import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.testng.annotations.Test;
-import jalview.datamodel.Alignment;
-import jalview.datamodel.SequenceI;
-
/**
* Test file for {@link PhylipFile}.
*
*
* @throws Exception
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSequentialDataExtraction() throws Exception
{
testDataExtraction(sequentialFile);
*
* @throws Exception
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testInterleavedDataExtraction() throws Exception
{
testDataExtraction(interleavedFile);
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
*
* @throws Exception
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testSequentialIO() throws Exception
{
testIO(sequentialFile);
*
* @throws Exception
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testInterleavedIO() throws Exception
{
testIO(interleavedFile);
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
- Alignment al = rf.readFile(file, AppletFormatAdapter.FILE,
+ AlignmentI al = rf.readFile(file, AppletFormatAdapter.FILE,
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
- Alignment al_input = new AppletFormatAdapter().readFile(outputfile,
+ AlignmentI al_input = new AppletFormatAdapter().readFile(outputfile,
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);