JAL-2593 don't filter out 'colour by label' features

[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 de1ee5e..231cfbe 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -559,7 +559,8 @@ public abstract class FeatureRendererModel implements
    * Returns the configured colour for a particular feature instance. This
    * includes calculation of 'colour by label', or of a graduated score colour,
    * if applicable. It does not take into account feature visibility or colour
-   * transparency.
+   * transparency. Returns null for a score feature whose score value lies
+   * outside any colour threshold.
    * 
    * @param feature
    * @return
@@ -571,19 +572,6 @@ public abstract class FeatureRendererModel implements
   }
 
   /**
-   * Answers true unless the feature has a graduated colour scheme and the
-   * feature value lies outside the current threshold for display
-   * 
-   * @param sequenceFeature
-   * @return
-   */
-  protected boolean showFeature(SequenceFeature sequenceFeature)
-  {
-    FeatureColourI fc = getFeatureStyle(sequenceFeature.type);
-    return fc.isColored(sequenceFeature);
-  }
-
-  /**
    * Answers true if the feature type is currently selected to be displayed,
    * else false
    * 
@@ -1005,7 +993,9 @@ public abstract class FeatureRendererModel implements
   /**
    * Removes from the list of features any that have a feature group that is not
    * displayed, or duplicate the location of a feature of the same type (unless
-   * a graduated colour scheme is applied)
+   * a graduated colour scheme or colour by label is applied). Should be used
+   * only for features of the same feature colour (which normally implies the
+   * same feature type).
    * 
    * @param features
    * @param fc
@@ -1018,7 +1008,7 @@ public abstract class FeatureRendererModel implements
       return;
     }
     SequenceFeatures.sortFeatures(features, true);
-    boolean graduated = fc != null && fc.isGraduatedColour();
+    boolean simpleColour = fc == null || fc.isSimpleColour();
     SequenceFeature lastFeature = null;
 
     Iterator<SequenceFeature> it = features.iterator();
@@ -1037,7 +1027,7 @@ public abstract class FeatureRendererModel implements
        * (checking type and isContactFeature as a fail-safe here, although
        * currently they are guaranteed to match in this context)
        */
-      if (!graduated)
+      if (simpleColour)
       {
         if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
                 && sf.getEnd() == lastFeature.getEnd()