X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=ab79f104f43b0fbbd265a3f32fdb98d9f5c3591e;hb=dc56d975105f135b5fd37a22913d164df51a02d8;hp=7e387bd7fdc4e3725b61823f21bb3bde364566f9;hpb=bb9e5fdd698bc2ccfbe37293f4d25178c407c811;p=jalview.git

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 7e387bd..ab79f10 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -21,20 +21,34 @@
 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.UniprotEntry;
+import jalview.datamodel.SequenceI;
+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.Assert;
+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>"
@@ -46,9 +60,16 @@ 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>"
+          + "<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>"
+          + "<feature type=\"sequence variant\" description=\"Foo\"><variation>L</variation><variation>LMV</variation><original>M</original><location><position position=\"42\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Foo\"><variation>LL</variation><variation>LMV</variation><original>ML</original><location><begin position=\"42\"/><end position=\"43\"/></location></feature>"
+          + "<feature type=\"sequence variant\" description=\"Foo Too\"><variation>LL</variation><variation>LMVK</variation><original>MLML</original><location><begin position=\"42\"/><end position=\"45\"/></location></feature>"
           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
           + "</uniprot>";
 
@@ -83,65 +104,161 @@ 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(9, features.size());
+    UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
     assertNull(sf.getStatus());
-    assertEquals(1, sf.getPosition()); // wrong - Castor bug??
     assertEquals(1, sf.getBegin());
     assertEquals(18, sf.getEnd());
     sf = features.get(1);
     assertEquals("propeptide", sf.getType());
     assertEquals("Activation peptide", sf.getDescription());
-    assertEquals(19, sf.getPosition()); // wrong - Castor bug??
+    assertEquals(19, sf.getPosition());
     assertEquals(19, sf.getBegin());
     assertEquals(20, sf.getEnd());
     sf = features.get(2);
     assertEquals("chain", sf.getType());
     assertEquals("Granzyme B", sf.getDescription());
-    assertEquals(21, sf.getPosition()); // wrong - Castor bug??
+    assertEquals(21, sf.getPosition());
     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());
+
+    sf = features.get(6);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Foo",
+            sf.getDescription());
+    assertEquals(42, sf.getPosition());
+    assertEquals(42, sf.getBegin());
+    assertEquals(42, sf.getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "p.Met42Leu" + "\n" + "p.Met42LeuMetVal Foo");
+
+    sf = features.get(7);
+    assertEquals(42, sf.getBegin());
+    assertEquals(43, sf.getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "p.MetLeu42LeuLeu" + "\n" + "p.MetLeu42LeuMetVal Foo");
+
+    sf = features.get(8);
+    assertEquals(42, sf.getBegin());
+    assertEquals(45, sf.getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "p.MLML42LeuLeu" + "\n" + "p.MLML42LMVK Foo Too");
+
     /*
      * 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());
     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());
+    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
+
   }
 
   /**
-   * Test the method that formats the sequence name in Fasta style
+   * Test the method that formats the sequence id
    */
   @Test(groups = { "Functional" })
-  public void testConstructSequenceFastaHeader()
+  public void testGetUniprotEntryId()
   {
-    Uniprot u = new Uniprot();
-    Reader reader = new StringReader(UNIPROT_XML);
-    Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
-    UniprotEntry entry = entries.get(0);
+    UniprotEntry entry = new Uniprot().getUniprotEntries(
+            new StringReader(UNIPROT_XML)).get(0);
+
+    /*
+     * name formatted with Uniprot Entry name
+     */
+    String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
+    assertEquals(expectedName,
+            Uniprot.getUniprotEntryId(entry));
+  }
 
-    // source + accession ids + names
-    String expectedName = "UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
-    // protein names
-    String expectedDescription = "Mitogen-activated protein kinase 13 Henry ";
+  /**
+   * Test the method that formats the sequence description
+   */
+  @Test(groups = { "Functional" })
+  public void testGetUniprotEntryDescription()
+  {
+    UniprotEntry entry = new Uniprot().getUniprotEntries(
+            new StringReader(UNIPROT_XML)).get(0);
 
-    assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+    /*
+     * recommended names concatenated with space separator
+     */
+    String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
     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");
+    Vector<String> vars = new Vector();
+    vars.add("y");
+    uf.setVariation(vars);
+    assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(uf));
+
+    vars.clear();
+    vars.add("z"); // unknown variant - fails gracefully
+    uf.setVariation(vars);
+    assertEquals("p.Lys23z Hello", Uniprot.getDescription(uf));
+
+    uf.setVariation(null); // variant missing - is ignored
+    assertEquals("Hello", Uniprot.getDescription(uf));
+  }
 }