X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceFeature.java;h=c330df9174a748ddc35df84cddd516314047c8d0;hb=5299e0d9142887a30889e8277d12039f10e5c36f;hp=c75d6f24cfd98e77f16737e88064d840a0b0b9c3;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index c75d6f2..c330df9 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.FeatureLocationI;
+
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
@@ -30,7 +32,7 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public class SequenceFeature
+public class SequenceFeature implements FeatureLocationI
 {
   private static final String STATUS = "status";
 
@@ -208,7 +210,9 @@ public class SequenceFeature
     }
 
     SequenceFeature sf = (SequenceFeature) o;
-    if (begin != sf.begin || end != sf.end || score != sf.score)
+    boolean sameScore = Float.isNaN(score) ? Float.isNaN(sf.score)
+            : score == sf.score;
+    if (begin != sf.begin || end != sf.end || !sameScore)
     {
       return false;
     }
@@ -266,6 +270,7 @@ public class SequenceFeature
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getBegin()
   {
     return begin;
@@ -281,6 +286,7 @@ public class SequenceFeature
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getEnd()
   {
     return end;
@@ -530,4 +536,21 @@ public class SequenceFeature
     return s.hashCode() + getBegin() + getEnd() + (int) getScore()
             + getStrand();
   }
+
+  /**
+   * Answers true if the feature's start/end values represent two related
+   * positions, rather than ends of a range. Such features may be visualised or
+   * reported differently to features on a range.
+   */
+  @Override
+  public boolean isContactFeature()
+  {
+    // TODO abstract one day to a FeatureType class
+    if ("disulfide bond".equalsIgnoreCase(type)
+            || "disulphide bond".equalsIgnoreCase(type))
+    {
+      return true;
+    }
+    return false;
+  }
 }