JAL-2781 mark aligned positions via StructureMapping’s Mapping object, and transfer...

[jalview.git] / src / jalview / ws / sifts / SiftsClient.java

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 289030e..e1b539e 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -448,8 +448,6 @@ public class SiftsClient implements SiftsClientI
     HashMap<Integer, int[]> mapping = getGreedyMapping(chain, seq, ps);
 
     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);
 
@@ -514,15 +512,61 @@ public class SiftsClient implements SiftsClientI
     {
       throw new SiftsException("SIFTS mapping failed");
     }
+    // also construct a mapping object between the seq-coord sys and the PDB seq's coord sys
 
     Integer[] keys = mapping.keySet().toArray(new Integer[0]);
     Arrays.sort(keys);
     seqStart = keys[0];
     seqEnd = keys[keys.length - 1];
-
+    List<int[]> from=new ArrayList<>(),to=new ArrayList<>();
+    int[]_cfrom=null,_cto=null;
     String matchedSeq = originalSeq;
-    if (seqStart != UNASSIGNED)
+    if (seqStart != UNASSIGNED) // fixme! seqStart can map to -1 for a pdb sequence that starts <-1
     {
+      for (int seqps:keys)
+      {
+        int pdbpos = mapping.get(seqps)[PDBE_POS];
+        if (pdbpos == UNASSIGNED)
+        {
+          // not correct - pdbpos might be -1, but leave it for now
+          continue;
+        }
+        if (_cfrom==null || seqps!=_cfrom[1]+1)
+        {
+          _cfrom = new int[] { seqps,seqps};
+          from.add(_cfrom);
+          _cto = null; // discontinuity
+        } else {
+          _cfrom[1]= seqps;
+        }
+        if (_cto==null || pdbpos!=1+_cto[1])
+        {
+          _cto = new int[] { pdbpos,pdbpos};
+          to.add(_cto);
+        } else {
+          _cto[1] = pdbpos;
+        }
+      }
+      _cfrom = new int[from.size() * 2];
+      _cto = new int[to.size() * 2];
+      int p = 0;
+      for (int[] range : from)
+      {
+        _cfrom[p++] = range[0];
+        _cfrom[p++] = range[1];
+      }
+      ;
+      p = 0;
+      for (int[] range : to)
+      {
+        _cto[p++] = range[0];
+        _cto[p++] = range[1];
+      }
+      ;
+
+      seqFromPdbMapping = new jalview.datamodel.Mapping(null, _cto, _cfrom,
+              1,
+              1);
       pdbStart = mapping.get(seqStart)[PDB_RES_POS];
       pdbEnd = mapping.get(seqEnd)[PDB_RES_POS];
       int orignalSeqStart = seq.getStart();
@@ -575,6 +619,8 @@ public class SiftsClient implements SiftsClientI
     TreeMap<Integer, String> resNumMap = shp.getResNumMap();
     List<Integer> omitNonObserved = shp.getOmitNonObserved();
     int nonObservedShiftIndex = shp.getNonObservedShiftIndex();
+    int pdbeNonObservedCount = shp.getPdbeNonObserved();
+    int firstPDBResNum = UNASSIGNED;
     for (Segment segment : segments)
     {
       // System.out.println("Mapping segments : " + segment.getSegId() + "\\"s