JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overri...

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index ccbad44..5a2d5dc 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -20,15 +20,16 @@
  */
 package jalview.schemes;
 
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+
+import jalview.api.AlignViewportI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-import java.util.List;
-import java.util.Map;
-
 public class ClustalxColourScheme extends ResidueColourScheme
 {
   private static final int EIGHTY_FIVE = 85;
@@ -94,7 +95,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public void alignmentChanged(AnnotatedCollectionI alignment,
+  public synchronized void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
     int maxWidth = alignment.getWidth();
@@ -107,19 +108,18 @@ 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]++;
       }
@@ -278,7 +278,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  protected Color findColour(char c, int j, SequenceI seq)
+  protected synchronized Color findColour(char c, int j, SequenceI seq)
   {
     // TODO why the test for includeGaps here?
     if (cons2.length <= j || Comparison.isGap(c)
@@ -336,11 +336,11 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
-          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  public ColourSchemeI getInstance(AlignViewportI view,
+          AnnotatedCollectionI sg)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,
-            hiddenRepSequences);
+            view == null ? null : view.getHiddenRepSequences());
     css.includeGaps = includeGaps;
     return css;
   }