JAL-3829 ignore the fake ID generated when a PDB format file without embedded ID...

[jalview.git] / src / jalview / io / StructureFile.java

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 16ae0a1..94a832b 100644 (file)
--- 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)
     {
@@ -341,8 +342,15 @@ public abstract class StructureFile extends AlignFile
     }
     StructureImportSettings.setShowSeqFeatures(true);
   }
-
-  public PDBChain findChain(String id) throws Exception
+  
+  /**
+   * Answers the first PDBChain found matching the given id, or null if none 
+   * is found
+   * 
+   * @param id
+   * @return
+   */
+  public PDBChain findChain(String id)
   {
     for (PDBChain chain : getChains())
     {
@@ -351,7 +359,7 @@ public abstract class StructureFile extends AlignFile
         return chain;
       }
     }
-    throw new Exception("PDB chain not Found!");
+    return null;
   }
 
   public void makeResidueList()