From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 31 Aug 2016 16:13:22 +0000 (+0100)
Subject: JAL-1926 JAL-2106 fix PDB primary DBRef semantics: must have a matching PDBEntry... 
X-Git-Tag: Release_2_10_0~47^2~4^2~24
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ffedfec94d6a9f8ec8ba0775c2b4259368f6f149;p=jalview.git

JAL-1926 JAL-2106 fix PDB primary DBRef semantics: must have a matching PDBEntry with non-null File. type field doesn’t matter
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 2bbc278..0018ea1 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1449,13 +1449,12 @@ public class Sequence extends ASequence implements SequenceI
         {
           // PDB dbrefs imply there should be a PDBEntry associated
           // TODO: tighten PDB dbrefs
-          // formally imply Jalview has actually downlaoded and
+          // formally imply Jalview has actually downloaded and
           // parsed the pdb file. That means there should be a cached file
           // handle on the PDBEntry, and a real mapping between sequence and
           // extracted sequence from PDB file
           PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
-          if (pdbentry != null && pdbentry.getType() != null
-                  && pdbentry.getType().equalsIgnoreCase("PDB"))
+          if (pdbentry != null && pdbentry.getFile() != null)
           {
             primaries.add(ref);
           }