package jalview.util;
-import static org.testng.AssertJUnit.assertSame;
+
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
-import java.awt.Color;
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
+import java.awt.Color;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.testng.annotations.Test;
+
public class MappingUtilsTest
{
private AlignViewportI dnaView;
/**
* Simple test of mapping with no intron involved.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testBuildSearchResults()
{
final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
/**
* Simple test of mapping with introns involved.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testBuildSearchResults_withIntron()
{
final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapSequenceGroup_sequences() throws IOException
{
/*
protected AlignmentI loadAlignment(final String data, String format)
throws IOException
{
- Alignment a = new FormatAdapter().readFile(data,
+ AlignmentI a = new FormatAdapter().readFile(data,
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapColumnSelection_proteinToDna() throws IOException
{
setupMappedAlignments();
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapColumnSelection_dnaToProtein() throws IOException
{
setupMappedAlignments();
assertEquals("[0, 1, 3]", cs.getSelected().toString());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testMapColumnSelection_null() throws IOException
{
setupMappedAlignments();
* Tests for the method that converts a series of [start, end] ranges to
* single positions
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testFlattenRanges()
{
assertEquals("[1, 2, 3, 4]",
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapSequenceGroup_columns() throws IOException
{
/*
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapSequenceGroup_region() throws IOException
{
/*
assertEquals(4, mappedGroup.getEndRes());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testFindMappingsForSequence()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");