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 759f527..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 +36,8 @@ 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;
 import jalview.ws.SequenceFetcher;
@@ -46,10 +47,19 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class CrossRefTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Functional" })
   public void testFindXDbRefs()
   {
@@ -96,7 +106,7 @@ public class CrossRefTest
   public void testFindXrefSourcesForSequence_proteinToDna()
   {
     SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
-    List<String> sources = new ArrayList<String>();
+    List<String> sources = new ArrayList<>();
     AlignmentI al = new Alignment(new SequenceI[] {});
 
     /*
@@ -122,8 +132,9 @@ public class CrossRefTest
     sources = new CrossRef(new SequenceI[] { seq }, al)
             .findXrefSourcesForSequences(false);
     // method is patched to remove EMBL from the sources to match
-    assertEquals(3, sources.size());
-    assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+    assertEquals(4, sources.size());
+    assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]",
+            sources.toString());
 
     /*
      * add a sequence to the alignment which has a dbref to UNIPROT|A1234
@@ -251,8 +262,7 @@ public class CrossRefTest
      */
     SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
     Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList(
-            new int[] { 1, 21 }, new int[] {
-        1, 7 }, 3, 1));
+            new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1));
     DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
     dna1.addDBRef(dbref);
     dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
@@ -261,7 +271,7 @@ public class CrossRefTest
     pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
     AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
 
-    List<SequenceI> result = new ArrayList<SequenceI>();
+    List<SequenceI> result = new ArrayList<>();
 
     /*
      * first search for a dbref nowhere on the alignment:
@@ -282,7 +292,7 @@ public class CrossRefTest
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
     found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
             acf, false); // search dataset with a protein xref from a dna
-                          // sequence to locate the protein product
+                         // sequence to locate the protein product
     assertTrue(found);
     assertEquals(1, result.size());
     assertSame(pep1, result.get(0));
@@ -296,14 +306,14 @@ public class CrossRefTest
     dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
     found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
             acf, false); // search dataset with a protein's direct dbref to
-                          // locate dna sequences with matching xref
+                         // locate dna sequences with matching xref
     assertTrue(found);
     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();
@@ -417,7 +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)
@@ -444,7 +454,7 @@ public class CrossRefTest
     assertSame(pep2, xrefs.getSequenceAt(1));
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceFetcherFactory.setSequenceFetcher(null);
@@ -495,7 +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)
@@ -641,7 +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;