From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 26 Aug 2016 12:20:51 +0000 (+0100)
Subject: JAL-2154 don’t add any remaining xrefed sequences of the wrong molecule type to the... 
X-Git-Tag: Release_2_10_0~47^2~4^2~43^2~6
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5f92754aa0aa65d11c2ccf7f1daa29fb5a7b421c

JAL-2154 don’t add any remaining xrefed sequences of the wrong molecule type to the alignment
---

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index cc80384..e0ec22b 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -2596,7 +2596,7 @@ public class AlignmentUtils
   {
     AlignmentI copy = new Alignment(new Alignment(seqs));
     copy.setDataset(dataset);
-
+    boolean isProtein = !copy.isNucleotide();
     SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
     if (xrefs != null)
     {
@@ -2607,7 +2607,8 @@ public class AlignmentUtils
         {
           for (DBRefEntry dbref : dbrefs)
           {
-            if (dbref.getMap() == null || dbref.getMap().getTo() == null)
+            if (dbref.getMap() == null || dbref.getMap().getTo() == null
+                    || dbref.getMap().getTo().isProtein() != isProtein)
             {
               continue;
             }