JAL-2069 update spike branch with latest

[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 6461748..c2f5bb7 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -490,7 +490,8 @@ public abstract class FeatureRendererModel
               if (mmrange != null)
               {
                 FeatureColourI fc = featureColours.get(oldRender[j]);
-                if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
+                if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+                        && !fc.isColourByAttribute())
                 {
                   fc.updateBounds(mmrange[0][0], mmrange[0][1]);
                 }
@@ -520,7 +521,8 @@ public abstract class FeatureRendererModel
         if (mmrange != null)
         {
           FeatureColourI fc = featureColours.get(newf[i]);
-          if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled())
+          if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+                  && !fc.isColourByAttribute())
           {
             fc.updateBounds(mmrange[0][0], mmrange[0][1]);
           }
@@ -586,7 +588,8 @@ public abstract class FeatureRendererModel
    */
   protected boolean showFeatureOfType(String type)
   {
-    return type == null ? false : av.getFeaturesDisplayed().isVisible(type);
+    return type == null ? false : (av.getFeaturesDisplayed() == null ? true
+            : av.getFeaturesDisplayed().isVisible(type));
   }
 
   @Override
@@ -1000,23 +1003,19 @@ public abstract class FeatureRendererModel
 
   /**
    * Removes from the list of features any that duplicate the location of a
-   * feature of the same type (unless feature is filtered out, or 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).
+   * feature of the same type. Should be used only for features of the same,
+   * simple, feature colour (which normally implies the same feature type). Does
+   * not check visibility settings for feature type or feature group.
    * 
    * @param features
-   * @param fc
    */
-  public void filterFeaturesForDisplay(List<SequenceFeature> features,
-          FeatureColourI fc)
+  public void filterFeaturesForDisplay(List<SequenceFeature> features)
   {
     if (features.isEmpty())
     {
       return;
     }
     SequenceFeatures.sortFeatures(features, true);
-    boolean simpleColour = fc == null || fc.isSimpleColour();
     SequenceFeature lastFeature = null;
 
     Iterator<SequenceFeature> it = features.iterator();
@@ -1030,15 +1029,12 @@ public abstract class FeatureRendererModel
        * (checking type and isContactFeature as a fail-safe here, although
        * currently they are guaranteed to match in this context)
        */
-      if (simpleColour)
+      if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+              && sf.getEnd() == lastFeature.getEnd()
+              && sf.isContactFeature() == lastFeature.isContactFeature()
+              && sf.getType().equals(lastFeature.getType()))
       {
-        if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
-                && sf.getEnd() == lastFeature.getEnd()
-                && sf.isContactFeature() == lastFeature.isContactFeature()
-                && sf.getType().equals(lastFeature.getType()))
-        {
-          it.remove();
-        }
+        it.remove();
       }
       lastFeature = sf;
     }