JAL-2480 JAL-2505 guard against duplicating links

[jalview.git] / src / jalview / datamodel / SequenceFeature.java

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 15f54b9..8eacb68 100755 (executable)
--- 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";
 
@@ -268,6 +270,7 @@ public class SequenceFeature
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getBegin()
   {
     return begin;
@@ -283,6 +286,7 @@ public class SequenceFeature
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getEnd()
   {
     return end;
@@ -340,7 +344,10 @@ public class SequenceFeature
       links = new Vector<String>();
     }
 
-    links.insertElementAt(labelLink, 0);
+    if (!links.contains(labelLink))
+    {
+      links.insertElementAt(labelLink, 0);
+    }
   }
 
   public float getScore()
@@ -538,6 +545,7 @@ public class SequenceFeature
    * 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
@@ -548,4 +556,14 @@ public class SequenceFeature
     }
     return false;
   }
+
+  /**
+   * Answers true if the sequence has zero start and end position
+   * 
+   * @return
+   */
+  public boolean isNonPositional()
+  {
+    return begin == 0 && end == 0;
+  }
 }