JAL-2593 avoid redundant rendering of co-located features

diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index 5e071f9..8f4f139 100644 (file)
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -21,6 +21,7 @@
 package jalview.renderer.seqfeatures;
 
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.util.Comparison;
@@ -290,8 +291,12 @@ public class FeatureRenderer extends FeatureRendererModel
         continue;
       }
 
+      FeatureColourI fc = getFeatureStyle(type);
       List<SequenceFeature> overlaps = seq.findFeatures(start + 1, end + 1,
               type);
+
+      filterFeaturesForDisplay(overlaps, fc);
+
       for (SequenceFeature sf : overlaps)
       {
         /*
@@ -303,7 +308,7 @@ public class FeatureRenderer extends FeatureRendererModel
           continue;
         }
 
-        Color featureColour = getColour(sf);
+        Color featureColour = fc.getColor(sf);
         boolean isContactFeature = sf.isContactFeature();
 
         int featureStartCol = seq.findIndex(sf.begin);

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index a568341..de1ee5e 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -26,6 +26,7 @@ import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.util.ColorUtils;
@@ -38,6 +39,7 @@ import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -1000,4 +1002,53 @@ public abstract class FeatureRendererModel implements
     return result;
   }
 
+  /**
+   * 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)
+   * 
+   * @param features
+   * @param fc
+   */
+  public void filterFeaturesForDisplay(List<SequenceFeature> features,
+          FeatureColourI fc)
+  {
+    if (features.isEmpty())
+    {
+      return;
+    }
+    SequenceFeatures.sortFeatures(features, true);
+    boolean graduated = fc != null && fc.isGraduatedColour();
+    SequenceFeature lastFeature = null;
+
+    Iterator<SequenceFeature> it = features.iterator();
+    while (it.hasNext())
+    {
+      SequenceFeature sf = it.next();
+      if (featureGroupNotShown(sf))
+      {
+        it.remove();
+        continue;
+      }
+
+      /*
+       * a feature is redundant for rendering purposes if it has the
+       * 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)
+       */
+      if (!graduated)
+      {
+        if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+                && sf.getEnd() == lastFeature.getEnd()
+                && sf.isContactFeature() == lastFeature.isContactFeature()
+                && sf.getType().equals(lastFeature.getType()))
+        {
+          it.remove();
+        }
+      }
+      lastFeature = sf;
+    }
+  }
+
 }

diff --git a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
index 31348c6..3e27aba 100644 (file)
--- a/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureRendererTest.java
@@ -14,6 +14,7 @@ import jalview.io.FileLoader;
 import jalview.schemes.FeatureColour;
 
 import java.awt.Color;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
@@ -252,4 +253,105 @@ public class FeatureRendererTest
     assertEquals(features.size(), 1);
     assertTrue(features.contains(sf8));
   }
+
+  @Test(groups = "Functional")
+  public void testFilterFeaturesForDisplay()
+  {
+    String seqData = ">s1\nabcdef\n";
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+            DataSourceType.PASTE);
+    AlignViewportI av = af.getViewport();
+    FeatureRenderer fr = new FeatureRenderer(av);
+
+    List<SequenceFeature> features = new ArrayList<>();
+    fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
+
+    SequenceI seq = av.getAlignment().getSequenceAt(0);
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, "group1");
+    seq.addSequenceFeature(sf1);
+    SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, "group2");
+    seq.addSequenceFeature(sf2);
+    SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, "group3");
+    seq.addSequenceFeature(sf3);
+    SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, "group4");
+    seq.addSequenceFeature(sf4);
+    SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, "group4");
+    seq.addSequenceFeature(sf5);
+
+    fr.findAllFeatures(true);
+
+    features = seq.getSequenceFeatures();
+    assertEquals(features.size(), 5);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf4));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * filter out duplicate (co-located) features
+     * note: which gets removed is not guaranteed
+     */
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertTrue(features.contains(sf2) || features.contains(sf3));
+    assertFalse(features.contains(sf2) && features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 3 - sf3 is removed, sf2 is retained
+     */
+    fr.setGroupVisibility("group3", false);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertTrue(features.contains(sf2));
+    assertFalse(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * hide group 2, show group 3 - sf2 is removed, sf3 is retained
+     */
+    fr.setGroupVisibility("group2", false);
+    fr.setGroupVisibility("group3", true);
+    features = seq.getSequenceFeatures();
+    fr.filterFeaturesForDisplay(features, null);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertFalse(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+
+    /*
+     * no filtering of co-located features with graduated colour scheme
+     * sf2 is removed as its group is hidden
+     */
+    features = seq.getSequenceFeatures();
+    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));
+
+    /*
+     * filtering of co-located features with colour by label
+     */
+    features = seq.getSequenceFeatures();
+    FeatureColour fc = new FeatureColour(Color.black);
+    fc.setColourByLabel(true);
+    fr.filterFeaturesForDisplay(features, fc);
+    assertEquals(features.size(), 3);
+    assertTrue(features.contains(sf1) || features.contains(sf4));
+    assertFalse(features.contains(sf1) && features.contains(sf4));
+    assertFalse(features.contains(sf2));
+    assertTrue(features.contains(sf3));
+    assertTrue(features.contains(sf5));
+  }
 }