Merge branch 'Release_2_9_0b1_Branch'

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index c3fd4e3..2f62110 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,9 +20,10 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+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;
@@ -34,7 +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
 {
@@ -42,13 +43,13 @@ public class StockholmFileTest
   static String PfamFile = "examples/PF00111_seed.stk",
           RfamFile = "examples/RF00031_folded.stk";
 
-  @Test
+  @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(PfamFile), "STH", -1, 0);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void pfamFileDataExtraction() throws Exception
   {
     AppletFormatAdapter af = new AppletFormatAdapter();
@@ -57,9 +58,9 @@ public class StockholmFileTest
     int numpdb = 0;
     for (SequenceI sq : al.getSequences())
     {
-      if (sq.getPDBId() != null)
+      if (sq.getAllPDBEntries() != null)
       {
-        numpdb += sq.getPDBId().size();
+        numpdb += sq.getAllPDBEntries().size();
       }
     }
     assertTrue(
@@ -67,7 +68,7 @@ public class StockholmFileTest
             numpdb > 0);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void rfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(RfamFile), "STH", 2, 1);
@@ -83,6 +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)
   {
@@ -134,7 +136,7 @@ public class StockholmFileTest
       if (naliannot > -1)
       {
         assertEquals("Number of alignment annotations", naliannot,
-              numaliannot);
+                numaliannot);
       }
 
       assertTrue(
@@ -266,7 +268,7 @@ public class StockholmFileTest
                           + (ignoreFeatures ? " ignoring." : ""),
                   ignoreFeatures
                           || (seq_original[i].getSequenceFeatures() == null && seq_new[in]
-                          .getSequenceFeatures() == null)
+                                  .getSequenceFeatures() == null)
                           || (seq_original[i].getSequenceFeatures() != null && seq_new[in]
                                   .getSequenceFeatures() != null));
           // compare sequence features
@@ -349,9 +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()