From: Jim Procter <jprocter@issues.jalview.org>
Date: Sat, 6 Jun 2015 17:00:53 +0000 (+0100)
Subject: JAL-653 make sure dummy sequences created during GFF parsing are actually resolved... 
X-Git-Tag: Release_2_10_0~296^2~150
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=96b4831c8077728623cb84cfd6940ac5b37df2c4;p=jalview.git

JAL-653 make sure dummy sequences created during GFF parsing are actually resolved and annotated
---

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;
   }