From 984b32fdd9ae57c1a03021d70556484215317bf2 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 9 Feb 2018 09:46:25 +0000
Subject: [PATCH] =?utf8?q?Use=20the=20=E2=80=9CPDBe=E2=80=9D=20or=20=E2=80=9C?=
 =?utf8?q?PDB=E2=80=9D=20numbering=20(starts=20from=201,=20corresponds=20wit?=
 =?utf8?q?h=20the=20PDB=20SEQRES=20record)=20to=20map=20to=20the=20dataset=20?=
 =?utf8?q?sequence=20if=20its=20primary=20coord=20system=20is=20PDB.=20(fixe?=
 =?utf8?q?s=20StructureSelectionManagerTest.testMapping=5FEqualsSeqFeatures=20?=
 =?utf8?q?with=204im2=5Fmissing.pdb).?=
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---
 src/jalview/ws/sifts/SiftsClient.java |   34 +++++++++++++++++++++++++++------
 1 file changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index d2db9cf..29f0ffe 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -571,6 +571,8 @@ public class SiftsClient implements SiftsClientI
       List<Residue> residues = segment.getListResidue().getResidue();
       for (Residue residue : residues)
       {
+        int pdbeIndex = getLeadingIntegerValue(residue.getDbResNum(),
+                UNASSIGNED);
         int currSeqIndex = UNASSIGNED;
         List<CrossRefDb> cRefDbs = residue.getCrossRefDb();
         CrossRefDb pdbRefDb = null;
@@ -591,11 +593,35 @@ public class SiftsClient implements SiftsClientI
             }
           }
         }
+        if (seqCoordSys == seqCoordSys.PDB) // FIXME: is seqCoordSys ever PDBe
+                                            // ???
+        {
+          // if the sequence has a primary reference to the PDB, then we are
+          // dealing with a sequence extracted directly from the PDB. In that
+          // case, numbering is PDBe - non-observed residues
+          currSeqIndex = pdbeIndex;
+        }
         if (currSeqIndex == UNASSIGNED)
         {
           continue;
         }
-        if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
+        if (!isResidueObserved(residue)
+                && seqCoordSys != seqCoordSys.UNIPROT)
+        {
+          // 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
+                                                                         // is
+                                                                         // not
+                                                                         // up
+                                                                         // to
+                                                                         // seq.getEnd()
         {
 
           int resNum = (pdbRefDb == null)
@@ -612,11 +638,7 @@ public class SiftsClient implements SiftsClientI
                             .getCanonicalAminoAcid(residue.getDbResName()));
             resNumMap.put(currSeqIndex, String.valueOf(resCharCode));
           }
-          else
-          {
-            omitNonObserved.add(currSeqIndex);
-            ++nonObservedShiftIndex;
-          }
+
           mapping.put(currSeqIndex - nonObservedShiftIndex,
                   new int[]
                   { Integer.valueOf(resNum), UNASSIGNED });
-- 
1.7.10.2