JAL-736 JAL-1645 brief documentation about physicochemical property conservation...

[jalview.git] / test / MCview / PDBfileTest.java

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 05680af..3e24f52 100644 (file)
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -15,6 +15,7 @@ import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 
 import java.io.IOException;
+import java.util.List;
 
 import org.testng.annotations.Test;
 
@@ -70,8 +71,8 @@ public class PDBfileTest
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, chainA.sequence.getPDBId().size());
-    PDBEntry pdb = chainA.sequence.getPDBId().get(0);
+    assertEquals(1, chainA.sequence.getAllPDBEntries().size());
+    PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
     assertEquals("A", pdb.getChainCode());
     assertEquals("PDB", pdb.getType());
     assertEquals("3W5V", pdb.getId());
@@ -96,6 +97,21 @@ public class PDBfileTest
     assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
     assertTrue(chainD.sequence.getSequenceAsString().endsWith("KEEELT"));
     assertEquals("3W5V|D", chainD.sequence.getName());
+
+    /*
+     * verify PDB-related data in parsed sequences
+     */
+    List<SequenceI> seqs = pf.getSeqs();
+    assertEquals(4, seqs.size());
+    assertEquals("3W5V|A", seqs.get(0).getName());
+    assertEquals("3W5V|B", seqs.get(1).getName());
+    assertEquals("3W5V|C", seqs.get(2).getName());
+    assertEquals("3W5V|D", seqs.get(3).getName());
+    assertEquals(1, seqs.get(0).getAllPDBEntries().size());
+    PDBEntry pdbe = seqs.get(0).getAllPDBEntries().get(0);
+    assertEquals("A", pdbe.getChainCode());
+    assertEquals("3W5V", pdbe.getId());
+    assertEquals(PDBEntry.Type.PDB.toString(), pdbe.getType());
   }
 
   /**