Merge branch 'feature/JAL-3187linkedFeatures' into feature/JAL-3251biotypedMappings

[jalview.git] / test / jalview / analysis / CrossRefTest.java

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 0265af3..2809004 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -29,7 +29,6 @@ import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -37,6 +36,7 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceMapping;
 import jalview.gui.JvOptionPane;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
@@ -311,9 +311,9 @@ public class CrossRefTest
     assertEquals(1, result.size());
     assertSame(dna1, result.get(0));
     // should now have a mapping from dna to pep1
-    List<SequenceToSequenceMapping> mappings = acf.getMappings();
+    List<SequenceMapping> mappings = acf.getMappings();
     assertEquals(1, mappings.size());
-    SequenceToSequenceMapping mapping = mappings.get(0);
+    SequenceMapping mapping = mappings.get(0);
     assertSame(dna1, mapping.getFromSeq());
     assertSame(pep1, mapping.getMapping().getTo());
     MapList mapList = mapping.getMapping().getMap();
@@ -427,7 +427,7 @@ public class CrossRefTest
      * argument false suppresses adding DAS sources
      * todo: define an interface type SequenceFetcherI and mock that
      */
-    SequenceFetcher mockFetcher = new SequenceFetcher(false)
+    SequenceFetcher mockFetcher = new SequenceFetcher()
     {
       @Override
       public boolean isFetchable(String source)
@@ -454,7 +454,7 @@ public class CrossRefTest
     assertSame(pep2, xrefs.getSequenceAt(1));
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceFetcherFactory.setSequenceFetcher(null);
@@ -505,7 +505,7 @@ public class CrossRefTest
      * argument false suppresses adding DAS sources
      * todo: define an interface type SequenceFetcherI and mock that
      */
-    SequenceFetcher mockFetcher = new SequenceFetcher(false)
+    SequenceFetcher mockFetcher = new SequenceFetcher()
     {
       @Override
       public boolean isFetchable(String source)
@@ -651,7 +651,7 @@ public class CrossRefTest
      * passed in calls to getSequences() - important to verify that
      * duplicate sequence fetches are not requested
      */
-    SequenceFetcher mockFetcher = new SequenceFetcher(false)
+    SequenceFetcher mockFetcher = new SequenceFetcher()
     {
       int call = 0;