JAL-2089 patch broken merge to master for Release 2.10.0b1

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

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index cbdbc40..9ec3a92 100644 (file)
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -30,13 +30,12 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
+import jalview.io.StructureFile;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
-
 public class Mapping
 {
 
@@ -67,7 +66,7 @@ public class Mapping
       { 303, 315 }, sheets[] = new int[] { 267, 268, 269, 270 };
 
       StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-      PDBfile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
+      StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
               new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
               jalview.io.FormatAdapter.FILE);
       assertTrue(pmap != null);
@@ -138,8 +137,9 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     // Associate the 1GAQ pdb file with the subsequence 'imported' from another
     // source
-    PDBfile pde = ssm.setMapping(true, new SequenceI[] { sq }, new String[]
-    { "A" }, inFile = "examples/1gaq.txt", jalview.io.FormatAdapter.FILE);
+    StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
+            new String[] { "A" }, inFile = "examples/1gaq.txt",
+            jalview.io.FormatAdapter.FILE);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
     assertTrue("No mappings made.", mp != null && mp.length > 0);
@@ -234,7 +234,7 @@ public class Mapping
                     FormatAdapter.PASTE, "FASTA");
     SequenceI newseq = seqf.getViewport().getAlignment().getSequenceAt(0);
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+    StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "examples/3W5V.pdb",
             jalview.io.FormatAdapter.FILE);
     if (pmap == null)
@@ -250,6 +250,7 @@ public class Mapping
   @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
+    StructureImportSettings.setShowSeqFeatures(true);
     AlignFrame ref = new FileLoader(false)
             .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
                     jalview.io.FormatAdapter.FILE);
@@ -262,7 +263,7 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     ssm.setProcessSecondaryStructure(true);
     ssm.setAddTempFacAnnot(true);
-    PDBfile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
+    StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
             jalview.io.FormatAdapter.FILE);
     assertTrue(pmap != null);