X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=2f30e9463a994ed8c7ad9d7eaa9b6260932551dc;hb=refs%2Fheads%2Fportforward%2FJAL-2675_2102b1to2103;hp=1d09dcacbe5bd2d069338c47c3fdf193e3efbd54;hpb=fb2d7072a283815141262d70d5f11a5e966d500b;p=jalview.git

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 1d09dca..2f30e94 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -45,8 +45,8 @@ import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 
-public abstract class FeatureRendererModel implements
-        jalview.api.FeatureRenderer
+public abstract class FeatureRendererModel
+        implements jalview.api.FeatureRenderer
 {
 
   /**
@@ -215,7 +215,8 @@ public abstract class FeatureRendererModel implements
       if (r[0] != 0 || mm[0] < 0.0)
       {
         r[0] = 1;
-        r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
+        r[1] = (byte) ((int) 128.0
+                + 127.0 * (sequenceFeature.score / mm[1]));
       }
       else
       {
@@ -462,7 +463,8 @@ public abstract class FeatureRendererModel implements
         {
           if (initOrders)
           {
-            setOrder(oldRender[j], (1 - (1 + (float) j) / oldRender.length));
+            setOrder(oldRender[j],
+                    (1 - (1 + (float) j) / oldRender.length));
           }
           if (allfeatures.contains(oldRender[j]))
           {
@@ -686,7 +688,8 @@ public abstract class FeatureRendererModel implements
       }
       else
       {
-        av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+        av.setFeaturesDisplayed(
+                av_featuresdisplayed = new FeaturesDisplayed());
       }
     }
     else
@@ -798,11 +801,12 @@ public abstract class FeatureRendererModel implements
   {
     // conflict between applet and desktop - featureGroups returns the map in
     // the desktop featureRenderer
-    return (featureGroups == null) ? Arrays.asList(new String[0]) : Arrays
-            .asList(featureGroups.keySet().toArray(new String[0]));
+    return (featureGroups == null) ? Arrays.asList(new String[0])
+            : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
   }
 
-  public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
+  public boolean checkGroupVisibility(String group,
+          boolean newGroupsVisible)
   {
     if (featureGroups == null)
     {
@@ -993,7 +997,9 @@ 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
@@ -1006,7 +1012,7 @@ 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();
@@ -1025,7 +1031,7 @@ 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()