X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=86f5602d856d988c27fda2f3be500eb6c5912074;hb=0173acde216fc54fb54d935c2f7d2550e4c25016;hp=57980b864ab5eb82569c246078b633792a5fd126;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 57980b8..86f5602 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -23,49 +23,73 @@ package jalview.ws.dbsources;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.datamodel.UniprotEntry;
+import jalview.gui.JvOptionPane;
+import jalview.xml.binding.uniprot.DbReferenceType;
+import jalview.xml.binding.uniprot.Entry;
+import jalview.xml.binding.uniprot.FeatureType;
+import jalview.xml.binding.uniprot.LocationType;
+import jalview.xml.binding.uniprot.PositionType;
 
-import java.io.Reader;
-import java.io.StringReader;
-import java.util.Vector;
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.math.BigInteger;
+import java.util.List;
 
+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>"
+          + "<uniprot xmlns=\"http://uniprot.org/uniprot\">"
           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
           + "<accession>A9CKP4</accession>"
           + "<accession>A9CKP5</accession>"
           + "<name>A9CKP4_AGRT5</name>"
           + "<name>A9CKP4_AGRT6</name>"
-          + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
+          + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</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>";
 
   /**
    * Test the method that unmarshals XML to a Uniprot model
+   * 
+   * @throws UnsupportedEncodingException
    */
   @Test(groups = { "Functional" })
-  public void testGetUniprotEntries()
+  public void testGetUniprotEntries() throws UnsupportedEncodingException
   {
     Uniprot u = new Uniprot();
-    Reader reader = new StringReader(UNIPROT_XML);
-    Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
+    InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+    List<Entry> entries = u.getUniprotEntries(is);
     assertEquals(1, entries.size());
-    UniprotEntry entry = entries.get(0);
+    Entry entry = entries.get(0);
     assertEquals(2, entry.getName().size());
     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
@@ -73,113 +97,211 @@ public class UniprotTest
     assertEquals("A9CKP4", entry.getAccession().get(0));
     assertEquals("A9CKP5", entry.getAccession().get(1));
 
-    /*
-     * UniprotSequence drops any space characters
-     */
-    assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
+    assertEquals("MHAPL VSKDL", entry.getSequence().getValue());
 
-    assertEquals(2, entry.getProtein().getName().size());
     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
-            .getName().get(0));
-    assertEquals("Henry", entry.getProtein().getName().get(1));
+            .getRecommendedName().getFullName().getValue());
 
     /*
      * Check sequence features
      */
-    Vector<SequenceFeature> features = entry.getFeature();
-    assertEquals(3, features.size());
-    SequenceFeature sf = features.get(0);
+    List<FeatureType> features = entry.getFeature();
+    assertEquals(9, features.size());
+    FeatureType 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());
+    assertNull(sf.getLocation().getPosition());
+    assertEquals(1, sf.getLocation().getBegin().getPosition().intValue());
+    assertEquals(18, sf.getLocation().getEnd().getPosition().intValue());
     sf = features.get(1);
     assertEquals("propeptide", sf.getType());
     assertEquals("Activation peptide", sf.getDescription());
-    assertEquals(19, sf.getPosition());
-    assertEquals(19, sf.getBegin());
-    assertEquals(20, sf.getEnd());
+    assertNull(sf.getLocation().getPosition());
+    assertEquals(19, sf.getLocation().getBegin().getPosition().intValue());
+    assertEquals(20, sf.getLocation().getEnd().getPosition().intValue());
     sf = features.get(2);
     assertEquals("chain", sf.getType());
     assertEquals("Granzyme B", sf.getDescription());
-    assertEquals(21, sf.getPosition());
-    assertEquals(21, sf.getBegin());
-    assertEquals(247, sf.getEnd());
+    assertNull(sf.getLocation().getPosition());
+    assertEquals(21, sf.getLocation().getBegin().getPosition().intValue());
+    assertEquals(247, sf.getLocation().getEnd().getPosition().intValue());
+
+    sf = features.get(3);
+    assertEquals("sequence variant", sf.getType());
+    assertNull(sf.getDescription());
+    assertEquals(41,
+            sf.getLocation().getPosition().getPosition().intValue());
+    assertNull(sf.getLocation().getBegin());
+    assertNull(sf.getLocation().getEnd());
+
+    sf = features.get(4);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Pathogenic", sf.getDescription());
+    assertEquals(41,
+            sf.getLocation().getPosition().getPosition().intValue());
+    assertNull(sf.getLocation().getBegin());
+    assertNull(sf.getLocation().getEnd());
+
+    sf = features.get(5);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Pathogenic", sf.getDescription());
+    assertEquals(41,
+            sf.getLocation().getPosition().getPosition().intValue());
+    assertNull(sf.getLocation().getBegin());
+    assertNull(sf.getLocation().getEnd());
+
+    sf = features.get(6);
+    assertEquals("sequence variant", sf.getType());
+    assertEquals("Foo",
+            sf.getDescription());
+    assertEquals(42,
+            sf.getLocation().getPosition().getPosition().intValue());
+    assertNull(sf.getLocation().getBegin());
+    assertNull(sf.getLocation().getEnd());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "<html>p.Met42Leu" + "<br/>&nbsp;&nbsp;"
+                    + "p.Met42LeuMetVal Foo</html>");
+
+    sf = features.get(7);
+    assertNull(sf.getLocation().getPosition());
+    assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
+    assertEquals(43, sf.getLocation().getEnd().getPosition().intValue());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "<html>p.MetLeu42LeuLeu" + "<br/>&nbsp;&nbsp;"
+                    + "p.MetLeu42LeuMetVal Foo</html>");
+
+    sf = features.get(8);
+    assertNull(sf.getLocation().getPosition());
+    assertEquals(42, sf.getLocation().getBegin().getPosition().intValue());
+    assertEquals(45, sf.getLocation().getEnd().getPosition().intValue());
+    Assert.assertEquals(Uniprot.getDescription(sf),
+            "<html>p.MLML42LeuLeu" + "<br/>&nbsp;&nbsp;"
+                    + "p.MLML42LMVK Foo Too</html>");
 
