Merge branch 'features/JAL-1541_BioJsMSAViewer-export-option' of https://source.jalvi...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7a1b100..175a249 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -28,7 +28,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
+import jalview.io.AppletFormatAdapter;
 import jalview.util.MessageManager;
 
 import java.io.PrintStream;
@@ -276,7 +276,7 @@ public class StructureSelectionManager
     {
       pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
       if (pdb.id != null && pdb.id.trim().length() > 0
-              && FormatAdapter.FILE.equals(protocol))
+              && AppletFormatAdapter.FILE.equals(protocol))
       {
         registerPDBFile(pdb.id.trim(), pdbFile);
       }
@@ -380,7 +380,10 @@ public class StructureSelectionManager
               + (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
 
       maxChain.makeExactMapping(maxAlignseq, sequence[s]);
-
+      jalview.datamodel.Mapping sqmpping = maxAlignseq
+              .getMappingFromS1(false);
+      jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
+              sqmpping.getMap().getInverse());
       maxChain.transferRESNUMFeatures(sequence[s], null);
 
       // allocate enough slots to store the mapping from positions in
@@ -426,7 +429,7 @@ public class StructureSelectionManager
 
         mappings[mappings.length - 1] = newMapping;
       }
-      maxChain.transferResidueAnnotation(newMapping);
+      maxChain.transferResidueAnnotation(newMapping, sqmpping);
     }
     // ///////