Any character non aa or nucleotide is a space

[jalview.git] / src / jalview / schemes / ResidueProperties.java

diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java
index 5604ca3..17f6a41 100755 (executable)
--- a/src/jalview/schemes/ResidueProperties.java
+++ b/src/jalview/schemes/ResidueProperties.java
@@ -35,9 +35,9 @@ public class ResidueProperties
 
   static
   {
-    aaIndex = new int[132];
-    for(int i=0; i<132; i++)
-      aaIndex[i] = -1;
+    aaIndex = new int[255];
+    for(int i=0; i<255; i++)
+      aaIndex[i] = 23;
 
     aaIndex['A'] = 0;
     aaIndex['R'] = 1;
@@ -87,16 +87,12 @@ public class ResidueProperties
     aaIndex['z'] = 21;
     aaIndex['x'] = 22;
     aaIndex['u'] = 22;
-    aaIndex['-'] = 23;
-    aaIndex['*'] = 23;
-    aaIndex['.'] = 23;
-    aaIndex[' '] = 23;
   }
 
   static
   {
-    nucleotideIndex = new int[132];
-    for (int i = 0; i < 132; i++)
+    nucleotideIndex = new int[255];
+    for (int i = 0; i < 255; i++)
       nucleotideIndex[i] = -1;
 
     nucleotideIndex['A'] = 0;