From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 27 Jan 2015 17:18:05 +0000 (+0000)
Subject: JAL-674 JAL-1270 added settings to ensure temperature and secondary
X-Git-Tag: Jalview_2_9~104
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=0703daae05998509e4f5b301224c61ccec3b77e2;p=jalview.git

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
--- 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())
     {