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 4a7706f..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";
 
@@ -39,6 +41,13 @@ 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 +60,10 @@ 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;
@@ -111,26 +124,57 @@ public class SequenceFeature
     }
   }
 
+  /**
+   * Constructor including a Status value
+   * 
+   * @param type
+   * @param desc
+   * @param status
+   * @param begin
+   * @param end
+   * @param featureGroup
+   */
   public SequenceFeature(String type, String desc, String status,
           int begin, int end, String featureGroup)
   {
+    this(type, desc, begin, end, featureGroup);
+    setStatus(status);
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param type
+   * @param desc
+   * @param begin
+   * @param end
+   * @param featureGroup
+   */
+  SequenceFeature(String type, String desc, int begin, int end,
+          String featureGroup)
+  {
     this.type = type;
     this.description = desc;
-    setValue(STATUS, status);
     this.begin = begin;
     this.end = end;
     this.featureGroup = featureGroup;
   }
 
+  /**
+   * Constructor including a score value
+   * 
+   * @param type
+   * @param desc
+   * @param begin
+   * @param end
+   * @param score
+   * @param featureGroup
+   */
   public SequenceFeature(String type, String desc, int begin, int end,
           float score, String featureGroup)
   {
-    this.type = type;
-    this.description = desc;
-    this.begin = begin;
-    this.end = end;
+    this(type, desc, begin, end, featureGroup);
     this.score = score;
-    this.featureGroup = featureGroup;
   }
 
   /**
@@ -166,7 +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;
     }
@@ -224,6 +270,7 @@ public class SequenceFeature
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getBegin()
   {
     return begin;
@@ -239,6 +286,7 @@ public class SequenceFeature
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getEnd()
   {
     return end;
@@ -296,7 +344,10 @@ public class SequenceFeature
       links = new Vector<String>();
     }
 
-    links.insertElementAt(labelLink, 0);
+    if (!links.contains(labelLink))
+    {
+      links.insertElementAt(labelLink, 0);
+    }
   }
 
   public float getScore()
@@ -445,6 +496,26 @@ 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
    */
@@ -468,4 +539,31 @@ 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;
+  }
+
+  /**
+   * Answers true if the sequence has zero start and end position
+   * 
+   * @return
+   */
+  public boolean isNonPositional()
+  {
+    return begin == 0 && end == 0;
+  }
 }