Merge branch 'develop' into features/JAL-2068groovyAnnotationWorker

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

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 53642b5..66a075e 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -98,6 +98,82 @@ public class DBRefEntry implements DBRefEntryI
   }
 
   /**
+   * Answers true if this object is either equivalent to, or can be 'improved'
+   * by, the given entry. Specifically, answers true if
+   * <ul>
+   * <li>source and accession are identical (ignoring case)</li>
+   * <li>version is identical (ignoring case), or this version is of the format
+   * "someSource:0", in which case the version for the other entry replaces it</li>
+   * <li>mappings are not compared but if this entry has no mapping, replace
+   * with that for the other entry</li>
+   * </ul>
+   * 
+   * @param other
+   * @return
+   */
+  @Override
+  public boolean updateFrom(DBRefEntryI other)
+  {
+    if (other == null)
+    {
+      return false;
+    }
+    if (other == this)
+    {
+      return true;
+    }
+
+    /*
+     * source must either match or be both null
+     */
+    String otherSource = other.getSource();
+    if ((source == null && otherSource != null)
+            || (source != null && otherSource == null)
+            || (source != null && !source.equalsIgnoreCase(otherSource)))
+    {
+      return false;
+    }
+
+    /*
+     * accession id must either match or be both null
+     */
+    String otherAccession = other.getAccessionId();
+    if ((accessionId == null && otherAccession != null)
+            || (accessionId != null && otherAccession == null)
+            || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+    {
+      return false;
+    }
+
+    /*
+     * if my version is null, "0" or "source:0" then replace with other version,
+     * otherwise the versions have to match
+     */
+    String otherVersion = other.getVersion();
+    if ((version == null || version.equals("0") || version.endsWith(":0"))
+            && otherVersion != null)
+    {
+      setVersion(otherVersion);
+    }
+    else
+    {
+      if (!version.equalsIgnoreCase(otherVersion))
+      {
+        return false;
+      }
+    }
+
+    /*
+     * if I have no mapping, take that of the other dbref
+     */
+    if (map == null)
+    {
+      setMap(other.getMap());
+    }
+    return true;
+  }
+
+  /**
    * test for similar DBRef attributes, except for the map object.
    * 
    * @param entry
@@ -106,6 +182,7 @@ public class DBRefEntry implements DBRefEntryI
   @Override
   public boolean equalRef(DBRefEntryI entry)
   {
+    // TODO is this method and equals() not needed?
     if (entry == null)
     {
       return false;