JAL-2388 Unit tests and tidies

[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 7ff9adf..8468329 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -28,7 +28,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.seqfeatures.FeatureRenderer;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
 
 import java.awt.Color;
 import java.beans.PropertyChangeListener;
@@ -288,8 +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]);
         }
@@ -538,7 +542,7 @@ public abstract class FeatureRendererModel implements
     FeatureColourI fc = featureColours.get(featureType);
     if (fc == null)
     {
-      Color col = UserColourScheme.createColourFromName(featureType);
+      Color col = ColorUtils.createColourFromName(featureType);
       fc = new FeatureColour(col);
       featureColours.put(featureType, fc);
     }