X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=80fffff5a890420e2a5ab1218bff4eefd693fef1;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=411086363a3f3cb90a8bd1370e5fa03cbffa4b93;hpb=e53e39aae1128c6e11e5a3b1529521e86ca6f9d8;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 4110863..80fffff 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -20,11 +20,16 @@
  */
 package jalview.ext.paradise;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.io.FastaFile;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
@@ -34,15 +39,22 @@ import java.util.Iterator;
 
 import org.testng.Assert;
 import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import MCview.PDBfile;
-
 import compbio.util.FileUtil;
+import mc_view.PDBfile;
 
 public class TestAnnotate3D
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = { "Network" }, enabled = true)
   public void test1GIDbyId() throws Exception
   {
@@ -101,7 +113,7 @@ public class TestAnnotate3D
   public void testPDBfileVsRNAML() throws Exception
   {
     PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
@@ -128,7 +140,7 @@ public class TestAnnotate3D
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
       final String lines = sb.toString();
       AlignmentI al = new FormatAdapter().readFile(lines,
-              FormatAdapter.PASTE, "RNAML");
+              DataSourceType.PASTE, FileFormat.Rnaml);
       if (al == null || al.getHeight() == 0)
       {
         System.out.println(lines);
@@ -141,11 +153,11 @@ public class TestAnnotate3D
         {
           {
             SequenceI struseq = null;
-            String sq_ = new String(sq.getSequence()).toLowerCase();
+            String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
             for (SequenceI _struseq : pdbf.getSeqsAsArray())
             {
-              final String lowerCase = new String(_struseq.getSequence())
-                      .toLowerCase();
+              final String lowerCase = _struseq.getSequenceAsString()
+                      .toLowerCase(Locale.ROOT);
               if (lowerCase.equals(sq_))
               {
                 struseq = _struseq;
@@ -156,11 +168,11 @@ public class TestAnnotate3D
             {
               AssertJUnit
                       .fail("Couldn't find this sequence in original input:\n"
-                              + new FastaFile()
-                                      .print(new SequenceI[] { sq })
+                              + new FastaFile().print(
+                                      new SequenceI[] { sq }, true)
                               + "\n\nOriginal input:\n"
-                              + new FastaFile().print(pdbf.getSeqsAsArray())
-                              + "\n");
+                              + new FastaFile().print(
+                                      pdbf.getSeqsAsArray(), true) + "\n");
             }
           }
         }