JAL-2018 export graduated feature colours correctly

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 5b55e05..ec2c591 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -68,6 +68,12 @@ public abstract class FeatureRendererModel implements
 
   protected AlignmentViewport av;
 
+  /*
+   * map holds per feature type, {{min, max}, {min, max}} feature score
+   * values for positional and non-positional features respectively
+   */
+  private Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+
   @Override
   public AlignViewportI getViewport()
   {
@@ -194,9 +200,7 @@ public abstract class FeatureRendererModel implements
     renderOrder = neworder;
   }
 
-  protected Hashtable minmax = new Hashtable();
-
-  public Hashtable getMinMax()
+  public Map<String, float[][]> getMinMax()
   {
     return minmax;
   }
@@ -210,7 +214,7 @@ public abstract class FeatureRendererModel implements
    */
   protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
   {
-    float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
+    float[] mm = minmax.get(sequenceFeature.type)[0];
     final byte[] r = new byte[] { 0, (byte) 255 };
     if (mm != null)
     {
@@ -341,7 +345,7 @@ public abstract class FeatureRendererModel implements
     }
     if (minmax == null)
     {
-      minmax = new Hashtable();
+      minmax = new Hashtable<String, float[][]>();
     }
     AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
@@ -396,7 +400,7 @@ public abstract class FeatureRendererModel implements
         if (!Float.isNaN(features[index].score))
         {
           int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
-          float[][] mm = (float[][]) minmax.get(features[index].getType());
+          float[][] mm = minmax.get(features[index].getType());
           if (mm == null)
           {
             mm = new float[][] { null, null };
@@ -557,31 +561,6 @@ public abstract class FeatureRendererModel implements
   }
 
   /**
-   * return a nominal colour for this feature
-   * 
-   * @param featureType
-   * @return standard color, or maximum colour for graduated colourscheme
-   */
-  public Color getColour(String featureType)
-  {
-    Object fc = getFeatureStyle(featureType);
-
-    if (fc instanceof Color)
-    {
-      return (Color) fc;
-    }
-    else
-    {
-      if (fc instanceof GraduatedColor)
-      {
-        return ((GraduatedColor) fc).getMaxColor();
-      }
-    }
-    throw new Error("Implementation Error: Unrecognised render object "
-            + fc.getClass() + " for features of type " + featureType);
-  }
-
-  /**
    * calculate the render colour for a specific feature using current feature
    * settings.
    * 
@@ -819,7 +798,7 @@ public abstract class FeatureRendererModel implements
     changeSupport.removePropertyChangeListener(listener);
   }
 
-  public Set getAllFeatureColours()
+  public Set<String> getAllFeatureColours()
   {
     return featureColours.keySet();
   }
@@ -834,6 +813,9 @@ public abstract class FeatureRendererModel implements
     return renderOrder != null;
   }
 
+  /**
+   * Returns feature types in ordering of rendering, where last means on top
+   */
   public List<String> getRenderOrder()
   {
     if (renderOrder == null)
@@ -943,7 +925,7 @@ public abstract class FeatureRendererModel implements
     while (en.hasNext())
     {
       String col = en.next();
-      fcols.put(col, getColour(col));
+      fcols.put(col, featureColours.get(col));
     }
     return fcols;
   }