X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBfileTest.java;h=3e24f520922aad6c59e1c7f055c5916d7ba7f1e8;hb=23278fe32b704fa2d246d34ac17699e9555d00ee;hp=5d69a00fe3f69b97a302d9f73e0690cd7dd409de;hpb=3de63f1530eb6fb6bca7996fe5e2002af3c811e9;p=jalview.git

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 5d69a00..3e24f52 100644
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -1,10 +1,11 @@
 package MCview;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -14,13 +15,13 @@ import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
 
 import java.io.IOException;
+import java.util.List;
 
-import org.junit.Ignore;
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 public class PDBfileTest
 {
-  @Test
+  @Test(groups ={ "Functional" })
   public void testIsRna()
   {
     SequenceI seq = new Sequence("Seq1", "CGAU");
@@ -42,7 +43,7 @@ public class PDBfileTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testParse() throws IOException
   {
     /*
@@ -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());
   }
 
   /**
@@ -104,7 +120,7 @@ public class PDBfileTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testParse_withAnnotations_noSS() throws IOException
   {
     PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
@@ -162,7 +178,7 @@ public class PDBfileTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testParse_withJmol_noAnnotations() throws IOException
   {
     PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
@@ -191,7 +207,7 @@ public class PDBfileTest
    * 
    * @throws IOException
    */
-  @Test
+  @Test(groups ={ "Functional" })
   public void testParse_withJmolAddAlignmentAnnotations()
           throws IOException
   {
@@ -247,8 +263,9 @@ public class PDBfileTest
    * 
    * @throws IOException
    */
-  @Test
-  @Ignore
+
+  @Test(groups =
+  { "Functional" }, enabled = false)
   public void testParse_withAnnotate3D() throws IOException
   {
     // TODO requires a mock for Annotate3D processing
@@ -265,7 +282,7 @@ public class PDBfileTest
   private AlignmentAnnotation[] getAlignmentAnnotations(PDBfile pf)
   {
     AlignmentI al = new Alignment(pf.getSeqsAsArray());
-    pf.addAnnotations((Alignment) al);
+    pf.addAnnotations(al);
     return al.getAlignmentAnnotation();
   }
   }