X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=43b0550e998dc1d7ab50949123be2321f50740ad;hb=b7cb4c78d9d787e918c9d88f917a41642dd90a7a;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..43b0550 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
 {
 
   /**
@@ -54,9 +54,9 @@ public abstract class FeatureRendererModel implements
    */
   protected float transparency = 1.0f;
 
-  protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<String, FeatureColourI>();
+  protected Map<String, FeatureColourI> featureColours = new ConcurrentHashMap<>();
 
-  protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<String, Boolean>();
+  protected Map<String, Boolean> featureGroups = new ConcurrentHashMap<>();
 
   protected String[] renderOrder;
 
@@ -156,7 +156,7 @@ public abstract class FeatureRendererModel implements
     {
       av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
     }
-    List<String> nft = new ArrayList<String>();
+    List<String> nft = new ArrayList<>();
     for (String featureType : featureTypes)
     {
       if (!fdi.isRegistered(featureType))
@@ -192,7 +192,7 @@ public abstract class FeatureRendererModel implements
     renderOrder = neworder;
   }
 
-  protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+  protected Map<String, float[][]> minmax = new Hashtable<>();
 
   public Map<String, float[][]> getMinMax()
   {
@@ -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
       {
@@ -270,7 +271,7 @@ public abstract class FeatureRendererModel implements
      * include features at the position provided their feature type is 
      * displayed, and feature group is null or marked for display
      */
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
     if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
     {
       return result;
@@ -319,7 +320,7 @@ public abstract class FeatureRendererModel implements
     }
     FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
 
-    Set<String> oldfeatures = new HashSet<String>();
+    Set<String> oldfeatures = new HashSet<>();
     if (renderOrder != null)
     {
       for (int i = 0; i < renderOrder.length; i++)
@@ -332,7 +333,7 @@ public abstract class FeatureRendererModel implements
     }
 
     AlignmentI alignment = av.getAlignment();
-    List<String> allfeatures = new ArrayList<String>();
+    List<String> allfeatures = new ArrayList<>();
 
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -412,7 +413,7 @@ public abstract class FeatureRendererModel implements
      */
     if (minmax == null)
     {
-      minmax = new Hashtable<String, float[][]>();
+      minmax = new Hashtable<>();
     }
     synchronized (minmax)
     {
@@ -449,7 +450,7 @@ public abstract class FeatureRendererModel implements
    */
   private void updateRenderOrder(List<String> allFeatures)
   {
-    List<String> allfeatures = new ArrayList<String>(allFeatures);
+    List<String> allfeatures = new ArrayList<>(allFeatures);
     String[] oldRender = renderOrder;
     renderOrder = new String[allfeatures.size()];
     boolean initOrders = (featureOrder == null);
@@ -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]))
           {
@@ -615,7 +617,7 @@ public abstract class FeatureRendererModel implements
   {
     if (featureOrder == null)
     {
-      featureOrder = new Hashtable<String, Float>();
+      featureOrder = new Hashtable<>();
     }
     featureOrder.put(type, new Float(position));
     return position;
@@ -674,7 +676,7 @@ public abstract class FeatureRendererModel implements
      * note visible feature ordering and colours before update
      */
     List<String> visibleFeatures = getDisplayedFeatureTypes();
-    Map<String, FeatureColourI> visibleColours = new HashMap<String, FeatureColourI>(
+    Map<String, FeatureColourI> visibleColours = new HashMap<>(
             getFeatureColours());
 
     FeaturesDisplayedI av_featuresdisplayed = null;
@@ -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)
     {
@@ -832,7 +836,7 @@ public abstract class FeatureRendererModel implements
   {
     if (featureGroups != null)
     {
-      List<String> gp = new ArrayList<String>();
+      List<String> gp = new ArrayList<>();
 
       for (String grp : featureGroups.keySet())
       {
@@ -878,7 +882,7 @@ public abstract class FeatureRendererModel implements
   @Override
   public Map<String, FeatureColourI> getDisplayedFeatureCols()
   {
-    Map<String, FeatureColourI> fcols = new Hashtable<String, FeatureColourI>();
+    Map<String, FeatureColourI> fcols = new Hashtable<>();
     if (getViewport().getFeaturesDisplayed() == null)
     {
       return fcols;
@@ -906,7 +910,7 @@ public abstract class FeatureRendererModel implements
   public List<String> getDisplayedFeatureTypes()
   {
     List<String> typ = getRenderOrder();
-    List<String> displayed = new ArrayList<String>();
+    List<String> displayed = new ArrayList<>();
     FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
     if (feature_disp != null)
     {
@@ -927,7 +931,7 @@ public abstract class FeatureRendererModel implements
   @Override
   public List<String> getDisplayedFeatureGroups()
   {
-    List<String> _gps = new ArrayList<String>();
+    List<String> _gps = new ArrayList<>();
     for (String gp : getFeatureGroups())
     {
       if (checkGroupVisibility(gp, false))
@@ -962,7 +966,7 @@ public abstract class FeatureRendererModel implements
   public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
           int resNo)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
     if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
     {
       return result;
@@ -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
@@ -1005,8 +1011,9 @@ 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();
@@ -1024,8 +1031,10 @@ public abstract class FeatureRendererModel implements
        * same extent as another (so would just redraw the same colour);
        * (checking type and isContactFeature as a fail-safe here, although
        * currently they are guaranteed to match in this context)
+       * don't remove 'redundant' features if transparency is applied 
+       * (as feature count affects depth of feature colour)
        */
-      if (!graduated)
+      if (simpleColour && transparency == 1f)
       {
         if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
                 && sf.getEnd() == lastFeature.getEnd()