From 3a8dc0dd7261853a53c7e4c3cde1b6d53d0e3e93 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Mon, 20 Sep 2021 11:13:12 +0100
Subject: [PATCH] JAL-3829 allow PDBEntry with file and ID with mismatching
 case to override one without a file

---
 src/jalview/datamodel/PDBEntry.java      |   34 ++++++++++++++++++++++--------
 test/jalview/datamodel/PDBEntryTest.java |    2 +-
 test/mc_view/PDBChainTest.java           |    2 +-
 3 files changed, 27 insertions(+), 11 deletions(-)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 672a59e..793fbd7 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -384,21 +384,37 @@ public class PDBEntry
       return false; // shouldn't happen
     }
 
-    /*
-     * id has to match (ignoring case)
-     */
-    if (!getId().equalsIgnoreCase(newId))
-    {
-      return false;
-    }
+    boolean idMatches = getId().equalsIgnoreCase(newId);
 
     /*
      * Don't update if associated with different structure files
      */
     String newFile = newEntry.getFile();
-    if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+    if (newFile != null && getFile() != null)
     {
-      return false;
+      if (!newFile.equals(getFile()))
+      {
+        return false;
+      }
+      else
+      {
+        // files match.
+        if (!idMatches)
+        {
+          // 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
+          return false;
+        }
+      }
+    }
+    else
+    {
+      // one has data, one doesn't ..
+      if (!idMatches)
+      {
+        return false;
+      } // otherwise maybe can update
     }
 
     /*
diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index cf4294e..198cde3 100644
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -208,7 +208,7 @@ public class PDBEntryTest
     assertTrue(pdb1.updateFrom(pdb2));
     assertEquals(pdb1.getFile(), "filePath");
     assertEquals(pdb1.getType(), Type.FILE.toString());
-
+    assertEquals(pdb1.getChainCode(),"B");
     /*
      * change of file is not allowed
      */
diff --git a/test/mc_view/PDBChainTest.java b/test/mc_view/PDBChainTest.java
index 14ec1e7..0f748ce 100644
--- a/test/mc_view/PDBChainTest.java
+++ b/test/mc_view/PDBChainTest.java
@@ -68,7 +68,7 @@ public class PDBChainTest
   {
     System.out.println("setup");
     StructureImportSettings.setShowSeqFeatures(true);
-    c = new PDBChain("1GAQ", "A", false);
+    c = new PDBChain("1GAQ", "A");
   }
 
   @Test(groups = { "Functional" })
-- 
1.7.10.2