JAL-3763 (for whatever reason) need to increase timeout for command line ops to 10...

[jalview.git] / test / jalview / io / EmblFlatFileTest.java

diff --git a/test/jalview/io/EmblFlatFileTest.java b/test/jalview/io/EmblFlatFileTest.java
index c893c09..7775c8f 100644 (file)
--- a/test/jalview/io/EmblFlatFileTest.java
+++ b/test/jalview/io/EmblFlatFileTest.java
@@ -47,7 +47,6 @@ public class EmblFlatFileTest
     File dataFile = new File("test/jalview/io/J03321.embl.txt");
     FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
     EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
-    parser.parse();
     List<SequenceI> seqs = parser.getSeqs();
 
     assertEquals(seqs.size(), 1);
@@ -231,6 +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()
@@ -263,7 +278,6 @@ public class EmblFlatFileTest
             + "     ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga        40\n";
     FileParse fp = new FileParse(data, DataSourceType.PASTE);
     EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
-    parser.parse();
     List<SequenceI> seqs = parser.getSeqs();
     assertEquals(seqs.size(), 1);
     SequenceI seq = seqs.get(0);