JAL-2335 patched FeatureRendererModel.findFeaturesAtRes to honour isContactFeature

[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 a4e4348..c1ad465 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
 import jalview.schemes.UserColourScheme;
-import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
@@ -64,7 +63,7 @@ public abstract class FeatureRendererModel implements
   protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
           this);
 
-  protected AlignmentViewport av;
+  protected AlignViewportI av;
 
   @Override
   public AlignViewportI getViewport()
@@ -289,8 +288,12 @@ public abstract class FeatureRendererModel implements
           continue;
         }
 
-        if ((features[i].getBegin() <= res)
-                && (features[i].getEnd() >= res))
+        // check if start/end are at res, and if not a contact feature, that res
+        // lies between start and end
+        if ((features[i].getBegin() == res || features[i].getEnd() == res)
+                || (!features[i].isContactFeature()
+                        && (features[i].getBegin() < res) && (features[i]
+                        .getEnd() >= res)))
         {
           tmp.add(features[i]);
         }
@@ -565,15 +568,22 @@ public abstract class FeatureRendererModel implements
     return fc.isColored(sequenceFeature);
   }
 
+  /**
+   * Answers true if the feature type is currently selected to be displayed,
+   * else false
+   * 
+   * @param type
+   * @return
+   */
   protected boolean showFeatureOfType(String type)
   {
-    return av.getFeaturesDisplayed().isVisible(type);
+    return type == null ? false : av.getFeaturesDisplayed().isVisible(type);
   }
 
   @Override
   public void setColour(String featureType, FeatureColourI col)
   {
-     featureColours.put(featureType, col);
+    featureColours.put(featureType, col);
   }
 
   public void setTransparency(float value)