X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fmc_view%2FPDBChain.java;h=2970ccf05e136b2b3a04a9d5f2a19e62c7b8ae55;hb=c43deb1df17a3860fc6c9b21c00e1bd62e53ff8e;hp=5413a3c648181f629af4c29343b2436a69ee373b;hpb=3380595c6eb44d914e9a25958bc09c4e292e1c32;p=jalview.git

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 5413a3c..2970ccf 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -39,6 +39,7 @@ import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
 import jalview.util.Comparison;
+import jalview.ws.datamodel.MappableContactMatrixI;
 
 public class PDBChain
 {
@@ -536,6 +537,7 @@ public class PDBChain
                       ? tfacTemplate.getDescription()
                       : tfacTemplate.getName()) + " for " + pdbid + id,
               annots, min, max, AlignmentAnnotation.LINE_GRAPH);
+      tfactorann.setTFType(tfacTemplate.getTFType());
       tfactorann.setCalcId(getClass().getName());
 
       tfactorann.setSequenceRef(sequence);
@@ -699,9 +701,10 @@ public class PDBChain
               ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
               dsq.addAlignmentAnnotation(ana);
-              if (cm != null)
+              if (cm != null && cm instanceof MappableContactMatrixI)
               {
-                dsq.addContactListFor(ana, cm);
+                dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
+                        .liftOver(dsq, sqmpping));
               }
             }
             else
@@ -716,8 +719,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         float min = -1, max = 0;
         Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-        for (int i = sq.getStart(), j = sq.getEnd(),
-                k = 0; i <= j; i++, k++)
+        for (int i = sq.getStart(), j = sq
+                .getEnd(), k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);