JAL-3855 JAL-2349 download PAE matrix along with alpha fold structure from EBI and...

[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 a7e5806..bf34ea5 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -20,12 +20,14 @@
  */
 package jalview.ws.seqfetcher;
 
+import static org.testng.Assert.assertNotEquals;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
@@ -35,6 +37,7 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.JvOptionPane;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
+import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.Uniprot;
 
@@ -42,6 +45,7 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
+import org.junit.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
@@ -202,4 +206,29 @@ public class DbRefFetcherTest
     assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
             proteinSeq.getName());
   }
+
+  /**
+   * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+   * availability of network and the EMBLCDS service.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "External" })
+  public void testAlphaFoldClien() throws Exception
+  {
+    DbSourceProxy alphafold = new EBIAlfaFold();
+    AlignmentI resp = alphafold.getSequenceRecords(alphafold.getTestQuery());
+    assertNotNull(resp);
+    assertEquals("One sequence only",resp.getHeight(), 1);
+    for (AlignmentAnnotation aa:resp.getAlignmentAnnotation()) {
+      if (aa.graph == AlignmentAnnotation.CUSTOMRENDERER)
+      {
+        assertTrue("Contact map didn't provide valid contact",resp.getContactListFor(aa, 1).getContactAt(1)!=-1d);
+        // test passes
+        return;
+      }
+    }
+    Assert.fail();
+  }
+
 }