JAL-2446 merged to spike branch

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 2beb4cf..056a167 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -20,15 +20,16 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
-import java.util.Hashtable;
-import java.util.Map;
-
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
+import java.awt.Color;
+import java.util.Hashtable;
+import java.util.Map;
+
 /**
  * Looks at the information computed from an RNA Stockholm format file on the
  * secondary structure of the alignment. Extracts the information on the
@@ -41,15 +42,10 @@ public class RNAHelicesColour extends ResidueColourScheme
 {
 
   /**
-   * Stores random colors generated for the number of helices
-   */
-  public Hashtable helixcolorhash = new Hashtable();
-
-  /**
    * Maps sequence positions to the RNA helix they belong to. Key: position,
-   * Value: helix
+   * Value: helix TODO: Revise or drop in favour of annotation position numbers
    */
-  public Hashtable positionsToHelix = new Hashtable();
+  public Hashtable<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
 
   /**
    * Number of helices in the RNA secondary structure
@@ -59,18 +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);
   }
 
@@ -82,7 +88,6 @@ public class RNAHelicesColour extends ResidueColourScheme
   public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
   {
     super(ResidueProperties.nucleotideIndex);
-    helixcolorhash = rnaHelicesColour.helixcolorhash;
     annotation = rnaHelicesColour.annotation;
     refresh();
   }
@@ -95,11 +100,16 @@ 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++)
     {
 
       // is this a sensible way of determining type of annotation?
-      if (annotations[i].getRNAStruc() != null)
+      if (annotations[i].visible && annotations[i].isRNA()
+              && annotations[i].isValidStruc())
       {
         annotation = annotations[i];
         break;
@@ -122,7 +132,7 @@ public class RNAHelicesColour extends ResidueColourScheme
       annotation.getRNAStruc();
       lastrefresh = annotation._rnasecstr.hashCode();
       numHelix = 0;
-      positionsToHelix = new Hashtable();
+      positionsToHelix = new Hashtable<Integer, String>();
 
       // Figure out number of helices
       // Length of rnasecstr is the number of pairs of positions that base pair
@@ -149,16 +159,7 @@ public class RNAHelicesColour extends ResidueColourScheme
         }
 
       }
-
-      // Generate random colors and store
-      for (int j = 0; j <= numHelix; j++)
-      {
-        if (!helixcolorhash.containsKey(Integer.toString(j)))
-        {
-          helixcolorhash.put(Integer.toString(j),
-                  jalview.util.ColorUtils.generateRandomColor(Color.white));
-        }
-      }
+      ColourSchemeProperty.initRnaHelicesShading(numHelix);
     }
   }
 
@@ -185,7 +186,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * @param c
    *          Character in sequence
    * @param j
-   *          Threshold
+   *          position in sequence - used to locate helix
    * 
    * @return Color in RGB
    */
@@ -195,22 +196,54 @@ public class RNAHelicesColour extends ResidueColourScheme
     refresh();
     Color currentColour = Color.white;
     String currentHelix = null;
-    currentHelix = (String) positionsToHelix.get(j);
-
+    currentHelix = positionsToHelix.get(j);
     if (currentHelix != null)
     {
-      currentColour = (Color) helixcolorhash.get(currentHelix);
+      currentColour = ColourSchemeProperty.rnaHelices[Integer
+              .parseInt(currentHelix)];
     }
-
-    // System.out.println(c + " " + j + " helix " + currentHelix + " " +
-    // currentColour);
     return currentColour;
   }
 
   @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;
   }
 }