X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=6d54f156b1116182de18036e227ef0c26369e3a2;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=85fc039210839192f24aba36a052b0aa88d8c340;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 85fc039..6d54f15 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -20,6 +20,8 @@
  */
 package jalview.ext.paradise;
 
+import java.util.Locale;
+
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
@@ -40,9 +42,8 @@ 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
 {
@@ -69,14 +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
       {
@@ -116,9 +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);
   }
 
@@ -152,11 +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;
@@ -165,13 +165,13 @@ public class TestAnnotate3D
             }
             if (struseq == null)
             {
-              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");
+              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");
             }
           }
         }