X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFeaturesFile.java;fp=src%2Fjalview%2Fio%2FFeaturesFile.java;h=d6c3c21d8386670f7d0a7981f99c6ba83a799843;hb=96b4831c8077728623cb84cfd6940ac5b37df2c4;hp=4085fc15da04e94aadc60088cb0c69d1cf8f066d;hpb=e0c1dde5b241a8ac5b8c960f1f55f0940da55788;p=jalview.git

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 4085fc1..d6c3c21 100755
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -1082,6 +1082,16 @@ public class FeaturesFile extends AlignFile
     else
     {
       match = align.findName(seqId, true);
+      if (match == null && newseqs != null)
+      {
+        for (SequenceI m : newseqs)
+        {
+          if (seqId.equals(m.getName()))
+          {
+            return m;
+          }
+        }
+      }
       
     }
     if (match==null && newseqs!=null)
@@ -1092,6 +1102,8 @@ public class FeaturesFile extends AlignFile
         matcher.addAll(Arrays.asList(new SequenceI[]
         { match }));
       }
+      // add dummy sequence to the newseqs list
+      newseqs.add(match);
     }
     return match;
   }