From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 23 Sep 2021 16:00:53 +0000 (+0100)
Subject: JAL-3821 failing test
X-Git-Tag: Release_2_11_2_0~32^2^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=722717410cce1e398f1153bdf23ed96b79e40e8a;p=jalview.git

JAL-3821 failing test
---

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index ee853f3..7775c8f 100644
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -230,6 +230,22 @@ public class EmblFlatFileTest
     }
     assertEquals(uniprotCount, 8);
   }
+  /**
+   * A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
+   * one of them reverse strand
+   * 
+   * @throws MalformedURLException
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testParseToRNA() throws MalformedURLException, IOException
+  {
+    File dataFile = new File("test/jalview/io/J03321_rna.embl.txt");
+    FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
+    EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
+    List<SequenceI> seqs = parser.getSeqs();
+    assertTrue(seqs.get(0).getSequenceAsString().indexOf("u")>-1);
+  }
 
   @Test(groups = "Functional")
   public void testParse_codonStartNot1()