JAL-2157 JAL-1803 refactored Sequence.updatePDBIds, parse DBRefs with

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index c7e53a9..8c5073b 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -884,4 +884,87 @@ public class SequenceTest
     assertTrue(primaryDBRefs.contains(dbr1));
     assertTrue(primaryDBRefs.contains(dbr3));
   }
+
+  /**
+   * Test the method that updates the list of PDBEntry from any new DBRefEntry
+   * for PDB
+   */
+  @Test(groups = { "Functional" })
+  public void testUpdatePDBIds()
+  {
+    PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
+    seq.addPDBId(pdbe1);
+    seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
+    seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
+    seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
+    seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
+    // 7 is not a valid chain code:
+    seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
+    
+    seq.updatePDBIds();
+    List<PDBEntry> pdbIds = seq.getAllPDBEntries();
+    assertEquals(4, pdbIds.size());
+    assertSame(pdbe1, pdbIds.get(0));
+    // chain code got added to 3A6S:
+    assertEquals("B", pdbe1.getChainCode());
+    assertEquals("1A70", pdbIds.get(1).getId());
+    // 4BQGA is parsed into id + chain
+    assertEquals("4BQG", pdbIds.get(2).getId());
+    assertEquals("a", pdbIds.get(2).getChainCode());
+    assertEquals("2GIS7", pdbIds.get(3).getId());
+    assertNull(pdbIds.get(3).getChainCode());
+  }
+
+  /**
+   * Test the method that either adds a pdbid or updates an existing one
+   */
+  @Test(groups = { "Functional" })
+  public void testAddPDBId()
+  {
+    PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
+    seq.addPDBId(pdbe);
+    assertEquals(1, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getPDBEntry("3A6S"));
+    assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
+
+    // add the same entry
+    seq.addPDBId(pdbe);
+    assertEquals(1, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getPDBEntry("3A6S"));
+
+    // add an identical entry
+    seq.addPDBId(new PDBEntry("3A6S", null, null, null));
+    assertEquals(1, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getPDBEntry("3A6S"));
+
+    // add a different entry
+    PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
+    seq.addPDBId(pdbe2);
+    assertEquals(2, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getAllPDBEntries().get(0));
+    assertSame(pdbe2, seq.getAllPDBEntries().get(1));
+
+    // update pdbe with chain code, file, type
+    PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
+    seq.addPDBId(pdbe3);
+    assertEquals(2, seq.getAllPDBEntries().size());
+    assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
+    assertEquals("3A6S", pdbe.getId()); // unchanged
+    assertEquals("A", pdbe.getChainCode()); // updated
+    assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
+    assertEquals("filepath", pdbe.getFile()); // updated
+    assertSame(pdbe2, seq.getAllPDBEntries().get(1));
+
+    // add with a different file path
+    PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
+    seq.addPDBId(pdbe4);
+    assertEquals(3, seq.getAllPDBEntries().size());
+    assertSame(pdbe4, seq.getAllPDBEntries().get(2));
+
+    // add with a different chain code
+    PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
+    seq.addPDBId(pdbe5);
+    assertEquals(4, seq.getAllPDBEntries().size());
+    assertSame(pdbe5, seq.getAllPDBEntries().get(3));
+  }
 }