Merge remote-tracking branch 'origin/develop' into bug/JAL-2665-2.10.3

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index f13a90c..ec13343 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -43,8 +43,8 @@ public class ClustalxColourScheme extends ResidueColourScheme
   {
     RED(0.9f, 0.2f, 0.1f), BLUE(0.5f, 0.7f, 0.9f), GREEN(0.1f, 0.8f, 0.1f),
     ORANGE(0.9f, 0.6f, 0.3f), CYAN(0.1f, 0.7f, 0.7f),
-    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f), YELLOW(0.8f, 0.8f,
-            0.0f);
+    PINK(0.9f, 0.5f, 0.5f), MAGENTA(0.8f, 0.3f, 0.8f),
+    YELLOW(0.8f, 0.8f, 0.0f);
 
     final Color colour;
 
@@ -53,6 +53,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
       colour = new Color(r, g, b);
     }
   }
+
   private class ConsensusColour
   {
     Consensus[] cons;
@@ -106,19 +107,18 @@ 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]++;
       }
@@ -297,8 +297,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     for (int k = 0; k < residueColour[i].cons.length; k++)
     {
-      if (residueColour[i].cons[k].isConserved(cons2, j, size,
-              includeGaps))
+      if (residueColour[i].cons[k].isConserved(cons2, j, size, includeGaps))
       {
         colour = residueColour[i].c;
       }