X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fstructure%2FMapping.java;h=4bee3f5ad73614f1912c83110d8b78e4e9592cdc;hb=06b709e1b942293188d561999a3c0d1042633868;hp=13387dbe409ae4647b5cc465cbefc218f845c1a7;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 13387db..4bee3f5 100644
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -28,6 +28,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileLoader;
@@ -35,11 +36,19 @@ import jalview.io.StructureFile;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class Mapping
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /*
    * more test data
    * 
@@ -69,7 +78,7 @@ public class Mapping
       StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
       StructureFile pmap = ssm.setMapping(true, new SequenceI[] { uprot },
               new String[] { "A" }, "test/jalview/ext/jmol/1QCF.pdb",
-              jalview.io.DataSourceType.FILE);
+              DataSourceType.FILE);
       assertTrue(pmap != null);
       SequenceI protseq = pmap.getSeqsAsArray()[0];
       AlignmentAnnotation pstra = protseq
@@ -140,7 +149,7 @@ public class Mapping
     // source
     StructureFile pde = ssm.setMapping(true, new SequenceI[] { sq },
             new String[]
-    { "A" }, inFile = "examples/1gaq.txt", jalview.io.DataSourceType.FILE);
+    { "A" }, inFile = "examples/1gaq.txt", DataSourceType.FILE);
     assertTrue("PDB File couldn't be found", pde != null);
     StructureMapping[] mp = ssm.getMapping(inFile);
     assertTrue("No mappings made.", mp != null && mp.length > 0);
@@ -237,7 +246,7 @@ public class Mapping
     StructureSelectionManager ssm = new jalview.structure.StructureSelectionManager();
     StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "examples/3W5V.pdb",
-            jalview.io.DataSourceType.FILE);
+            DataSourceType.FILE);
     if (pmap == null)
     {
       AssertJUnit.fail("Couldn't make a mapping for 3W5V to FER1_MAIZE");
@@ -251,10 +260,12 @@ public class Mapping
   @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
     StructureImportSettings.setShowSeqFeatures(true);
     AlignFrame ref = new FileLoader(false)
             .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",
-                    jalview.io.DataSourceType.FILE);
+                    DataSourceType.FILE);
     SequenceI refseq = ref.getViewport().getAlignment().getSequenceAt(0);
     SequenceI newseq = new Sequence(refseq.getName() + "Copy",
             refseq.getSequenceAsString());
@@ -266,7 +277,7 @@ public class Mapping
     ssm.setAddTempFacAnnot(true);
     StructureFile pmap = ssm.setMapping(true, new SequenceI[] { newseq },
             new String[] { null }, "test/jalview/ext/jmol/1QCF.pdb",
-            jalview.io.DataSourceType.FILE);
+            DataSourceType.FILE);
     assertTrue(pmap != null);
     assertEquals("Original and copied sequence of different lengths.",
             refseq.getLength(), newseq.getLength());