From 584ab9644955bec02d96448361b8aac5b9542599 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 14 Feb 2022 14:03:39 +0000
Subject: [PATCH] JAL-3956 - PDBEntry objects constructed from 3D-Beacons have
 authoritative IDs overriding any embedded IDs

---
 src/jalview/datamodel/PDBEntry.java                |   30 ++++++++++++++++++--
 .../ThreeDBStructureChooserQuerySource.java        |    1 +
 test/jalview/datamodel/PDBEntryTest.java           |   17 ++++++++++-
 3 files changed, 45 insertions(+), 3 deletions(-)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index adcefb3..741ef07 100755
--- 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
diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index 23b96c9..669e58a 100644
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -415,6 +415,7 @@ public class ThreeDBStructureChooserQuerySource
       {
         pdbEntry = new PDBEntry();
         pdbEntry.setId(pdbIdStr);
+        pdbEntry.setAuthoritative(true);
         try
         {
           pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index 198cde3..80b7376 100644
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -90,7 +90,7 @@ public class PDBEntryTest
     PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
     // different file only
     PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
-
+    
     /*
      * assertEquals will invoke PDBEntry.equals()
      */
@@ -269,6 +269,21 @@ public class PDBEntryTest
     pdb2.setProperty("hello", "moon");
     assertTrue(pdb1.updateFrom(pdb2));
     assertEquals(pdb1.getProperty("hello"), "moon");
+    
+    /*
+    * different id but authoritative
+    */
+    pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
+    pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
+    pdb1.setAuthoritative(true);
+
+    assertTrue(pdb1.isAuthoritative());
+    assertFalse(pdb2.isAuthoritative());
+    // can update pdb1 (authoritative) from pdb2 (non-authoritative)
+    assertTrue(pdb1.updateFrom(pdb2));
+    // but the ID must remain the same
+    assertEquals(pdb1.getId(),"af:1xyz");
+    
   }
 
   @Test(groups = { "Functional" })
-- 
1.7.10.2