JAL-2920 use HGVS notation for protein variant feature

[jalview.git] / test / jalview / ws / dbsources / UniprotTest.java

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 57980b8..0ee4388 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -21,22 +21,33 @@
 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 jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.gui.JvOptionPane;
 
 import java.io.Reader;
 import java.io.StringReader;
 import java.util.Vector;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class UniprotTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
           + "<uniprot>"
@@ -52,6 +63,9 @@ public class UniprotTest
           + "<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>"
+          + "<feature type=\"sequence variant\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><variation>L</variation><location><position position=\"41\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Pathogenic\"><original>M</original><location><position position=\"41\"/></location></feature>"
           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
           + "</uniprot>";
 
@@ -86,13 +100,12 @@ public class UniprotTest
     /*
      * Check sequence features
      */
-    Vector<SequenceFeature> features = entry.getFeature();
-    assertEquals(3, features.size());
-    SequenceFeature sf = features.get(0);
+    Vector<UniprotFeature> features = entry.getFeature();
+    assertEquals(6, features.size());
+    UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
     assertNull(sf.getStatus());
-    assertEquals(1, sf.getPosition());
     assertEquals(1, sf.getBegin());
     assertEquals(18, sf.getEnd());
     sf = features.get(1);
@@ -108,6 +121,26 @@ public class UniprotTest
     assertEquals(21, sf.getBegin());
     assertEquals(247, sf.getEnd());
 
+    sf = features.get(3);
+    assertEquals("sequence variant", sf.getType());
+    assertNull(sf.getDescription());
+    assertEquals(41, sf.getPosition());
+    assertEquals(41, sf.getBegin());
+    assertEquals(41, sf.getEnd());
+
+    sf = features.get(4);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Pathogenic", sf.getDescription());
+    assertEquals(41, sf.getPosition());
+    assertEquals(41, sf.getBegin());
+    assertEquals(41, sf.getEnd());
+
+    sf = features.get(5);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Pathogenic", sf.getDescription());
+    assertEquals(41, sf.getPosition());
+    assertEquals(41, sf.getBegin());
+    assertEquals(41, sf.getEnd());
     /*
      * Check cross-references
      */
@@ -117,25 +150,19 @@ public class UniprotTest
     PDBEntry xref = xrefs.get(0);
     assertEquals("2FSQ", xref.getId());
     assertEquals("PDB", xref.getType());
-    assertEquals(2, xref.getProperty().size());
-    assertEquals("X-ray", xref.getProperty().get("method"));
-    assertEquals("1.40", xref.getProperty().get("resolution"));
+    assertEquals("X-ray", xref.getProperty("method"));
+    assertEquals("1.40", xref.getProperty("resolution"));
 
     xref = xrefs.get(1);
     assertEquals("2FSR", xref.getId());
     assertEquals("PDBsum", xref.getType());
-    assertNull(xref.getProperty());
+    assertFalse(xref.getProperties().hasMoreElements());
 
     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());
-
+    assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
+    assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
   }
 
   @Test(groups = { "Functional" })
@@ -159,11 +186,11 @@ public class UniprotTest
             new StringReader(UNIPROT_XML)).get(0);
 
     /*
-     * name formatted as source | accession ids | names
-     * source database converted to Jalview canonical name
+     * name formatted with Uniprot Entry name
      */
-    String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
-    assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+    String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
+    assertEquals(expectedName,
+            Uniprot.getUniprotEntryId(entry));
   }
 
   /**
@@ -182,4 +209,25 @@ public class UniprotTest
     assertEquals(expectedDescription,
             Uniprot.getUniprotEntryDescription(entry));
   }
+
+  @Test(groups = { "Functional" })
+  public void testGetDescription()
+  {
+    UniprotFeature uf = new UniprotFeature();
+    assertEquals("", Uniprot.getDescription(uf));
+
+    uf.setDescription("Hello");
+    assertEquals("Hello", Uniprot.getDescription(uf));
+
+    uf.setPosition(23);
+    uf.setOriginal("K");
+    uf.setVariation("y");
+    assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
+
+    uf.setVariation("z"); // unknown variant - fails gracefully
+    assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
+
+    uf.setVariation(null); // variant missing - is ignored
+    assertEquals("Hello", Uniprot.getDescription(uf));
+  }
 }