JAL-2416 JAL-2403 remove unused '*' row/column from score matrices

diff --git a/resources/scoreModel/blosum62.scm b/resources/scoreModel/blosum62.scm
index 50e74cc..0d6ffab 100644 (file)
--- a/resources/scoreModel/blosum62.scm
+++ b/resources/scoreModel/blosum62.scm
@@ -7,31 +7,28 @@ ScoreMatrix BLOSUM62
 # 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 -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
-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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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 -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      -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 

diff --git a/resources/scoreModel/pam250.scm b/resources/scoreModel/pam250.scm
index 57922a4..10a46ec 100644 (file)
--- a/resources/scoreModel/pam250.scm
+++ b/resources/scoreModel/pam250.scm
@@ -5,31 +5,28 @@ ScoreMatrix PAM250
 # 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      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
-D      0       -1      2       4       -5      2       3       1       1       -2      -4      0       -3      -6      -1      0       0       -7      -4      -2      3       3       -1      -8      -8
-C      -2      -4      -4      -5      12      -5      -5      -3      -3      -2      -6      -5      -5      -4      -3      0       -2      -8      0       -2      -4      -5      -3      -8      -8      
-Q      0       1       1       2       -5      4       2       -1      3       -2      -2      1       -1      -5      0       -1      -1      -5      -4      -2      1       3       -1      -8      -8      
-E      0       -1      1       3       -5      2       4       0       1       -2      -3      0       -2      -5      -1      0       0       -7      -4      -2      3       3       -1      -8      -8      
-G      1       -3      0       1       -3      -1      0       5       -2      -3      -4      -2      -3      -5      0       1       0       -7      -5      -1      0       0       -1      -8      -8      
-H      -1      2       2       1       -3      3       1       -2      6       -2      -2      0       -2      -2      0       -1      -1      -3      0       -2      1       2       -1      -8      -8      
-I      -1      -2      -2      -2      -2      -2      -2      -3      -2      5       2       -2      2       1       -2      -1      0       -5      -1      4       -2      -2      -1      -8      -8      
-L      -2      -3      -3      -4      -6      -2      -3      -4      -2      2       6       -3      4       2       -3      -3      -2      -2      -1      2       -3      -3      -1      -8      -8      
-K      -1      3       1       0       -5      1       0       -2      0       -2      -3      5       0       -5      -1      0       0       -3      -4      -2      1       0       -1      -8      -8      
-M      -1      0       -2      -3      -5      -1      -2      -3      -2      2       4       0       6       0       -2      -2      -1      -4      -2      2       -2      -2      -1      -8      -8      
-F      -3      -4      -3      -6      -4      -5      -5      -5      -2      1       2       -5      0       9       -5      -3      -3      0       7       -1      -4      -5      -2      -8      -8      
-P      1       0       0       -1      -3      0       -1      0       0       -2      -3      -1      -2      -5      6       1       0       -6      -5      -1      -1      0       -1      -8      -8      
-S      1       0       1       0       0       -1      0       1       -1      -1      -3      0       -2      -3      1       2       1       -2      -3      -1      0       0        0      -8      -8      
-T      1       -1      0       0       -2      -1      0       0       -1      0       -2      0       -1      -3      0       1       3       -5      -3      0       0       -1       0      -8      -8      
-W      -6      2       -4      -7      -8      -5      -7      -7      -3      -5      -2      -3      -4      0       -6      -2      -5      17      0       -6      -5      -6      -4      -8      -8      
-Y      -3      -4      -2      -4      0       -4      -4      -5      0       -1      -1      -4      -2      7       -5      -3      -3      0       10      -2      -3      -4      -2      -8      -8      
-V      0       -2      -2      -2      -2      -2      -2      -1      -2      4       2       -2      2       -1      -1      -1      0       -6      -2      4       -2      -2      -1      -8      -8      
-B      0       -1      2       3       -4      1       3       0       1       -2      -3      1       -2      -4      -1      0       0       -5      -3      -2      3       2       -1      -8      -8      
-Z      0       0       1       3       -5      3       3       0       2       -2      -3      0       -2      -5      0       0       -1      -6      -4      -2      2       3       -1      -8      -8      
-X      0       -1      0       -1      -3      -1      -1      -1      -1      -1      -1      -1      -1      -2      -1      0       0       -4      -2      -1      -1      -1      -1      -8      -8      
