Merge commit 'ab43013b7e357b84b4abade0dba949668dfb2a0e' into develop

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

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index d09eb2a..74e6a31 100644 (file)
--- 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 +107,20 @@ 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