Merge develop to Release_2_8_3_Branch

[jalview.git] / test / jalview / structure / Mapping.java

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index b0144fc..cc8138c 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -3,6 +3,13 @@ package jalview.structure;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
+
+import org.junit.Assert;
+import org.junit.Ignore;
+import org.junit.Test;
+
+import MCview.PDBfile;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
@@ -11,11 +18,6 @@ import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 
-import org.junit.Assert;
-import org.junit.Test;
-
-import MCview.PDBfile;
-
 public class Mapping
 {
 
@@ -27,6 +29,7 @@ public class Mapping
    * msd numbering, not pdb res numbering.
    */
   @Test
+  @Ignore
   public void pdbEntryPositionMap() throws Exception
   {
     fail("This test intentionally left to fail");
@@ -109,6 +112,7 @@ public class Mapping
   }
 
   @Test
+  @Ignore
   public void testPDBentryMapping() throws Exception
   {
     fail("This test intentionally left to fail");
@@ -245,6 +249,8 @@ public class Mapping
     newseq.setStart(refseq.getStart() + 25);
     newseq.setEnd(refseq.getLength() + 25 + refseq.getStart());
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
+    ssm.setProcessSecondaryStructure(true);
+    ssm.setAddTempFacAnnot(true);
     PDBfile pmap = ssm.setMapping(true, new SequenceI[]
     { newseq }, new String[]
     { null }, "test/jalview/ext/jmol/1QCF.pdb",
@@ -252,7 +258,9 @@ public class Mapping
     assertTrue(pmap != null);
     assertEquals("Original and copied sequence of different lengths.",
             refseq.getLength(), newseq.getLength());
-    assertTrue(refseq.getAnnotation().length > 0
+    assertTrue(refseq.getAnnotation() != null
+            && refseq.getAnnotation().length > 0);
+    assertTrue(newseq.getAnnotation() != null
             && newseq.getAnnotation().length > 0);
     for (AlignmentAnnotation oannot : refseq.getAnnotation())
     {