JAL-653 JAL-1968 FeaturesFile now handles Jalview or GFF2 or GFF3

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

diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index 1b6498f..5fadb6f 100755 (executable)
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -20,7 +20,8 @@
  */
 package jalview.datamodel;
 
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
 /**
@@ -41,7 +42,7 @@ public class SequenceFeature
 
   public String description;
 
-  public Hashtable otherDetails;
+  public Map<String, Object> otherDetails;
 
   public Vector<String> links;
 
@@ -54,9 +55,9 @@ public class SequenceFeature
   }
 
   /**
-   * Constructs a duplicate feature. Note: Uses clone on the otherDetails so
-   * only shallow copies are made of additional properties and method will
-   * silently fail if unclonable objects are found in the hash.
+   * Constructs a duplicate feature. Note: Uses makes a shallow copy of the
+   * otherDetails map, so the new and original SequenceFeature may reference the
+   * same objects in the map.
    * 
    * @param cpy
    */
@@ -83,10 +84,11 @@ public class SequenceFeature
       {
         try
         {
-          otherDetails = (Hashtable) cpy.otherDetails.clone();
+          otherDetails = (Map<String, Object>) ((HashMap<String, Object>) cpy.otherDetails)
+                  .clone();
         } catch (Exception e)
         {
-          // Uncloneable objects in the otherDetails - don't complain
+          // ignore
         }
       }
       if (cpy.links != null && cpy.links.size() > 0)
@@ -248,6 +250,20 @@ public class SequenceFeature
   }
 
   /**
+   * Returns a property value for the given key if known, else the specified
+   * default value
+   * 
+   * @param key
+   * @param defaultValue
+   * @return
+   */
+  public Object getValue(String key, Object defaultValue)
+  {
+    Object value = getValue(key);
+    return value == null ? defaultValue : value;
+  }
+
+  /**
    * Used for setting values which are not in the basic set. eg STRAND, FRAME
    * for GFF file
    * 
@@ -262,7 +278,7 @@ public class SequenceFeature
     {
       if (otherDetails == null)
       {
-        otherDetails = new Hashtable();
+        otherDetails = new HashMap<String, Object>();
       }
 
       otherDetails.put(key, value);