JAL-4024 only render partially when new view overlaps with last rendered annotation...

[jalview.git] / resources / scoreModel / blosum62.scm

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
index 3df8833..b0e927d 100644 (file)
--- a/resources/scoreModel/blosum62.scm
+++ b/resources/scoreModel/blosum62.scm
@@ -1,42 +1,34 @@
 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)
-# 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
+# Scores are not symbol case sensitive, unless column(s) are provided for lower case characters
+# The 'guide symbol' at the start of each row of score values is optional
 # 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           *
-#
-       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
-       -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
-       -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
-       -2      -2      1       6       -3      0       2       -1      -1      -3      -4      -1      -3      -3      -1      0       -1      -4      -3      -3      4       1       -1      -4 -4
-       0       3       -3      -3      9       -3      -4      -3      -3      -1      -1      -3      -1      -2      -3      -1      -1      -2      -2      -1      -3      -3      -2      -4 -4
-       -1      1       0       0       -3      5       2       -2      0       -3      -2      1       0       -3      -1      0       -1      -2      -1      -2      0       3       -1      -4 -4
-       -1      0       0       2       -4      2       5       -2      0       -3      -3      1       -2      -3      -1      0       -1      -3      -2      -2      1       4       -1      -4 -4
-       0       -2      0       -1      -3      -2      -2      6       -2      -4      -4      -2      -3      -3      -2      0       -2      -2      -3      -3      -1      -2      -1      -4 -4
-       -2      0       1       -1      -3      0       0       -2      8       -3      -3      -1      -2      -1      -2      -1      -2      -2      2       -3      0       0       -1      -4 -4
-       -1      -3      -3      -3      -1      -3      -3      -4      -3      4       2       -3      1       0       -3      -2      -1      -3      -1      3       -3      -3      -1      -4 -4
-       -1      -2      -3      -4      -1      -2      -3      -4      -3      2       4       -2      2       0       -3      -2      -1      -2      -1      1       -4      -3      -1      -4 -4
-       -1      2       0       -1      -3      1       1       -2      -1      -3      -2      5       -1      -3      -1      0       -1      -3      -2      -2      0       1       -1      -4 -4
-       -1      -1      -2      -3      -1      0       -2      -3      -2      1       2       -1      5       0       -2      -1      -1      -1      -1      1       -3      -1      -1      -4 -4
-       -2      -3      -3      -3      -2      -3      -3      -3      -1      0       0       -3      0       6       -4      -2      -2      1       3       -1      -3      -3      -1      -4 -4
-       -1      -2      -2      -1      -3      -1      -1      -2      -2      -3      -3      -1      -2      -4      7       -1      -1      -4      -3      -2      -2      -1      -2      -4 -4
-       1       -1      1       0       -1      0       0       0       -1      -2      -2      0       -1      -2      -1      4       1       -3      -2      -2      0       0       0       -4 -4
-       0       -1      0       -1      -1      -1      -1      -2      -2      -1      -1      -1      -1      -2      -1      1       5       -2      -2      0       -1      -1      0       -4 -4
-       -3      -3      -4      -4      -2      -2      -3      -2      -2      -3      -2      -3      -1      1       -4      -3      -2      11      2       -3      -4      -3      -2      -4 -4
-       -2      -2      -2      -3      -2      -1      -2      -3      2       -1      -1      -2      -1      3       -3      -2      -2      2       7       -1      -3      -2      -1      -4 -4
-       0       -3      -3      -3      -1      -2      -2      -3      -3      3       1       -2      1       -1      -2      -2      0       -3      -1      4       -3      -2      -1      -4 -4
-       -2      -1      3       4       -3      0       1       -1      0       -3      -4      0       -3      -3      -2      0       -1      -4      -3      -3      4       1       -1      -4 -4
-       -1      0       0       1       -3      3       4       -2      0       -3      -3      1       -1      -3      -1      0       -1      -3      -2      -2      1       4       -1      -4 -4
