X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fdbsources%2FUniprotTest.java;h=72e599d924a429f40ac02f227cb2ddfd129606cd;hb=547575f4b08f2cc25adcd438e8bce24e4e7af04e;hp=c89324ba7fdc8d26a91c2e6b8daac47a139f85ad;hpb=ab22918ab8fc67d30dad1fb1ae0f37e51f49df95;p=jalview.git

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index c89324b..72e599d 100644
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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;
@@ -35,7 +55,7 @@ public class UniprotTest
   /**
    * Test the method that unmarshals XML to a Uniprot model
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetUniprotEntries()
   {
     Uniprot u = new Uniprot();
@@ -53,8 +73,7 @@ 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()
@@ -70,19 +89,19 @@ 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());
 
@@ -106,19 +125,36 @@ public class UniprotTest
   }
 
   /**
-   * 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()
+  @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);
 
-    // 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());
+    /*
+     * 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));
+  }
+
+  /**
+   * 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));
   }
 }