From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 13 Feb 2018 15:35:41 +0000 (+0000)
Subject: JAL-2780 JAL-2781 don’t create a mapping if sequence position was not assigned but... 
X-Git-Tag: Release_2_10_4~68^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=842713f26c299ec867320918a721ff5be9df7dbb;p=jalview.git

JAL-2780 JAL-2781 don’t create a mapping if sequence position was not assigned but still keep track of ‘unobserved’ counts for bookkeeping
---

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index 5050c34..b5f9653 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -690,6 +690,13 @@ public class SiftsClient implements SiftsClientI
             ++nonObservedShiftIndex;
           }
         }
+        if (currSeqIndex == UNASSIGNED)
+        {
+          // change in logic - unobserved residues with no currSeqIndex
+          // corresponding are still counted in both nonObservedShiftIndex and
+          // pdbeIndex...
+          continue;
+        }
         // if (currSeqIndex >= seq.getStart() && currSeqIndex <= seqlength) //
         // true
                                                                          // numbering