Merge develop to Release_2_8_3_Branch

[jalview.git] / test / jalview / ext / paradise / TestAnnotate3D.java

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index a7c439f..3365c52 100644 (file)
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,10 +21,6 @@
 package jalview.ext.paradise;
 
 import static org.junit.Assert.assertTrue;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
 import java.io.File;
@@ -35,9 +31,13 @@ import org.junit.Assert;
 import org.junit.Test;
 
 import MCview.PDBfile;
-
 import compbio.util.FileUtil;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
 public class TestAnnotate3D
 {
 
@@ -124,11 +124,12 @@ public class TestAnnotate3D
         sb.append(line + "\n");
       }
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
-      AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+      final String lines = sb.toString();
+      AlignmentI al = new FormatAdapter().readFile(lines,
               FormatAdapter.PASTE, "RNAML");
       if (al == null || al.getHeight() == 0)
       {
-        System.out.println(sb.toString());
+        System.out.println(lines);
       }
       assertTrue("No alignment returned.", al != null);
       assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
@@ -141,7 +142,8 @@ public class TestAnnotate3D
             String sq_ = new String(sq.getSequence()).toLowerCase();
             for (SequenceI _struseq : pdbf.getSeqsAsArray())
             {
-              if (new String(_struseq.getSequence()).toLowerCase().equals(
+              final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
+              if (lowerCase.equals(
                       sq_))
               {
                 struseq = _struseq;