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.testng.Assert;
import org.testng.annotations.Test;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.io.AnnotationFile.ViewDef;
-
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",
{ "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)
{
FormatAdapter rf = new FormatAdapter();
- AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
- new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+ AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+ new IdentifyFile().identify(ff, DataSourceType.FILE));
// make sure dataset is initialised ? not sure about this
for (int i = 0; i < al.getSequencesArray().length; ++i)
* f
*/
- // @Test
+ // @Test(groups ={ "Functional" })
public static void testAnnotationFileIO(String testname, File f,
File annotFile)
{
+ testname
+ "\nAlignment was not annotated - annotation file not imported.",
new AnnotationFile().readAnnotationFile(al, cs, af,
- FormatAdapter.FILE));
+ DataSourceType.FILE));
AnnotationFile aff = new AnnotationFile();
ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+ testname
+ "\nregenerated annotation file did not annotate alignment.",
new AnnotationFile().readAnnotationFile(al_new, anfileout,
- FormatAdapter.PASTE));
+ DataSourceType.PASTE));
// test for consistency in io
StockholmFileTest.testAlignmentEquivalence(al, al_new, false);