JAL-1492 JAL-1397 JAL-643 JAL-969 factory method to clone and apply colour scheme...

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index c3357ad..f619d07 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -51,7 +51,27 @@ public class AnnotationColourGradient extends FollowerColourScheme
   private boolean seqAssociated = false;
 
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
-
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+    acg.thresholdIsMinMax = thresholdIsMinMax;
+    acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+    acg.r1 = r1;
+    acg.g1 = g1;
+    acg.b1 = b1;
+    acg.rr = rr;
+    acg.gg = gg;
+    acg.bb = bb;
+    acg.dr = dr;
+    acg.dg = dg;
+    acg.db = db;
+    acg.predefinedColours = predefinedColours;
+    acg.seqAssociated = seqAssociated;
+    
+    return acg;
+  }
   /**
    * Creates a new AnnotationColourGradient object.
    */