X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=056a1676a4801cebe663a150a07e60437ce94af1;hb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;hp=ffc013d654ced7a2ad6b1e113356cbcc33070553;hpb=60b63ec67604be95d1be4ff04e51c5705b05b109;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index ffc013d..056a167 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -21,6 +21,7 @@
 package jalview.schemes;
 
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
@@ -40,7 +41,6 @@ import java.util.Map;
 public class RNAHelicesColour extends ResidueColourScheme
 {
 
-
   /**
    * Maps sequence positions to the RNA helix they belong to. Key: position,
    * Value: helix TODO: Revise or drop in favour of annotation position numbers
@@ -55,6 +55,14 @@ public class RNAHelicesColour extends ResidueColourScheme
   public AlignmentAnnotation annotation;
 
   /**
+   * Default constructor (required for ColourSchemes cache)
+   */
+  public RNAHelicesColour()
+  {
+
+  }
+
+  /**
    * Creates a new RNAHelicesColour object.
    */
   public RNAHelicesColour(AlignmentAnnotation annotation)
@@ -92,6 +100,10 @@ public class RNAHelicesColour extends ResidueColourScheme
     // This loop will find the first rna structure annotation by which to colour
     // the sequences.
     AlignmentAnnotation[] annotations = alignment.getAlignmentAnnotation();
+    if (annotations == null)
+    {
+      return;
+    }
     for (int i = 0; i < annotations.length; i++)
     {
 
@@ -194,9 +206,44 @@ public class RNAHelicesColour extends ResidueColourScheme
   }
 
   @Override
-  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+  public ColourSchemeI getInstance(AnnotatedCollectionI sg,
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
   {
-    return new RNAHelicesColour(this);
+    return new RNAHelicesColour(sg);
+  }
+
+  @Override
+  public boolean isNucleotideSpecific()
+  {
+    return true;
+  }
+
+  /**
+   * Answers true if the data has RNA secondary structure annotation
+   */
+  @Override
+  public boolean isApplicableTo(AnnotatedCollectionI ac)
+  {
+    if (ac instanceof AlignmentI && ((AlignmentI) ac).hasRNAStructure())
+    {
+      return true;
+    }
+
+    /*
+     * not currently supporting this option for group annotation / colouring
+     */
+    return false;
+  }
+
+  @Override
+  public String getSchemeName()
+  {
+    return JalviewColourScheme.RNAHelices.toString();
+  }
+
+  @Override
+  public boolean isSimple()
+  {
+    return false;
   }
-}
\ No newline at end of file
+}