JAL-2593 avoid redundant rendering of co-located features

[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 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;
+    }
+  }
+
 }