JAL-2416 amended to (as near as possible) strict NCBI format

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
index b793e04..50e74cc 100644 (file)
--- a/resources/scoreModel/blosum62.scm
+++ b/resources/scoreModel/blosum62.scm
@@ -1,5 +1,4 @@
 ScoreMatrix BLOSUM62
-ARNDCQEGHILKMFPSTWYVBZX-*
 #
 # The BLOSUM62 substitution matrix, as at https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
 # The first line declares a ScoreMatrix with the name BLOSUM62 (shown in menus)
@@ -9,7 +8,6 @@ ARNDCQEGHILKMFPSTWYVBZX-*
 # Values may be integer or floating point, delimited by tab, space, comma or combinations
 #
        A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X       -   *
-#
 A      4       -1      -2      -2      0       -1      -1      0       -2      -1      -1      -1      -1      -2      -1      1       0       -3      -2      0       -2      -1      0       -4 -4
 R      -1      5       0       -2      -3      1       0       -2      0       -3      -2      2       -1      -3      -2      -1      -1      -3      -2      -3      -1      0       -1      -4 -4
 N      -2      0       6       1       -3      0       0       0       1       -3      -3      0       -2      -3      -2      1       0       -4      -2      -3      3       0       -1      -4 -4

diff --git a/resources/scoreModel/dna.scm b/resources/scoreModel/dna.scm
index e66864a..c490931 100644 (file)
--- a/resources/scoreModel/dna.scm
+++ b/resources/scoreModel/dna.scm
@@ -1,5 +1,4 @@
 ScoreMatrix DNA
-ACGTUIXRYN-
 #
 # A DNA substitution matrix.
 # This is an ad-hoc matrix which, in addition to penalising mutations between the common 

diff --git a/resources/scoreModel/pam250.scm b/resources/scoreModel/pam250.scm
index 05404d0..57922a4 100644 (file)
--- a/resources/scoreModel/pam250.scm
+++ b/resources/scoreModel/pam250.scm
@@ -1,12 +1,11 @@
 ScoreMatrix PAM250
-ARNDCQEGHILKMFPSTWYVBZX-*
 #
 # The PAM250 substitution matrix
 # The first line declares a ScoreMatrix with the name PAM250 (shown in menus)
 # Scores are not case sensitive, unless column(s) are provided for lower case characters
 # Values may be integer or floating point, delimited by tab, space, comma or combinations
 #
-#      A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X       -       *
+       A       R       N       D       C       Q       E       G       H       I       L       K       M       F       P       S       T       W       Y       V       B       Z       X       -       *
 A      2       -2      0       0       -2      0       0       1       -1      -1      -2      -1      -1      -3      1       1       1       -6      -3      0       0       0       0       -8      -8
 R      -2      6       0       -1      -4      1       -1      -3      2       -2      -3      3       0       -4      0       0       -1      2       -4      -2      -1      0       -1      -8      -8
 N      0       0       2       2       -4      1       1       0       2       -2      -3      1       -2      -3      0       1       0       -4      -2      -2      2       1       0       -8      -8