X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Flegacyblosum62.scm;fp=examples%2Flegacyblosum62.scm;h=57072cf70594f45886925d4712ded1bb56afe51e;hb=001d029b058432b3ae0a4431e5bcd4116ee7694a;hp=0000000000000000000000000000000000000000;hpb=d7dd2118c0ae3cf0c0288b66fdd07146d53014d8;p=jalview.git

diff --git a/examples/legacyblosum62.scm b/examples/legacyblosum62.scm
new file mode 100644
index 0000000..57072cf
--- /dev/null
+++ b/examples/legacyblosum62.scm
@@ -0,0 +1,33 @@
+ScoreMatrix BLOSUM62Legacy
+#
+# The BLOSUM62 substitution matrix, as used in earlier versions of jalview
+#
+# 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	 * 
+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