import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.testng.annotations.Test;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;
import org.testng.annotations.Test;
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
private void testDataExtraction(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
public void testIO(String file) throws IOException
{
AppletFormatAdapter rf = new AppletFormatAdapter();
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
PhylipFile.FILE_DESC);
assertNotNull("Couldn't read supplied alignment data.", al);
String outputfile = rf.formatSequences(PhylipFile.FILE_DESC, al, true);
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);
AppletFormatAdapter.PASTE, PhylipFile.FILE_DESC);
assertNotNull("Couldn't parse reimported alignment data.", al_input);