JAL-3956 - PDBEntry objects constructed from 3D-Beacons have authoritative IDs overri...

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

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index adcefb3..741ef07 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -38,7 +38,14 @@ public class PDBEntry
 
   private static final int PDB_ID_LENGTH = 4;
 
+  /**
+   * property set when id is a 'manufactured' identifier from the structure data's filename
+   */
   private static final String FAKED_ID = "faked_pdbid";
+  /**
+   * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+   */
+  private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
 
   private String file;
 
@@ -406,7 +413,7 @@ public class PDBEntry
           // this shouldn't happen, but could do if the id from the
           // file is not the same as the id from the authority that provided
           // the file
-          if (!newEntry.fakedPDBId())
+          if (!newEntry.fakedPDBId() && !isAuthoritative())
           {
             return false;
           } // otherwise we can update
@@ -474,7 +481,7 @@ public class PDBEntry
        */
       String key = newProps.nextElement();
       Object value = newEntry.getProperty(key);
-      if (FAKED_ID.equals(key))
+      if (FAKED_ID.equals(key) || AUTHORITATIVE_ID.equals(key))
       {
         // we never update the fake ID property
         continue;
@@ -487,6 +494,25 @@ public class PDBEntry
     return true;
   }
   
+  public void setAuthoritative(boolean isAuthoritative)
+  {
+    setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
+  }
+  
+  /**
+   * 
+   * @return true if the identifier should be preferred over any identifiers
+   *         embedded in the structure data
+   */
+  public boolean isAuthoritative()
+  {
+    if (_hasProperty(AUTHORITATIVE_ID))
+    {
+      return ((Boolean)getProperty(AUTHORITATIVE_ID));
+    }
+    return false;
+  }
+
   /**
    * set when Jalview has manufactured the ID using a local filename
    * @return