JAL-1479 added basic support for SIFTs mapping - more work to follow

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index e9d736f..0b3696c 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -458,117 +458,61 @@ public class StructureSelectionManager
       {
         continue;
       }
-      final StringBuilder mappingDetails = new StringBuilder(128);
-      mappingDetails.append(NEWLINE).append("PDB Sequence is :")
-              .append(NEWLINE).append("Sequence = ")
-              .append(maxChain.sequence.getSequenceAsString());
-      mappingDetails.append(NEWLINE).append("No of residues = ")
-              .append(maxChain.residues.size()).append(NEWLINE)
-              .append(NEWLINE);
-      PrintStream ps = new PrintStream(System.out)
-      {
-        @Override
-        public void print(String x)
-        {
-          mappingDetails.append(x);
-        }
-
-        @Override
-        public void println()
-        {
-          mappingDetails.append(NEWLINE);
-        }
-      };
-
-      // mapWithNWAlignment();
-      // mapWithSIFTS();
-      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());
 
       if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
       {
         pdbFile = "INLINE" + pdb.id;
       }
-      // StructureMapping newMapping = new StructureMapping(seq, pdbFile,
-      // pdb.id, maxChainId, mapping, mappingDetails.toString());
-      StructureMapping newMapping = new SiftsClient(pdb.id)
-              .getSiftsMappingsFor(seq, pdbFile, maxChainId);
+
+      StructureMapping seqToStrucMapping = null;
+      boolean isMapViaSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
+              "MAP_WITH_SIFTS", "false"));
+      if (isMapViaSIFTs)
+      {
+        SiftsClient siftsClient = new SiftsClient(pdb.id);
+        seqToStrucMapping = siftsClient.getSiftsStructureMapping(seq,
+                pdbFile, maxChainId);
+        // TODO if SIFTs mapping fails.. then fallback to NW alignment
+      }
+      else
+      {
+        seqToStrucMapping = getNWMappings(seq, pdbFile,
+                maxChainId, maxChain, pdb,
+                maxAlignseq);
+      }
+
       if (forStructureView)
       {
-        mappings.add(newMapping);
+        mappings.add(seqToStrucMapping);
       }
-      maxChain.transferResidueAnnotation(newMapping, sqmpping);
     }
-    // ///////
-
     return pdb;
   }
 
-  private StructureMapping mapWithNWAlignment(StringBuilder mappingDetails,
-          PDBChain maxChain, AlignSeq maxAlignseq, SequenceI seq,
-          PrintStream ps)
+  private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
+          String maxChainId, PDBChain maxChain, PDBfile pdb,
+          AlignSeq maxAlignseq)
   {
-    maxAlignseq.printAlignment(ps);
+    final StringBuilder mappingDetails = new StringBuilder(128);
+    PrintStream ps = new PrintStream(System.out)
+    {
+      @Override
+      public void print(String x)
+      {
+        mappingDetails.append(x);
+      }
 
-    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));
+      @Override
+      public void println()
+      {
+        mappingDetails.append(NEWLINE);
+      }
+    };
 
+    maxAlignseq.printAlignment(ps);
     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
@@ -595,7 +539,10 @@ public class StructureSelectionManager
       index++;
     } while (index < maxChain.atoms.size());
 
-    return null;
+    StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
+            pdb.id, maxChainId, mapping, mappingDetails.toString());
+    maxChain.transferResidueAnnotation(nwMapping, sqmpping);
+    return nwMapping;
   }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)