X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=2df8be69fb71d97168519ec0a04cb68661d9c8ab;hb=1e943acf589b7393c666204f533d2ebce28d7471;hp=26fcaf03fca547a4b5a2a2a9357eb3e003932a8e;hpb=6c96743ff6c65895e4b96523d0e3d05f6dc3cb01;p=jalview.git

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 26fcaf0..2df8be6 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -22,10 +22,12 @@ package jalview.ws.dbsources;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 
 import java.io.Reader;
@@ -47,6 +49,7 @@ public class UniprotTest
           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
+          + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
@@ -110,7 +113,7 @@ public class UniprotTest
      * Check cross-references
      */
     Vector<PDBEntry> xrefs = entry.getDbReference();
-    assertEquals(2, xrefs.size());
+    assertEquals(3, xrefs.size());
 
     PDBEntry xref = xrefs.get(0);
     assertEquals("2FSQ", xref.getId());
@@ -122,6 +125,25 @@ public class UniprotTest
     assertEquals("2FSR", xref.getId());
     assertEquals("PDBsum", xref.getType());
     assertFalse(xref.getProperties().hasMoreElements());
+
+    xref = xrefs.get(2);
+    assertEquals("AE007869", xref.getId());
+    assertEquals("EMBL", xref.getType());
+    assertEquals("AAK85932.1",
+ xref.getProperty("protein sequence ID"));
+    assertEquals("Genomic_DNA",
+ xref.getProperty("molecule type"));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetUniprotSequence()
+  {
+    UniprotEntry entry = new Uniprot().getUniprotEntries(
+            new StringReader(UNIPROT_XML)).get(0);
+    SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+    assertNotNull(seq);
+    assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+
   }
 
   /**
@@ -149,7 +171,7 @@ public class UniprotTest
   {
     UniprotEntry entry = new Uniprot().getUniprotEntries(
             new StringReader(UNIPROT_XML)).get(0);
-  
+
     /*
      * recommended names concatenated with space separator
      */