JAL-674 JAL-1270 added settings to ensure temperature and secondary

structure are propagated and finer grain checks on presence of annotation

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index b0144fc..716755b 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -245,6 +245,8 @@ 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 +254,9 @@ 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())
     {