From cf02a7088e2835fa4764d034e662f4319073c8a9 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 21 Sep 2021 08:30:03 +0100
Subject: [PATCH] JAL-3829 ignore the fake ID generated when a PDB format file
 without embedded ID is imported for an existing PDBEntry

---
 src/jalview/datamodel/PDBEntry.java       |   38 ++++++++++++++++++++++++++++-
 src/jalview/io/StructureFile.java         |    1 +
 test/jalview/datamodel/SequenceTest.java  |   15 ++++++++++++
 test/jalview/ext/jmol/JmolParserTest.java |    4 +++
 4 files changed, 57 insertions(+), 1 deletion(-)

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index b3e17bf..fc4ee46 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -38,6 +38,8 @@ public class PDBEntry
 
   private static final int PDB_ID_LENGTH = 4;
 
+  private static final String FAKED_ID = "faked_pdbid";
+
   private String file;
 
   private String type;
@@ -404,7 +406,10 @@ 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
-          return false;
+          if (!newEntry.fakedPDBId())
+          {
+            return false;
+          } // otherwise we can update
         }
       }
     }
@@ -469,6 +474,11 @@ public class PDBEntry
        */
       String key = newProps.nextElement();
       Object value = newEntry.getProperty(key);
+      if (FAKED_ID.equals(key))
+      {
+        // we never update the fake ID property
+        continue;
+      }
       if (!value.equals(getProperty(key)))
       {
         setProperty(key, value);
@@ -477,6 +487,32 @@ public class PDBEntry
     return true;
   }
   
+  /**
+   * set when Jalview has manufactured the ID using a local filename
+   * @return
+   */
+  public boolean fakedPDBId()
+  {
+    if (_hasProperty(FAKED_ID))
+    {
+      return true;
+    }
+    return false;
+  }
+  public void setFakedPDBId(boolean faked)
+  {
+    if (faked)
+    {
+      setProperty(FAKED_ID, Boolean.TRUE);
+    }
+    else 
+    {
+      if (properties!=null) {
+        properties.remove(FAKED_ID);
+      }
+    }
+  }
+
   private boolean _hasProperty(final String key)
   {
     return (properties != null && properties.containsKey(key));
diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 084f886..94a832b 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -119,6 +119,7 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
+    entry.setFakedPDBId(!isPPDBIdAvailable());
     entry.setType(getStructureFileType());
     if (chain.id != null)
     {
diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index eb75645..5069759 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1460,6 +1460,21 @@ public class SequenceTest
     seq.addPDBId(pdbe5);
     assertEquals(4, seq.getAllPDBEntries().size());
     assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+    
+    // add with a fake pdbid 
+    // (models don't have an embedded ID)
+    String realId = "RealIDQ";
+    PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
+    PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
+    pdbe7.setFakedPDBId(true);
+    seq.addPDBId(pdbe6);
+    assertEquals(5,seq.getAllPDBEntries().size());
+    seq.addPDBId(pdbe7);
+    assertEquals(5,seq.getAllPDBEntries().size());
+    assertFalse(pdbe6.fakedPDBId());
+    assertSame(pdbe6,seq.getAllPDBEntries().get(4));
+    assertEquals("C",pdbe6.getChainCode());
+    assertEquals(realId, pdbe6.getId());
   }
 
   @Test(
diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 2832135..10882d3 100644
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -277,6 +277,10 @@ public class JmolParserTest
     assertEquals(structureData.getId(), "localstruct");
     assertNotNull(structureData.getSeqs());
     /*
+     * local structures have a fake ID
+     */
+    assertTrue(structureData.getSeqs().get(0).getAllPDBEntries().get(0).fakedPDBId());
+    /*
      * the ID is also the group for features derived from structure data 
      */
     String featureGroup = structureData.getSeqs().get(0)
-- 
1.7.10.2