Merge branch 'develop' into features/JAL-892varnaToProject

[jalview.git] / test / jalview / io / StockholmFileTest.java

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 806e4dc..45de531 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -20,10 +20,10 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import jalview.datamodel.Alignment;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -35,7 +35,7 @@ import java.util.BitSet;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 public class StockholmFileTest
 {
@@ -84,6 +84,7 @@ public class StockholmFileTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
+
   public static void testFileIOwithFormat(File f, String ioformat,
           int naliannot, int nminseqann)
   {
@@ -93,7 +94,7 @@ public class StockholmFileTest
     {
       AppletFormatAdapter rf = new AppletFormatAdapter();
 
-      Alignment al = rf.readFile(ff, AppletFormatAdapter.FILE,
+      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
               new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
 
       assertNotNull("Couldn't read supplied alignment data.", al);
@@ -107,7 +108,7 @@ public class StockholmFileTest
       System.out.println("Output file in '" + ioformat + "':\n"
               + outputfile + "\n<<EOF\n");
       // test for consistency in io
-      Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+      AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
               AppletFormatAdapter.PASTE, ioformat);
       assertNotNull("Couldn't parse reimported alignment data.", al_input);
 
@@ -350,9 +351,11 @@ public class StockholmFileTest
                 an_new.displayCharacter.trim())
                 || !("" + an_or.secondaryStructure).trim().equals(
                         ("" + an_new.secondaryStructure).trim())
-                || (an_or.description != an_new.description && (an_or.description == null
-                        || an_new.description == null || !an_or.description
-                          .equals(an_new.description))))
+                || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+                        .trim().length() == 0)
+                        || (an_new.description == null && an_or.description
+                                .trim().length() == 0) || an_or.description
+                        .trim().equals(an_new.description.trim()))))
         {
           System.err.println("Annotation Element Mismatch\nElement " + i
                   + " in original: " + annot_or.annotations[i].toString()