     /*
      * Check cross-references
      */
-    Vector<PDBEntry> xrefs = entry.getDbReference();
+    List<DbReferenceType> xrefs = entry.getDbReference();
     assertEquals(3, xrefs.size());
 
-    PDBEntry xref = xrefs.get(0);
+    DbReferenceType 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",
+            Uniprot.getProperty(xref.getProperty(), "method"));
+    assertEquals("1.40",
+            Uniprot.getProperty(xref.getProperty(), "resolution"));
 
     xref = xrefs.get(1);
     assertEquals("2FSR", xref.getId());
     assertEquals("PDBsum", xref.getType());
-    assertNull(xref.getProperty());
+    assertTrue(xref.getProperty().isEmpty());
 
     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"));
+            Uniprot.getProperty(xref.getProperty(), "protein sequence ID"));
     assertEquals("Genomic_DNA",
-            (String) xref.getProperty().get("molecule type"));
-    assertEquals(2, xref.getProperty().size());
-
+            Uniprot.getProperty(xref.getProperty(), "molecule type"));
   }
 
   @Test(groups = { "Functional" })
-  public void testGetUniprotSequence()
+  public void testGetUniprotSequence() throws UnsupportedEncodingException
   {
-    UniprotEntry entry = new Uniprot().getUniprotEntries(
-            new StringReader(UNIPROT_XML)).get(0);
-    SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+    InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+    Entry entry = new Uniprot().getUniprotEntries(
+            is).get(0);
+    SequenceI seq = new Uniprot().uniprotEntryToSequence(entry);
     assertNotNull(seq);
     assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+    assertEquals(seq.getSequenceAsString(),
+            seq.createDatasetSequence().getSequenceAsString());
 
   }
 
   /**
    * Test the method that formats the sequence id
+   * 
+   * @throws UnsupportedEncodingException
    */
   @Test(groups = { "Functional" })
-  public void testGetUniprotEntryId()
+  public void testGetUniprotEntryId() throws UnsupportedEncodingException
   {
-    UniprotEntry entry = new Uniprot().getUniprotEntries(
-            new StringReader(UNIPROT_XML)).get(0);
+    InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+    Entry entry = new Uniprot().getUniprotEntries(is).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));
   }
 
   /**
    * Test the method that formats the sequence description
+   * 
+   * @throws UnsupportedEncodingException
    */
   @Test(groups = { "Functional" })
   public void testGetUniprotEntryDescription()
+          throws UnsupportedEncodingException
   {
-    UniprotEntry entry = new Uniprot().getUniprotEntries(
-            new StringReader(UNIPROT_XML)).get(0);
+    InputStream is = new ByteArrayInputStream(UNIPROT_XML.getBytes());
+    Entry entry = new Uniprot().getUniprotEntries(is).get(0);
+
+    assertEquals("Mitogen-activated protein kinase 13",
+            Uniprot.getUniprotEntryDescription(entry));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetDescription()
+  {
+    FeatureType ft = new FeatureType();
+    assertEquals("", Uniprot.getDescription(ft));
+
+    ft.setDescription("Hello");
+    assertEquals("Hello", Uniprot.getDescription(ft));
+
+    ft.setLocation(new LocationType());
+    ft.getLocation().setPosition(new PositionType());
+    ft.getLocation().getPosition().setPosition(BigInteger.valueOf(23));
+    ft.setOriginal("K");
+    ft.getVariation().add("y");
+    assertEquals("p.Lys23Tyr Hello", Uniprot.getDescription(ft));
+
+    // multiple variants generate an html description over more than one line
+    ft.getVariation().add("W");
+    assertEquals("<html>p.Lys23Tyr<br/>&nbsp;&nbsp;p.Lys23Trp Hello</html>",
+            Uniprot.getDescription(ft));
 
     /*
-     * recommended names concatenated with space separator
+     * indel cases
+     * up to 3 bases (original or variant) are shown using 3 letter code
      */
-    String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
-    assertEquals(expectedDescription,
-            Uniprot.getUniprotEntryDescription(entry));
+    ft.getVariation().clear();
+    ft.getVariation().add("KWE");
+    ft.setOriginal("KLS");
+    assertEquals("p.LysLeuSer23LysTrpGlu Hello",
+            Uniprot.getDescription(ft));
+
+    // adding a fourth original base switches to single letter code
+    ft.setOriginal("KLST");
+    assertEquals("p.KLST23LysTrpGlu Hello", Uniprot.getDescription(ft));
+
+    // adding a fourth variant switches to single letter code
+    ft.getVariation().clear();
+    ft.getVariation().add("KWES");
+    assertEquals("p.KLST23KWES Hello", Uniprot.getDescription(ft));
+
+    ft.getVariation().clear();
+    ft.getVariation().add("z"); // unknown variant - fails gracefully
+    ft.setOriginal("K");
+    assertEquals("p.Lys23z Hello", Uniprot.getDescription(ft));
+
+    ft.getVariation().clear(); // variant missing - is ignored
+    assertEquals("Hello", Uniprot.getDescription(ft));
   }
 }