*/
package jalview.analysis;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import java.util.Map;
import java.util.Set;
-import org.junit.Test;
+import org.testng.annotations.Test;
-public class AlignmentUtilsTests
+public class AlignmentUtilsTests
{
// @formatter:off
private static final String TEST_DATA =
public static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
- @Test
+ @Test(groups ={ "Functional" })
public void testExpandContext()
{
AlignmentI al = new Alignment(new Sequence[] {});
/**
* Test that annotations are correctly adjusted by expandContext
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testExpandContext_annotation()
{
AlignmentI al = new Alignment(new Sequence[]
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testGetSequencesByName() throws IOException
{
final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
*/
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 testMapProteinToCdna_noXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
/**
* Test for the alignSequenceAs method that takes two sequences and a mapping.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_withMapping_noIntrons()
{
MapList map = new MapList(new int[]
/**
* Test for the alignSequenceAs method that takes two sequences and a mapping.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_withMapping_withIntrons()
{
/*
/**
* Test for the case where not all of the protein sequence is mapped to cDNA.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_withMapping_withUnmappedProtein()
{
/**
* Test for the alignSequenceAs method where we preserve gaps in introns only.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignSequenceAs_keepIntronGapsOnly()
{
* Test for the method that generates an aligned translated sequence from one
* mapping.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testGetAlignedTranslation_dnaLikeProtein()
{
// dna alignment will be replaced
/**
* Test the method that realigns protein to match mapped codon alignment.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testAlignProteinAsDna()
{
// seq1 codons are [1,2,3] [4,5,6] [7,8,9] [10,11,12]
* Test the method that tests whether a CDNA sequence translates to a protein
* sequence
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testTranslatesAs()
{
assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_withStartAndStopCodons()
throws IOException
{
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_withXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapProteinToCdna_prioritiseXrefs() throws IOException
{
List<SequenceI> protseqs = new ArrayList<SequenceI>();
* Test the method that shows or hides sequence annotations by type(s) and
* selection group.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testShowOrHideSequenceAnnotations()
{
SequenceI seq1 = new Sequence("Seq1", "AAA");
/**
* Tests for the method that checks if one sequence cross-references another
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testHasCrossRef()
{
assertFalse(AlignmentUtils.hasCrossRef(null, null));
* Tests for the method that checks if either sequence cross-references the
* other
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testHaveCrossRef()
{
assertFalse(AlignmentUtils.hasCrossRef(null, null));
/**
* Test the method that extracts the exon-only part of a dna alignment.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExonAlignment()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
* already has a protein product (Uniprot translation) which in turn has an
* x-ref to the EMBLCDS record.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExonSequences()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
* its product mappings, for the case where there are multiple exon mappings
* to different protein products.
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMakeExonAlignment_multipleProteins()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");