Merge branch 'develop' into releases/Release_2_11_2_Branch

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 9df7ab8..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;
@@ -43,8 +44,8 @@ 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 +54,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
       colour = new Color(r, g, b);
     }
   }
+
   private class ConsensusColour
   {
     Consensus[] cons;
@@ -93,7 +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();
@@ -276,7 +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)
@@ -296,8 +298,7 @@ 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;
       }
@@ -335,11 +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;
   }