From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 22 Aug 2016 12:00:07 +0000 (+0100)
Subject: JAL-2154 regression warning - should never recover a sequence ‘like’ an xref’s mappin... 
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~23
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=20ff4429a9545eeea6857818b55ec29eaf0388ad;p=jalview.git

JAL-2154 regression warning - should never recover a sequence ‘like’ an xref’s mapping.getTo() sequence!
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 578b18f..81fad27 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -271,6 +271,18 @@ public class CrossRef
              * but findInDataset() matches ENSP when looking for Uniprot...
              */
             SequenceI matchInDataset = findInDataset(xref);
+            if (matchInDataset != null && xref.getMap().getTo() != null
+                    && matchInDataset != xref.getMap().getTo())
+            {
+              System.err
+                      .println("Implementation problem (reopen JAL-2154): CrossRef.findInDataset seems to have recovered a different sequence than the one explicitly mapped for xref."
+                              + "Found:"
+                              + matchInDataset
+                              + "\nExpected:"
+                              + xref.getMap().getTo()
+                              + "\nFor xref:"
+                              + xref);
+            }
             /*matcher.findIdMatch(mappedTo);*/
             if (matchInDataset != null)
             {