Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/jalview/schemes/RNAHelicesColour.java b/src/jalview/schemes/RNAHelicesColour.java
index 57fcba5..d17f510 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColour.java
+++ b/src/jalview/schemes/RNAHelicesColour.java
@@ -20,15 +20,15 @@
  */
 package jalview.schemes;
 
-import java.awt.*;
-import java.util.Hashtable;
-import java.util.Map;
-
 import jalview.datamodel.AlignmentAnnotation;
 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 +41,10 @@ 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
@@ -65,15 +60,29 @@ public class RNAHelicesColour extends ResidueColourScheme
   {
     super(ResidueProperties.nucleotideIndex);
     this.annotation = annotation;
+    ColourSchemeProperty.resetRnaHelicesShading();
     refresh();
   }
 
   public RNAHelicesColour(AnnotatedCollectionI alignment)
   {
     super(ResidueProperties.nucleotideIndex);
+    ColourSchemeProperty.resetRnaHelicesShading();
     alignmentChanged(alignment, null);
   }
 
+  /**
+   * clones colour settings and annotation row data
+   * 
+   * @param rnaHelicesColour
+   */
+  public RNAHelicesColour(RNAHelicesColour rnaHelicesColour)
+  {
+    super(ResidueProperties.nucleotideIndex);
+    annotation = rnaHelicesColour.annotation;
+    refresh();
+  }
+
   @Override
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
@@ -86,7 +95,8 @@ public class RNAHelicesColour extends ResidueColourScheme
     {
 
       // 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;
@@ -109,7 +119,7 @@ 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
@@ -136,16 +146,7 @@ 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);
     }
   }
 
@@ -172,7 +173,7 @@ public class RNAHelicesColour extends ResidueColourScheme
    * @param c
    *          Character in sequence
    * @param j
-   *          Threshold
+   *          position in sequence - used to locate helix
    * 
    * @return Color in RGB
    */
@@ -182,15 +183,19 @@ 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,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    return new RNAHelicesColour(this);
+  }
+}
\ No newline at end of file