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[jalview.git]
/
test
/
jalview
/
util
/
MappingUtilsTest.java
diff --git
a/test/jalview/util/MappingUtilsTest.java
b/test/jalview/util/MappingUtilsTest.java
index
2d197be
..
2c0045b
100644
(file)
--- a/
test/jalview/util/MappingUtilsTest.java
+++ b/
test/jalview/util/MappingUtilsTest.java
@@
-1,11
+1,12
@@
package jalview.util;
package jalview.util;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertSame;
-import static org.junit.Assert.assertTrue;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertSame;
+import static org.testng.AssertJUnit.assertTrue;
+
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignedCodonFrame;
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.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.SearchResults;
@@
-16,6
+17,7
@@
import jalview.datamodel.SequenceI;
import jalview.gui.AlignViewport;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
import jalview.gui.AlignViewport;
import jalview.io.AppletFormatAdapter;
import jalview.io.FormatAdapter;
+
import java.awt.Color;
import java.io.IOException;
import java.util.Arrays;
import java.awt.Color;
import java.io.IOException;
import java.util.Arrays;
@@
-24,8
+26,7
@@
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.List;
import java.util.Set;
-import org.junit.Test;
-
+import org.testng.annotations.Test;
public class MappingUtilsTest
{
public class MappingUtilsTest
{
@@
-35,7
+36,7
@@
public class MappingUtilsTest
/**
* Simple test of mapping with no intron involved.
*/
/**
* 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");
public void testBuildSearchResults()
{
final Sequence seq1 = new Sequence("Seq1", "C-G-TA-GC");
@@
-88,7
+89,7
@@
public class MappingUtilsTest
/**
* Simple test of mapping with introns involved.
*/
/**
* 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");
public void testBuildSearchResults_withIntron()
{
final Sequence seq1 = new Sequence("Seq1", "C-G-TAGA-GCAGCTT");
@@
-165,7
+166,7
@@
public class MappingUtilsTest
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapSequenceGroup_sequences() throws IOException
{
/*
public void testMapSequenceGroup_sequences() throws IOException
{
/*
@@
-247,7
+248,7
@@
public class MappingUtilsTest
protected AlignmentI loadAlignment(final String data, String format)
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;
AppletFormatAdapter.PASTE, format);
a.setDataset(null);
return a;
@@
-258,7
+259,7
@@
public class MappingUtilsTest
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapColumnSelection_proteinToDna() throws IOException
{
setupMappedAlignments();
public void testMapColumnSelection_proteinToDna() throws IOException
{
setupMappedAlignments();
@@
-356,7
+357,7
@@
public class MappingUtilsTest
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapColumnSelection_dnaToProtein() throws IOException
{
setupMappedAlignments();
public void testMapColumnSelection_dnaToProtein() throws IOException
{
setupMappedAlignments();
@@
-383,7
+384,7
@@
public class MappingUtilsTest
assertEquals("[0, 1, 3]", cs.getSelected().toString());
}
assertEquals("[0, 1, 3]", cs.getSelected().toString());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testMapColumnSelection_null() throws IOException
{
setupMappedAlignments();
public void testMapColumnSelection_null() throws IOException
{
setupMappedAlignments();
@@
-396,7
+397,7
@@
public class MappingUtilsTest
* Tests for the method that converts a series of [start, end] ranges to
* single positions
*/
* 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]",
public void testFlattenRanges()
{
assertEquals("[1, 2, 3, 4]",
@@
-422,7
+423,7
@@
public class MappingUtilsTest
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapSequenceGroup_columns() throws IOException
{
/*
public void testMapSequenceGroup_columns() throws IOException
{
/*
@@
-505,7
+506,7
@@
public class MappingUtilsTest
*
* @throws IOException
*/
*
* @throws IOException
*/
- @Test
+ @Test(groups ={ "Functional" })
public void testMapSequenceGroup_region() throws IOException
{
/*
public void testMapSequenceGroup_region() throws IOException
{
/*
@@
-599,7
+600,7
@@
public class MappingUtilsTest
assertEquals(4, mappedGroup.getEndRes());
}
assertEquals(4, mappedGroup.getEndRes());
}
- @Test
+ @Test(groups ={ "Functional" })
public void testFindMappingsForSequence()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");
public void testFindMappingsForSequence()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");