X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=2df8be69fb71d97168519ec0a04cb68661d9c8ab;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=60a111130afbad500c555ccf8f88f03ebff88d44;hpb=3412b273e964fb1a9d22564b04a5f0c827ec2461;p=jalview.git

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 60a1111..2df8be6 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -1,16 +1,41 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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 org.testng.annotations.Test;
-import java.io.Reader;
-import java.io.StringReader;
-import java.util.Vector;
 
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 
+import java.io.Reader;
+import java.io.StringReader;
+import java.util.Vector;
+
+import org.testng.annotations.Test;
+
 public class UniprotTest
 {
   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
@@ -24,6 +49,7 @@ 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>"
@@ -33,7 +59,7 @@ public class UniprotTest
   /**
    * Test the method that unmarshals XML to a Uniprot model
    */
-  @Test
+  @Test(groups = { "Functional" })
   public void testGetUniprotEntries()
   {
     Uniprot u = new Uniprot();
@@ -51,8 +77,7 @@ public class UniprotTest
     /*
      * UniprotSequence drops any space characters
      */
-    assertEquals("MHAPLVSKDL", entry.getUniprotSequence()
-            .getContent());
+    assertEquals("MHAPLVSKDL", entry.getUniprotSequence().getContent());
 
     assertEquals(2, entry.getProtein().getName().size());
     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
@@ -68,19 +93,19 @@ public class UniprotTest
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
     assertNull(sf.getStatus());
-    assertEquals(1, sf.getPosition()); // wrong - Castor bug??
+    assertEquals(1, sf.getPosition());
     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());
 
@@ -88,35 +113,70 @@ 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());
     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
-  public void testConstructSequenceFastaHeader()
+  @Test(groups = { "Functional" })
+  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 as source | accession ids | names
+     * source database converted to Jalview canonical name
+     */
+    String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
+    assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+  }
 
-    // source + accession ids + names + protein names
-    String expectedName = ">UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6 Mitogen-activated protein kinase 13 Henry";
-    assertEquals(expectedName, Uniprot.constructSequenceFastaHeader(entry)
-            .toString());
+  /**
+   * 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);
+
+    /*
+     * recommended names concatenated with space separator
+     */
+    String expectedDescription = "Mitogen-activated protein kinase 13 Henry";
+    assertEquals(expectedDescription,
+            Uniprot.getUniprotEntryDescription(entry));
   }
 }