JAL-3013 resolve symlink to hmmer binaries folder

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

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index a85dcef..0265af3 100644 (file)
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -37,6 +37,7 @@ import jalview.datamodel.Mapping;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+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
@@ -260,7 +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: