From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 11 Feb 2018 11:03:27 +0000 (+0000)
Subject: JAL-2780 JAL-2781 use PDBe numbering to map between sequence extracted from PDB chain... 
X-Git-Tag: Release_2_10_4~68^2~20
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=38889ac4815d29d1fbb040ff1dbbc47fe89ea87e;p=jalview.git

JAL-2780 JAL-2781 use PDBe numbering to map between sequence extracted from PDB chain and Uniprot mapping
---

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index e1b539e..3899f04 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -108,6 +108,8 @@ public class SiftsClient implements SiftsClientI
 
   private static final int PDB_ATOM_POS = 1;
 
+  private static final int PDBE_POS = 2;
+
   private static final String NOT_OBSERVED = "Not_Observed";
 
   private static final String SIFTS_FTP_BASE_URL = "http://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
@@ -458,8 +460,8 @@ public class SiftsClient implements SiftsClientI
   public HashMap<Integer, int[]> getGreedyMapping(String entityId,
           SequenceI seq, java.io.PrintStream os) throws SiftsException
   {
-    List<Integer> omitNonObserved = new ArrayList<Integer>();
-    int nonObservedShiftIndex = 0;
+    List<Integer> omitNonObserved = new ArrayList<>();
+    int nonObservedShiftIndex = 0,pdbeNonObserved=0;
     // System.out.println("Generating mappings for : " + entityId);
     Entity entity = null;
     entity = getEntityById(entityId);
@@ -490,7 +492,7 @@ public class SiftsClient implements SiftsClientI
     TreeMap<Integer, String> resNumMap = new TreeMap<Integer, String>();
     List<Segment> segments = entity.getSegment();
     SegmentHelperPojo shp = new SegmentHelperPojo(seq, mapping, resNumMap,
-            omitNonObserved, nonObservedShiftIndex);
+            omitNonObserved, nonObservedShiftIndex,pdbeNonObserved);
     processSegments(segments, shp);
     try
     {
@@ -628,6 +630,7 @@ public class SiftsClient implements SiftsClientI
       List<Residue> residues = segment.getListResidue().getResidue();
       for (Residue residue : residues)
       {
+        boolean isObserved = isResidueObserved(residue);
         int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
                 UNASSIGNED);
         int currSeqIndex = UNASSIGNED;
@@ -638,6 +641,19 @@ public class SiftsClient implements SiftsClientI
           if (cRefDb.getDbSource().equalsIgnoreCase(DBRefSource.PDB))
           {
             pdbRefDb = cRefDb;
+            if (firstPDBResNum == UNASSIGNED)
+            {
+              firstPDBResNum = getLeadingIntegerValue(cRefDb.getDbResNum(),
+                      UNASSIGNED);
+            }
+            else
+            {
+              if (isObserved)
+              {
+                // after we find the first observed residue we just increment
+                firstPDBResNum++;
+              }
+            }
           }
           if (cRefDb.getDbCoordSys().equalsIgnoreCase(seqCoordSys.getName())
                   && isAccessionMatched(cRefDb.getDbAccessionId()))
@@ -650,6 +666,10 @@ public class SiftsClient implements SiftsClientI
             }
           }
         }
+        if (!isObserved)
+        {
+          ++pdbeNonObservedCount;
+        }
         if (seqCoordSys == seqCoordSys.PDB) // FIXME: is seqCoordSys ever PDBe
                                             // ???
         {
@@ -662,15 +682,18 @@ public class SiftsClient implements SiftsClientI
         {
           continue;
         }
-        if (!isResidueObserved(residue)
-                && seqCoordSys != seqCoordSys.UNIPROT)
+        if (!isObserved)
         {
-          // mapping to PDB or PDBe so we need to bookkeep for the non-observed
-          // SEQRES positions
-          omitNonObserved.add(currSeqIndex);
-          ++nonObservedShiftIndex;
+          if (seqCoordSys != CoordinateSys.UNIPROT) // FIXME: PDB or PDBe only
+                                                    // here
+          {
+            // mapping to PDB or PDBe so we need to bookkeep for the
+            // non-observed
+            // SEQRES positions
+            omitNonObserved.add(currSeqIndex);
+            ++nonObservedShiftIndex;
+          }
         }
-
         // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
         // true
                                                                          // numbering
@@ -695,10 +718,13 @@ public class SiftsClient implements SiftsClientI
                             .getCanonicalAminoAcid(residue.getDbResName()));
             resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
           }
-
+          // TODO: mapping should have SeqCoordSysNum => int[] {PDBeNum,
+          // PDBRESNUM, ATOMNUM }
           mapping.put(currSeqIndex - nonObservedShiftIndex,
                   new int[]
-                  { Integer.valueOf(resNum), UNASSIGNED });
+                  { Integer.valueOf(resNum), UNASSIGNED,
+                      isObserved ? firstPDBResNum
+                              : UNASSIGNED });
         }
       }
     }
@@ -988,17 +1014,36 @@ public class SiftsClient implements SiftsClientI
 
     private int nonObservedShiftIndex;
 
+    /**
+     * count of number of 'not observed' positions in the PDB record's SEQRES
+     * (total number of residues with coordinates == length(SEQRES) -
+     * pdbeNonObserved
+     */
+    private int pdbeNonObserved;
+
     public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
             TreeMap<Integer, String> resNumMap,
-            List<Integer> omitNonObserved, int nonObservedShiftIndex)
+            List<Integer> omitNonObserved, int nonObservedShiftIndex,
+            int pdbeNonObserved)
     {
       setSeq(seq);
       setMapping(mapping);
       setResNumMap(resNumMap);
       setOmitNonObserved(omitNonObserved);
       setNonObservedShiftIndex(nonObservedShiftIndex);
+      setPdbeNonObserved(pdbeNonObserved);
+
     }
 
+    public void setPdbeNonObserved(int pdbeNonObserved2)
+    {
+      this.pdbeNonObserved = pdbeNonObserved2;
+    }
+
+    public int getPdbeNonObserved()
+    {
+      return pdbeNonObserved;
+    }
     public SequenceI getSeq()
     {
       return seq;
@@ -1048,6 +1093,7 @@ public class SiftsClient implements SiftsClientI
     {
       this.nonObservedShiftIndex = nonObservedShiftIndex;
     }
+
   }
 
   @Override