X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;fp=test%2Fjalview%2Fio%2FAnnotationFileIOTest.java;h=3d4e841d10d11306a1df74df62b12906bbbe854c;hb=18a869338d12b9069496e3e07b994df01ffe78f4;hp=18e008ec823a91c96d5341f95f4ce8d0d0de7813;hpb=51afb2227c77bfab9c174f09ff03f996915e2479;p=jalview.git

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index 18e008e..3d4e841 100644
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -24,8 +24,11 @@ import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 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;
 
@@ -44,7 +47,9 @@ 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
   public void exampleAnnotationFileIO() throws Exception
@@ -102,17 +107,21 @@ 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));
 
+      ViewDef[] v = new ViewDef[1];
+      AnnotationFile aff = new AnnotationFile();
+      v[0] = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+              new Hashtable());
       String anfileout = new AnnotationFile().printAnnotations(
               al.getAlignmentAnnotation(), al.getGroups(),
-              al.getProperties());
+              al.getProperties(), v);
       assertTrue(
               "Test "
                       + testname