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 4c9aa05..71732aa 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -39,6 +39,13 @@ public class SequenceFeature
   // private key for Phase designed not to conflict with real GFF data
   private static final String PHASE = "!Phase";
 
+  // private key for ENA location designed not to conflict with real GFF data
+  private static final String LOCATION = "!Location";
+
+  /*
+   * ATTRIBUTES is reserved for the GFF 'column 9' data, formatted as
+   * name1=value1;name2=value2,value3;...etc
+   */
   private static final String ATTRIBUTES = "ATTRIBUTES";
 
   public int begin;
@@ -51,6 +58,10 @@ public class SequenceFeature
 
   public String description;
 
+  /*
+   * a map of key-value pairs; may be populated from GFF 'column 9' data,
+   * other data sources (e.g. GenBank file), or programmatically
+   */
   public Map<String, Object> otherDetails;
 
   public Vector<String> links;
@@ -121,8 +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);
@@ -197,7 +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;
     }
@@ -207,8 +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;
     }
@@ -476,6 +489,26 @@ public class SequenceFeature
   }
 
   /**
+   * Sets the 'raw' ENA format location specifier e.g. join(12..45,89..121)
+   * 
+   * @param loc
+   */
+  public void setEnaLocation(String loc)
+  {
+    setValue(LOCATION, loc);
+  }
+
+  /**
+   * Gets the 'raw' ENA format location specifier e.g. join(12..45,89..121)
+   * 
+   * @param loc
+   */
+  public String getEnaLocation()
+  {
+    return (String) getValue(LOCATION);
+  }
+
+  /**
    * Readable representation, for debug only, not guaranteed not to change
    * between versions
    */
@@ -499,4 +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;
+  }
 }