--      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8       1   1
-*      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8       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       2      -2       0       0      -2       0       0       1      -1      -1      -2      -1      -1      -3       1       1       1      -6      -3       0       0       0       0      -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
+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
+D       0      -1       2       4      -5       2       3       1       1      -2      -4       0      -3      -6      -1       0       0      -7      -4      -2       3       3      -1      -8
+C      -2      -4      -4      -5      12      -5      -5      -3      -3      -2      -6      -5      -5      -4      -3       0      -2      -8       0      -2      -4      -5      -3      -8
+Q       0       1       1       2      -5       4       2      -1       3      -2      -2       1      -1      -5       0      -1      -1      -5      -4      -2       1       3      -1      -8
+E       0      -1       1       3      -5       2       4       0       1      -2      -3       0      -2      -5      -1       0       0      -7      -4      -2       3       3      -1      -8
+G       1      -3       0       1      -3      -1       0       5      -2      -3      -4      -2      -3      -5       0       1       0      -7      -5      -1       0       0      -1      -8
+H      -1       2       2       1      -3       3       1      -2       6      -2      -2       0      -2      -2       0      -1      -1      -3       0      -2       1       2      -1      -8
+I      -1      -2      -2      -2      -2      -2      -2      -3      -2       5       2      -2       2       1      -2      -1       0      -5      -1       4      -2      -2      -1      -8
+L      -2      -3      -3      -4      -6      -2      -3      -4      -2       2       6      -3       4       2      -3      -3      -2      -2      -1       2      -3      -3      -1      -8
+K      -1       3       1       0      -5       1       0      -2       0      -2      -3       5       0      -5      -1       0       0      -3      -4      -2       1       0      -1      -8
+M      -1       0      -2      -3      -5      -1      -2      -3      -2       2       4       0       6       0      -2      -2      -1      -4      -2       2      -2      -2      -1      -8
+F      -3      -4      -3      -6      -4      -5      -5      -5      -2       1       2      -5       0      9       -5      -3      -3       0       7      -1      -4      -5      -2      -8
+P       1       0       0      -1      -3       0      -1       0       0      -2      -3      -1      -2      -5       6       1       0      -6      -5      -1      -1       0      -1      -8
+S       1       0       1       0       0      -1       0       1      -1      -1      -3       0      -2      -3       1       2       1      -2      -3      -1       0       0       0      -8
+T       1      -1       0       0      -2      -1       0       0      -1       0      -2       0      -1      -3       0       1       3      -5      -3       0       0      -1       0      -8
+W      -6       2      -4      -7      -8      -5      -7      -7      -3      -5      -2      -3      -4       0      -6      -2      -5      17       0      -6      -5      -6      -4      -8
+Y      -3      -4      -2      -4       0      -4      -4      -5       0      -1      -1      -4      -2       7      -5      -3      -3       0      10      -2      -3      -4      -2      -8
+V       0      -2      -2      -2      -2      -2      -2      -1      -2       4       2      -2       2      -1      -1      -1       0      -6      -2       4      -2      -2      -1      -8
+B       0      -1       2       3      -4       1       3       0       1      -2      -3       1      -2      -4      -1       0       0      -5      -3      -2       3       2      -1      -8
+Z       0       0       1       3      -5       3       3       0       2      -2      -3       0      -2      -5       0       0      -1      -6      -4      -2       2       3      -1      -8
+X       0      -1       0      -1      -3      -1      -1      -1      -1      -1      -1      -1      -1      -2      -1       0       0      -4      -2      -1      -1      -1      -1      -8
+-      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8      -8       1

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 55881d7..f4346c3 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -614,9 +614,7 @@ public class Conservation
       lengths[l] = seqNums.elementAt(l).length - 1;
     }
 
-    // todo ? remove '*' (unused?) from score matrix and
-    // use getSize() here instead of getSize() - 1 ??
-    final int symbolCount = blosum62.getSize() - 1; // 24;
+    final int symbolCount = blosum62.getSize();
     int gapIndex = blosum62.getGapIndex();
 
     for (j = startRes; j <= endRes; j++)