X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=c9b5f4a1f3ea2eca45b57e24c2778a7ebfca9d01;hb=44d74820a0af7a277c10c1eab98b59eb7fceddf6;hp=18e008ec823a91c96d5341f95f4ce8d0d0de7813;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 18e008e..c9b5f4a 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.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.
  * 
@@ -20,20 +20,23 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.io.AnnotationFile.ViewDef;
 
 import java.io.File;
+import java.util.Hashtable;
 
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.Test;
 
 public class AnnotationFileIOTest
 {
 
-  static String TestFiles[][] =
-  {
+  static String TestFiles[][] = {
       { "Test example annotation import/export", "examples/uniref50.fa",
           "examples/testdata/example_annot_file.jva" },
       { "Test multiple combine annotation statements import/export",
@@ -44,9 +47,11 @@ public class AnnotationFileIOTest
           "examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
       {
           "Test group only annotation file parsing results in parser indicating annotation was parsed",
-          "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
+          "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
+      { "Test hiding/showing of insertions on sequence_ref",
+          "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
 
-  @Test
+  @Test(groups = { "Functional" })
   public void exampleAnnotationFileIO() throws Exception
   {
     for (String[] testPair : TestFiles)
@@ -65,13 +70,12 @@ public class AnnotationFileIOTest
       FormatAdapter rf = new FormatAdapter();
 
       AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+              new IdentifyFile().identify(ff, AppletFormatAdapter.FILE));
 
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(
-                al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -79,7 +83,7 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    fail("Couln't read the alignment in file '" + f.toString() + "'");
+    Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
     return null;
   }
 
@@ -93,6 +97,8 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
+
+  // @Test(groups ={ "Functional" })
   public static void testAnnotationFileIO(String testname, File f,
           File annotFile)
   {
@@ -102,17 +108,20 @@ public class AnnotationFileIOTest
     try
     {
       AlignmentI al = readAlignmentFile(f);
-
+      ColumnSelection cs = new ColumnSelection();
       assertTrue(
               "Test "
                       + testname
                       + "\nAlignment was not annotated - annotation file not imported.",
-              new AnnotationFile().readAnnotationFile(al, af,
+              new AnnotationFile().readAnnotationFile(al, cs, af,
                       FormatAdapter.FILE));
 
+      AnnotationFile aff = new AnnotationFile();
+      ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+              new Hashtable());
       String anfileout = new AnnotationFile().printAnnotations(
               al.getAlignmentAnnotation(), al.getGroups(),
-              al.getProperties());
+              al.getProperties(), null, al, v);
       assertTrue(
               "Test "
                       + testname
@@ -136,13 +145,13 @@ public class AnnotationFileIOTest
                       FormatAdapter.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
       return;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
-    fail("Test "
+    Assert.fail("Test "
             + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
             + annotFile + "'.");