JAL-2780 JAL-2781 include a Mapping object in StructureMapping to pass to sequence...

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 948b23f..289030e 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -92,6 +92,14 @@ public class SiftsClient implements SiftsClientI
 
   private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT;
 
+  /**
+   * PDB sequence position to sequence coordinate mapping as derived from SIFTS
+   * record for the identified SeqCoordSys Used for lift-over from sequence
+   * derived from PDB (with first extracted PDBRESNUM as 'start' to the sequence
+   * being annotated with PDB data
+   */
+  private jalview.datamodel.Mapping seqFromPdbMapping;
+
   private static final int BUFFER_SIZE = 4096;
 
   public static final int UNASSIGNED = Integer.MIN_VALUE;
@@ -442,6 +450,9 @@ public class SiftsClient implements SiftsClientI
     String mappingOutput = mappingDetails.toString();
     StructureMapping siftsMapping = new StructureMapping(seq, pdbFile,
             pdbId, chain, mapping, mappingOutput);
+    StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile,
+            pdbId, chain, mapping, mappingOutput, seqFromPdbMapping);
+
     return siftsMapping;
   }