JAL-2136 JAL-2137 Improvements: enable STRUCTMODEL annotation statement to be less...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 671c325..5ff2da4 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -600,11 +600,15 @@ public class StructureSelectionManager
         setProgressBar(null);
         setProgressBar(MessageManager
                 .getString("status.obtaining_mapping_with_phyre2_template_alignment"));
+        String fastaFile = getPhyre2FastaFileFor(pdbFile);
         StructureMapping phyre2ModelMapping = new Phyre2Client(pdb)
-                .getStructureMapping(seq, pdbFile,
-                        getPhyre2FastaFileFor(pdbFile), " ");
-
+                .getStructureMapping(seq, pdbFile, fastaFile, " ");
         seqToStrucMapping.add(phyre2ModelMapping);
+        maxChain.makeExactMapping(maxAlignseq, seq);
+        maxChain.transferRESNUMFeatures(seq, null);
+        jalview.datamodel.Mapping sqmpping = maxAlignseq
+                .getMappingFromS1(false);
+        maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping);
         ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
       }
       else