X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColour.java;h=dbc9c03dd6ac5b3ab9c265f915eaa1997a45a1e7;hb=9e926ac4305fd9dff38b6e079e55b4f50664d544;hp=cc7f5cad8b8c15ffb07f3499e22a962440ed3b5a;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index cc7f5ca..dbc9c03 100644
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
@@ -54,6 +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)
@@ -91,6 +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++)
     {
 
@@ -112,9 +125,9 @@ public class RNAHelicesColour extends ResidueColourScheme
   public void refresh()
   {
 
-    if (annotation != null
-            && ((annotation._rnasecstr == null || lastrefresh != annotation._rnasecstr
-                    .hashCode()) && annotation.isValidStruc()))
+    if (annotation != null && ((annotation._rnasecstr == null
+            || lastrefresh != annotation._rnasecstr.hashCode())
+            && annotation.isValidStruc()))
     {
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
@@ -138,11 +151,11 @@ public class RNAHelicesColour extends ResidueColourScheme
         positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
                 this.annotation._rnasecstr[x].getFeatureGroup());
 
-        if (Integer.parseInt(this.annotation._rnasecstr[x]
-                .getFeatureGroup()) > numHelix)
+        if (Integer.parseInt(
+                this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
         {
-          numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
-                  .getFeatureGroup());
+          numHelix = Integer.parseInt(
+                  this.annotation._rnasecstr[x].getFeatureGroup());
         }
 
       }
@@ -193,9 +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
+}