JAL-2360 comment only

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

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 7ff1c65..2bb64fc 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -77,6 +77,14 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
   private boolean includeGaps = true;
 
+  /**
+   * Default constructor (required for Class.newInstance())
+   */
+  public ClustalxColourScheme()
+  {
+
+  }
+
   public ClustalxColourScheme(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
@@ -298,6 +306,9 @@ public class ClustalxColourScheme extends ResidueColourScheme
 
     if (i == 4)
     {
+      /*
+       * override to colour C pink if 100% conserved
+       */
       if (conses[27].isConserved(cons2, j, size, includeGaps))
       {
         currentColour = ClustalColour.PINK.colour;
@@ -330,7 +341,7 @@ public class ClustalxColourScheme extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
     ClustalxColourScheme css = new ClustalxColourScheme(sg,