JAL-2446 merged to spike branch

[jalview.git] / test / jalview / ws / seqfetcher / DbRefFetcherTest.java

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 63b1b9c..de91af3 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -21,6 +21,7 @@
 package jalview.ws.seqfetcher;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
@@ -31,12 +32,14 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.Uniprot;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
@@ -50,6 +53,13 @@ import org.testng.annotations.Test;
 public class DbRefFetcherTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * @throws java.lang.Exception
    */
@@ -62,7 +72,7 @@ public class DbRefFetcherTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
@@ -75,7 +85,9 @@ public class DbRefFetcherTest
   @Test(groups = { "Functional" })
   public void testStandardProtDbs()
   {
-    String[] defdb = DBRefSource.PROTEINDBS;
+    List<String> defdb = new ArrayList<String>();
+    defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
+    defdb.add(DBRefSource.PDB);
     List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
     SequenceFetcher sfetcher = new SequenceFetcher();
     boolean pdbFound = false;
@@ -162,24 +174,23 @@ public class DbRefFetcherTest
     SequenceI seq = alsq.getSequenceAt(0);
     assertEquals("Wrong sequence name", embl.getDbSource() + "|"
             + retrievalId, seq.getName());
-    SequenceFeature[] sfs = seq.getSequenceFeatures();
-    assertNotNull("Sequence features missing", sfs);
+    List<SequenceFeature> sfs = seq.getSequenceFeatures();
+    assertFalse("Sequence features missing", sfs.isEmpty());
     assertTrue(
             "Feature not CDS",
             FeatureProperties.isCodingFeature(embl.getDbSource(),
-                    sfs[0].getType()));
-    assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
+ sfs.get(0).getType()));
+    assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
     DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
-            new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
-                DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
+            new String[] { DBRefSource.UNIPROT });
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
     assertEquals("Expected cross reference map to be one amino acid", dr[0]
             .getMap().getMappedWidth(), 1);
     assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
             .getMap().getWidth(), 3);
-    AlignmentI sprods = CrossRef.findXrefSequences(
-            alsq.getSequencesArray(), true, dr[0].getSource(), alsq);
+    AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+            .findXrefSequences(dr[0].getSource(), true);
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);