X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FClustalxColourScheme.java;h=2bb64fce9249ae806a2005cce0c6bc9df45ce1f0;hb=8eb830995e6e2bf47d5e0a5e355faaf7a72d3711;hp=7ff1c65a3de6c1281c8fe4dd23fbc83aa8718ee8;hpb=b0cee3aaf7d8873910939f97b6acb217d518968d;p=jalview.git

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 7ff1c65..2bb64fc 100755
--- 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,