Merge branch 'feature/JAL-2664' into feature/JAL-2527

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 187d5c2..71732aa 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -132,8 +132,8 @@ public class SequenceFeature
    * @param end
    * @param featureGroup
    */
-  public SequenceFeature(String type, String desc, String status,
-          int begin, int end, String featureGroup)
+  public SequenceFeature(String type, String desc, String status, int begin,
+          int end, String featureGroup)
   {
     this(type, desc, begin, end, featureGroup);
     setStatus(status);
@@ -208,7 +208,9 @@ 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;
     }
@@ -218,8 +220,8 @@ public class SequenceFeature
       return false;
     }
 
-    if (!(type + description + featureGroup + getPhase()).equals(sf.type
-            + sf.description + sf.featureGroup + sf.getPhase()))
+    if (!(type + description + featureGroup + getPhase()).equals(
+            sf.type + sf.description + sf.featureGroup + sf.getPhase()))
     {
       return false;
     }
@@ -530,4 +532,20 @@ 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.
+   */
+  public boolean isContactFeature()
+  {
+    // TODO abstract one day to a FeatureType class
+    if ("disulfide bond".equalsIgnoreCase(type)
+            || "disulphide bond".equalsIgnoreCase(type))
+    {
+      return true;
+    }
+    return false;
+  }
 }