X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=77f8078981a010046c0572db1ea1de88ba0f3a37;hb=1986948868e6643ea811a70cd0018c8103a7b3f0;hp=ed3ac772598ce214ad884abdb29ed586ecc7a3d5;hpb=f225620636ce3b7ec768b4bed98ba000f09efc2a;p=jalview.git

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index ed3ac77..77f8078 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -21,10 +21,12 @@
 package jalview.ws.dbsources;
 
 import static org.testng.AssertJUnit.assertEquals;
+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;
@@ -46,6 +48,7 @@ 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>"
@@ -109,7 +112,7 @@ 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());
@@ -122,8 +125,29 @@ public class UniprotTest
     assertEquals("2FSR", xref.getId());
     assertEquals("PDBsum", xref.getType());
     assertNull(xref.getProperty());
+
+    xref = xrefs.get(2);
+    assertEquals("AE007869", xref.getId());
+    assertEquals("EMBL", xref.getType());
+    assertNotNull(xref.getProperty());
+    assertEquals("AAK85932.1",
+            (String) xref.getProperty().get("protein sequence ID"));
+    assertEquals("Genomic_DNA",
+            (String) xref.getProperty().get("molecule type"));
+    assertEquals(2, xref.getProperty().size());
+
   }
 
+  @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
+
+  }
   /**
    * Test the method that formats the sequence id
    */
@@ -135,8 +159,9 @@ public class UniprotTest
 
     /*
      * name formatted as source | accession ids | names
+     * source database converted to Jalview canonical name
      */
-    String expectedName = "UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
+    String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
     assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
   }