-       0       -1      -1      -1      -2      -1      -1      -1      -1      -1      -1      -1      -1      -1      -2      0       0       -2      -1      -1      -1      -1      -1      -4 -4
-       -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      1  1
-       -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      1  1
-#
-#      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       4      -1      -2      -2       0      -1      -1       0      -2      -1      -1      -1      -1      -2      -1       1       0      -3      -2       0      -2      -1       0      -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
+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
+D      -2      -2       1       6      -3       0       2      -1      -1      -3      -4      -1      -3      -3      -1       0      -1      -4      -3      -3       4       1      -1      -4
+C       0      -3      -3      -3       9      -3      -4      -3      -3      -1      -1      -3      -1      -2      -3      -1      -1      -2      -2      -1      -3      -3      -2      -4
+Q      -1       1       0       0      -3       5       2      -2       0      -3      -2       1       0      -3      -1       0      -1      -2      -1      -2       0       3      -1      -4
+E      -1       0       0       2      -4       2       5      -2       0      -3      -3       1      -2      -3      -1       0      -1      -3      -2      -2       1       4      -1      -4
+G       0      -2       0      -1      -3      -2      -2       6      -2      -4      -4      -2      -3      -3      -2       0      -2      -2      -3      -3      -1      -2      -1      -4
+H      -2       0       1      -1      -3       0       0      -2       8      -3      -3      -1      -2      -1      -2      -1      -2      -2       2      -3       0       0      -1      -4
+I      -1      -3      -3      -3      -1      -3      -3      -4      -3       4       2      -3       1       0      -3      -2      -1      -3      -1       3      -3      -3      -1      -4
+L      -1      -2      -3      -4      -1      -2      -3      -4      -3       2       4      -2       2       0      -3      -2      -1      -2      -1       1      -4      -3      -1      -4
+K      -1       2       0      -1      -3       1       1      -2      -1      -3      -2       5      -1      -3      -1       0      -1      -3      -2      -2       0       1      -1      -4
+M      -1      -1      -2      -3      -1       0      -2      -3      -2       1       2      -1       5       0      -2      -1      -1      -1      -1       1      -3      -1      -1      -4
+F      -2      -3      -3      -3      -2      -3      -3      -3      -1       0       0      -3       0       6      -4      -2      -2       1       3      -1      -3      -3      -1      -4
+P      -1      -2      -2      -1      -3      -1      -1      -2      -2      -3      -3      -1      -2      -4       7      -1      -1      -4      -3      -2      -2      -1      -2      -4
+S       1      -1       1       0      -1       0       0       0      -1      -2      -2       0      -1      -2      -1       4       1      -3      -2      -2       0       0       0      -4
+T       0      -1       0      -1      -1      -1      -1      -2      -2      -1      -1      -1      -1      -2      -1       1       5      -2      -2       0      -1      -1       0      -4
+W      -3      -3      -4      -4      -2      -2      -3      -2      -2      -3      -2      -3      -1       1      -4      -3      -2      11       2      -3      -4      -3      -2      -4
+Y      -2      -2      -2      -3      -2      -1      -2      -3       2      -1      -1      -2      -1       3      -3      -2      -2       2       7      -1      -3      -2      -1      -4
+V       0      -3      -3      -3      -1      -2      -2      -3      -3       3       1      -2       1      -1      -2      -2       0      -3      -1       4      -3      -2      -1      -4
+B      -2      -1       3       4      -3       0       1      -1       0      -3      -4       0      -3      -3      -2       0      -1      -4      -3      -3       4       1      -1      -4
+Z      -1       0       0       1      -3       3       4      -2       0      -3      -3       1      -1      -3      -1       0      -1      -3      -2      -2       1       4      -1      -4
+X       0      -1      -1      -1      -2      -1      -1      -1      -1      -1      -1      -1      -1      -1      -2       0       0      -2      -1      -1      -1      -1      -1      -4
+*      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4      -4       1