JAL-3063 Save/Load user defined colours using JAXB

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 74cc803..dbc9c03 100644 (file)
--- 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
@@ -55,18 +55,28 @@ 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)
   {
     super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
+    ColourSchemeProperty.resetRnaHelicesShading();
     refresh();
   }
 
   public RNAHelicesColour(AnnotatedCollectionI alignment)
   {
     super(ResidueProperties.nucleotideIndex);
+    ColourSchemeProperty.resetRnaHelicesShading();
     alignmentChanged(alignment, null);
   }
 
@@ -90,6 +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++)
     {
 
@@ -111,9 +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();
@@ -137,11 +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());
         }
 
       }
@@ -192,9 +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
+}