JAL-2624 additional tests for FeatureColour.getColour(),

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 3c9f095..9df7ab8 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -106,19 +106,18 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     for (SequenceI sq : seqs)
     {
-      char[] seq = sq.getSequence();
-
-      int end_j = seq.length - 1;
+      int end_j = sq.getLength() - 1;
+      int length = sq.getLength();
 
       for (int i = 0; i <= end_j; i++)
       {
-        if ((seq.length - 1) < i)
+        if (length - 1 < i)
         {
           res = 23;
         }
         else
         {
-          res = ResidueProperties.aaIndex[seq[i]];
+          res = ResidueProperties.aaIndex[sq.getCharAt(i)];
         }
         cons2[i][res]++;
       }
@@ -307,7 +306,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
     if (i == 4)
     {
       /*
-       * override to colour C pink if 100% conserved
+       * override to colour C pink if >85% conserved
        */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {