JAL-1479 refactored SequenceI interface - changed getDBRef() to getDBRefs() since...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 59d8631..e9d736f 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -33,6 +33,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.SiftsClient;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
@@ -479,6 +480,8 @@ public class StructureSelectionManager
         }
       };
 
+      // mapWithNWAlignment();
+      // mapWithSIFTS();
       maxAlignseq.printAlignment(ps);
 
       mappingDetails.append(NEWLINE).append("PDB start/end ");
@@ -528,8 +531,10 @@ public class StructureSelectionManager
       {
         pdbFile = "INLINE" + pdb.id;
       }
-      StructureMapping newMapping = new StructureMapping(seq, pdbFile,
-              pdb.id, maxChainId, mapping, mappingDetails.toString());
+      // StructureMapping newMapping = new StructureMapping(seq, pdbFile,
+      // pdb.id, maxChainId, mapping, mappingDetails.toString());
+      StructureMapping newMapping = new SiftsClient(pdb.id)
+              .getSiftsMappingsFor(seq, pdbFile, maxChainId);
       if (forStructureView)
       {
         mappings.add(newMapping);
@@ -541,6 +546,58 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  private StructureMapping mapWithNWAlignment(StringBuilder mappingDetails,
+          PDBChain maxChain, AlignSeq maxAlignseq, SequenceI seq,
+          PrintStream ps)
+  {
+    maxAlignseq.printAlignment(ps);
+
+    mappingDetails.append(NEWLINE).append("PDB start/end ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+            .append(" ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+    mappingDetails.append(NEWLINE).append("SEQ start/end ");
+    // TODO JAL-1887 should be fixed from here
+    mappingDetails.append(
+            String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
+            .append(" ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq1end + seq.getEnd()
+            - 1));
+
+    maxChain.makeExactMapping(maxAlignseq, seq);
+    jalview.datamodel.Mapping sqmpping = maxAlignseq
+            .getMappingFromS1(false);
+    jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(sqmpping
+            .getMap().getInverse());
+    maxChain.transferRESNUMFeatures(seq, null);
+
+    // allocate enough slots to store the mapping from positions in
+    // sequence[s] to the associated chain
+    int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
+    int resNum = -10000;
+    int index = 0;
+
+    do
+    {
+      Atom tmp = maxChain.atoms.elementAt(index);
+      if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+      {
+        resNum = tmp.resNumber;
+        if (tmp.alignmentMapping >= -1)
+        {
+          // TODO (JAL-1836) address root cause: negative residue no in PDB
+          // file
+          mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+          mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+        }
+      }
+
+      index++;
+    } while (index < maxChain.atoms.size());
+
+    return null;
+  }
+
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
     listeners.removeElement(svl);