import jalview.datamodel.ProfileI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
import jalview.datamodel.ProfileI;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileParse;
-import jalview.io.HMMFile;
-
-import java.io.IOException;
-import java.net.MalformedURLException;
@Test(groups = { "Functional" })
public void testGetHMMProfileFor()
throws MalformedURLException, IOException
{
@Test(groups = { "Functional" })
public void testGetHMMProfileFor()
throws MalformedURLException, IOException
{
HMMFile hmmFile = new HMMFile(new FileParse(
"test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
hmmFile.parse();
HMMFile hmmFile = new HMMFile(new FileParse(
"test/jalview/io/test_MADE1_hmm.txt", DataSourceType.FILE));
hmmFile.parse();
int[] expected2 = { 0, 4, 85, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
int[] actual2 = AAFrequency.getHMMProfileFor(hmm, 2, true);
for (int i = 0; i < actual.length; i++)
int[] expected2 = { 0, 4, 85, 'A', 85, 'C', 0, 'G', 0, 'T', 0 };
int[] actual2 = AAFrequency.getHMMProfileFor(hmm, 2, true);
for (int i = 0; i < actual.length; i++)