X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=4d67342736c147cb8fafbbabf3122394a42630c1;hb=53c54d0ada46fa839095ace36e18e30ddcf63aa0;hp=e1d075d344ba5e528659113b492ecead8fe62363;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index e1d075d..4d67342 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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[] {});
 
     /*
@@ -118,12 +128,13 @@ public class CrossRefTest
     seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347"));
     seq.addDBRef(new DBRefEntry("GENEDB", "0", "E2348"));
     seq.addDBRef(new DBRefEntry("ENSEMBL", "0", "E2349"));
-    seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
+    seq.addDBRef(new DBRefEntry("EnsemblFungi", "0", "E2350"));
     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("[EMBLCDS, GENEDB, ENSEMBL]",
+            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:
@@ -416,7 +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)
@@ -443,7 +454,7 @@ public class CrossRefTest
     assertSame(pep2, xrefs.getSequenceAt(1));
   }
 
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public void tearDown()
   {
     SequenceFetcherFactory.setSequenceFetcher(null);
@@ -494,7 +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)
@@ -640,7 +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;