JAL-2349 JAL-3855 Integrate pAE retrieval in StructureFile so it can be transferred...

[jalview.git] / src / mc_view / PDBChain.java

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index dc25368..035e608 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -28,6 +28,7 @@ import java.util.Vector;
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContactMatrixI;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
@@ -664,10 +665,16 @@ public class PDBChain
                   ana.getCalcId(), ana.label, ana.description);
           if (transfer == null || transfer.size() == 0)
           {
+            ContactMatrixI cm = shadow.getContactMatrixFor(ana);
             ana = new AlignmentAnnotation(ana);
+            // TODO map contact matrix under mapping
             ana.liftOver(sequence, shadowMap);
             ana.liftOver(dsq, sqmpping);
             dsq.addAlignmentAnnotation(ana);
+            if (cm != null)
+            {
+              dsq.addContactListFor(ana, cm);
+            }
           }
           else
           {
@@ -688,10 +695,14 @@ public class PDBChain
                             ana.description);
             if (transfer == null || transfer.size() == 0)
             {
+              ContactMatrixI cm = sequence.getContactMatrixFor(ana);
               ana = new AlignmentAnnotation(ana);
               ana.liftOver(dsq, sqmpping);
               dsq.addAlignmentAnnotation(ana);
-              // mapping.transfer(ana);
+              if (cm != null)
+              {
+                dsq.addContactListFor(ana, cm);
+              }
             }
             else
             {