JAL-3529 failing test for bug

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index ba4312a..d8d524f 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -20,17 +20,22 @@
  */
 package jalview.io;
 
+import static org.testng.Assert.assertTrue;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
 
 import java.io.File;
 import java.util.Arrays;
@@ -93,14 +98,44 @@ public class StockholmFileTest
   }
 
   /**
+   * JAL-3529 - verify uniprot refs for sequences are output for sequences
+   * retrieved via Pfam
+   */
+  @Test(groups = { "Functional" })
+  public void dbrefOutput() throws Exception
+  {
+    // sequences retrieved in a Pfam domain alignment also have a PFAM database
+    // reference
+    SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+    sq.addDBRef(new DBRefEntry("UNIPROT", "1", "P00224"));
+    sq.addDBRef(new DBRefEntry("PFAM", "1", "P00224.1"));
+    sq.addDBRef(new DBRefEntry("PFAM", "1", "PF00111"));
+    AppletFormatAdapter af = new AppletFormatAdapter();
+    String toStockholm = af.formatSequences(FileFormat.Stockholm,
+            new Alignment(new SequenceI[]
+            { sq }), false);
+    assertTrue(toStockholm.indexOf("P00224") > -1,
+            "Couldn't locate UNIPROT Accession in generated Stockholm file.");
+    AlignmentI fromStockholm = af.readFile(toStockholm,
+            DataSourceType.PASTE, FileFormat.Stockholm);
+    SequenceI importedSeq = fromStockholm.getSequenceAt(0);
+    List<DBRefEntry> dbrefs = DBRefUtils.searchRefs(importedSeq.getDBRefs(),
+            "P00224");
+    assertTrue(dbrefs.size() == 1,
+            "Couldn't find Uniprot DBRef on re-imported sequence.");
+
+  }
+
+  /**
    * test alignment data in given file can be imported, exported and reimported
    * with no dataloss
    * 
    * @param f
-   *          - source datafile (IdentifyFile.identify() should work with it)
+   *                               - source datafile (IdentifyFile.identify()
+   *                               should work with it)
    * @param ioformat
-   *          - label for IO class used to write and read back in the data from
-   *          f
+   *                               - label for IO class used to write and read
+   *                               back in the data from f
    * @param ignoreFeatures
    * @param ignoreRowVisibility
    * @param allowNullAnnotations