JAL-1920 JAL-3017 use newline not <br/> in description and update test to cover multi...

[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 2f548d0..c7f216e 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -26,15 +26,16 @@ 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.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
@@ -63,6 +64,11 @@ 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>"
+          + "<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>"
           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
           + "</uniprot>";
 
@@ -97,13 +103,12 @@ 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(8, 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);
@@ -119,9 +124,44 @@ public class UniprotTest
     assertEquals(21, sf.getBegin());
     assertEquals(247, sf.getEnd());
 
-    /*
-     * Check cross-references
-     */
+    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"); /*
+                                                                    * Check cross-references
+                                                                    */
     Vector<PDBEntry> xrefs = entry.getDbReference();
     assertEquals(3, xrefs.size());
 
@@ -139,10 +179,8 @@ public class UniprotTest
     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"));
+    assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
+    assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
   }
 
   @Test(groups = { "Functional" })
@@ -166,11 +204,11 @@ 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));
   }
 
   /**
@@ -189,4 +227,29 @@ 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");
+    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));
+  }
 }