Merge branch 'develop' into merge/develop_bug/JAL-2154projectMappings

[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 341d9ef..59bf445 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -37,6 +37,7 @@ 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;
@@ -75,7 +76,9 @@ 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;
@@ -178,8 +181,8 @@ public class DbRefFetcherTest
             .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);