JAL-2349 JAL-3855 fix failing tests

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

diff --git a/test/mc_view/PDBfileTest.java b/test/mc_view/PDBfileTest.java
index c99d185..cae183a 100644 (file)
--- a/test/mc_view/PDBfileTest.java
+++ b/test/mc_view/PDBfileTest.java
@@ -26,6 +26,13 @@ import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.IOException;
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -37,13 +44,6 @@ import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureImportSettings;
 
-import java.io.IOException;
-import java.util.List;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 public class PDBfileTest
 {
 
@@ -102,7 +102,8 @@ public class PDBfileTest
     assertEquals(0, chainA.seqend); // not set
     assertEquals(18, chainA.sequence.getStart());
     assertEquals(314, chainA.sequence.getEnd());
-    assertTrue(chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+    assertTrue(
+            chainA.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
@@ -122,7 +123,8 @@ public class PDBfileTest
     PDBChain chainC = pf.getChains().get(2);
     assertEquals(18, chainC.sequence.getStart());
     assertEquals(314, chainC.sequence.getEnd());
-    assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
+    assertTrue(
+            chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
     assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|C", chainC.sequence.getName());
 
@@ -243,8 +245,7 @@ public class PDBfileTest
    * @throws IOException
    */
   @Test(groups = { "Functional" })
-  public void testParse_withJmolAddAlignmentAnnotations()
-          throws IOException
+  public void testParse_withJmolAddAlignmentAnnotations() throws IOException
   {
     PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
             DataSourceType.FILE);
@@ -285,10 +286,10 @@ public class PDBfileTest
     for (int i = 0; i < 20; i++)
     {
       assertNull(anns[0].annotations[i]);
-      assertEquals("E", anns[0].annotations[20].displayCharacter);
+      assertNull(anns[0].annotations[20].displayCharacter);
       assertEquals('E', anns[0].annotations[20].secondaryStructure);
-      assertEquals("E", anns[2].annotations[18].displayCharacter);
-      assertEquals("H", anns[2].annotations[23].displayCharacter);
+      assertEquals('E', anns[2].annotations[18].secondaryStructure);
+      assertEquals('H', anns[2].annotations[23].secondaryStructure);
     }
   }