From b7cb4c78d9d787e918c9d88f917a41642dd90a7a Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 18 Apr 2018 12:28:37 +0100
Subject: [PATCH] JAL-2593 render 'duplicate' features if transparency is
 applied

---
 .../seqfeatures/FeatureRendererModel.java          |   37 +++++++++++---------
 .../renderer/seqfeatures/FeatureRendererTest.java  |   14 +++++---
 2 files changed, 30 insertions(+), 21 deletions(-)

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 2f30e94..43b0550 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -54,9 +54,9 @@ public abstract class FeatureRendererModel
    */
   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
     {
       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
     renderOrder = neworder;
   }
 
-  protected Map<String, float[][]> minmax = new Hashtable<String, float[][]>();
+  protected Map<String, float[][]> minmax = new Hashtable<>();
 
   public Map<String, float[][]> getMinMax()
   {
@@ -271,7 +271,7 @@ public abstract class FeatureRendererModel
      * 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;
@@ -320,7 +320,7 @@ public abstract class FeatureRendererModel
     }
     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++)
@@ -333,7 +333,7 @@ public abstract class FeatureRendererModel
     }
 
     AlignmentI alignment = av.getAlignment();
-    List<String> allfeatures = new ArrayList<String>();
+    List<String> allfeatures = new ArrayList<>();
 
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -413,7 +413,7 @@ public abstract class FeatureRendererModel
      */
     if (minmax == null)
     {
-      minmax = new Hashtable<String, float[][]>();
+      minmax = new Hashtable<>();
     }
     synchronized (minmax)
     {
@@ -450,7 +450,7 @@ public abstract class FeatureRendererModel
    */
   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);
@@ -617,7 +617,7 @@ public abstract class FeatureRendererModel
   {
     if (featureOrder == null)
     {
-      featureOrder = new Hashtable<String, Float>();
+      featureOrder = new Hashtable<>();
     }
     featureOrder.put(type, new Float(position));
     return position;
@@ -676,7 +676,7 @@ public abstract class FeatureRendererModel
      * 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;
@@ -836,7 +836,7 @@ public abstract class FeatureRendererModel
   {
     if (featureGroups != null)
     {
-      List<String> gp = new ArrayList<String>();
+      List<String> gp = new ArrayList<>();
 
       for (String grp : featureGroups.keySet())
       {
@@ -882,7 +882,7 @@ public abstract class FeatureRendererModel
   @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;
@@ -910,7 +910,7 @@ public abstract class FeatureRendererModel
   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)
     {
@@ -931,7 +931,7 @@ public abstract class FeatureRendererModel
   @Override
   public List<String> getDisplayedFeatureGroups()
   {
-    List<String> _gps = new ArrayList<String>();
+    List<String> _gps = new ArrayList<>();
     for (String gp : getFeatureGroups())
     {
       if (checkGroupVisibility(gp, false))
@@ -966,7 +966,7 @@ public abstract class FeatureRendererModel
   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;
@@ -1011,6 +1011,7 @@ public abstract class FeatureRendererModel
     {
       return;
     }
+
     SequenceFeatures.sortFeatures(features, true);
     boolean simpleColour = fc == null || fc.isSimpleColour();
     SequenceFeature lastFeature = null;
@@ -1030,8 +1031,10 @@ public abstract class FeatureRendererModel
        * 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 (simpleColour)
+      if (simpleColour && transparency == 1f)
       {
         if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
                 && sf.getEnd() == lastFeature.getEnd()
diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index d3cddf9..3d48097 100644
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -341,10 +341,7 @@ public class FeatureRendererTest
     fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
             Color.white, 0f, 1f));
     assertEquals(features.size(), 4);
-    assertTrue(features.contains(sf1));
-    assertTrue(features.contains(sf3));
-    assertTrue(features.contains(sf4));
-    assertTrue(features.contains(sf5));
+    assertFalse(features.contains(sf2));
 
     /*
      * co-located features with colour by label
@@ -359,5 +356,14 @@ public class FeatureRendererTest
     assertTrue(features.contains(sf3));
     assertTrue(features.contains(sf4));
     assertTrue(features.contains(sf5));
+
+    /*
+     * no filtering if transparency is applied
+     */
+    fr.setTransparency(0.5f);
+    features = seq.getSequenceFeatures();
+    fr.setGroupVisibility("group2", true);
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.RED));
+    assertEquals(features.size(), 5);
   }
 }
-- 
1.7.10.2