores are not case sensitive, unless column(s) are provided for lower case characters
+#
+#
+# Comment line with symbols is provided as a guide
+# Values may be integer or floating point, delimited by tab, space, comma or combinations
+#
+#      A       C       G       T       U       I       X       R       Y       N       -
+#
+       10      -8      -8      -8      -8      1       1       1       -8      1       1       1 
+       -8      10      -8      -8      -8      1       1       -8      1       1       1       1
+       -8      -8      10      -8      -8      1       1       1       -8      1       1       1
+       -8      -8      -8      10      10      1       1       -8      1       1       1       1
+       -8      -8      -8      10      10      1       1       -8      1       1       1       1
+       1       1       1       1       1       10      0       0       0       1       1       1
+       1       1       1       1       1       0       10      0       0       1       1       1
+       1       -8      1       -8      -8      0       0       10      -8      1       1       1
+       -8      1       -8      1       1       0       0       -8      10      1       1       1
+       1       1       1       1       1       1       1       1       1       10      1       1
+       1       1       1       1       1       1       1       1       1       1       1       1
+       1       1       1       1       1       1       1       1       1       1       1       1
+#
+#      A       C       G       T       U       I       X       R       Y       N       -