/*
- * 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.
*
*/
package jalview.io;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-import jalview.datamodel.AlignmentI;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
import java.io.File;
+import java.util.Hashtable;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
-import org.junit.Test;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.io.AnnotationFile.ViewDef;
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
{
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;
}
* - label for IO class used to write and read back in the data from
* f
*/
+
+ // @Test
public static void testAnnotationFileIO(String testname, File f,
File annotFile)
{
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
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 + "'.");