X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=6d54f156b1116182de18036e227ef0c26369e3a2;hb=20d8cc2bb3e2fab2b7f637a3d523c90ceb58903d;hp=c2be67ec89f89c7b83eed2d1444c7dfea7d1b0a2;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index c2be67e..6d54f15 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -20,10 +20,13 @@
  */
 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;
@@ -36,15 +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
   {
@@ -60,14 +70,14 @@ public class TestAnnotate3D
   {
     Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
     assertTrue("Didn't retrieve 2GIS by id.", ids != null);
-    Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(FileUtil
-            .readFileToString(new File("examples/2GIS.pdb")));
+    Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(
+            FileUtil.readFileToString(new File("examples/2GIS.pdb")));
     assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
     int i = 0;
     while (ids.hasNext() && files.hasNext())
     {
-      BufferedReader file = new BufferedReader(files.next()), id = new BufferedReader(
-              ids.next());
+      BufferedReader file = new BufferedReader(files.next()),
+              id = new BufferedReader(ids.next());
       String iline, fline;
       do
       {
@@ -107,9 +117,8 @@ public class TestAnnotate3D
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
-    Iterator<Reader> readers = Annotate3D
-            .getRNAMLForPDBFileAsString(FileUtil.readFileToString(new File(
-                    "examples/2GIS.pdb")));
+    Iterator<Reader> readers = Annotate3D.getRNAMLForPDBFileAsString(
+            FileUtil.readFileToString(new File("examples/2GIS.pdb")));
     testRNAMLcontent(readers, pdbf);
   }
 
@@ -143,11 +152,11 @@ 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;
@@ -156,12 +165,12 @@ public class TestAnnotate3D
             }
             if (struseq == null)
             {
-              AssertJUnit
-                      .fail("Couldn't find this sequence in original input:\n"
-                              + new FastaFile()
-                                      .print(new SequenceI[] { sq })
-                              + "\n\nOriginal input:\n"
-                              + new FastaFile().print(pdbf.getSeqsAsArray())
+              AssertJUnit.fail(
+                      "Couldn't find this sequence in original input:\n"
+                              + new FastaFile().print(new SequenceI[]
+                              { sq }, true) + "\n\nOriginal input:\n"
+                              + new FastaFile().print(pdbf.getSeqsAsArray(),
+                                      true)
                               + "\n");
             }
           }