X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=cf794b631327724b869d395424b2e29ec6dd40d2;hb=1b4069135fa518efcb11d9cb729e5031347b8fe0;hp=073772adbbb7ef5dfc6713378001f13b4bb2c4ed;hpb=834ebffc22ed9e72b139cadf5652d1a7006da9b3;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 073772a..cf794b6 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -29,8 +29,8 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
+import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
-import jalview.structure.StructureViewSettings;
 
 import java.awt.Color;
 import java.util.List;
@@ -82,7 +82,7 @@ public class PDBChain
 
   public PDBChain(String pdbid, String id)
   {
-    this.pdbid = pdbid.toLowerCase();
+    this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
     this.id = id;
   }
 
@@ -423,7 +423,7 @@ public class PDBChain
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
 
-    if (StructureViewSettings.isShowSeqFeatures())
+    if (StructureImportSettings.isShowSeqFeatures())
     {
     for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
     {
@@ -582,12 +582,13 @@ public class PDBChain
         {
           for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
-            List<AlignmentAnnotation> transfer = sq
+            List<AlignmentAnnotation> transfer = dsq
                     .getAlignmentAnnotations(ana.getCalcId(), ana.label);
             if (transfer == null || transfer.size() == 0)
             {
               ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
+              dsq.addAlignmentAnnotation(ana);
               // mapping.transfer(ana);
             }
             else